Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008421.1 Hibiscus syriacus cultivar Beakdansim tig00111201_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1159951
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:957379 original size:21 final size:19
Alignment explanation
Indices: 957349--957397 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
957339 ATTAATAATA
957349 ATAATA-ATAACAATAATACT
1 ATAATATATAACAATAA-A-T
* *
957369 ATAGTATATAATAATAAAT
1 ATAATATATAACAATAAAT
957388 ATAATATATA
1 ATAATATATA
957398 TTTTAATCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 9 0.36
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAATATATAACAATAAAT
Found at i:957737 original size:90 final size:90
Alignment explanation
Indices: 957579--957890 Score: 520
Period size: 90 Copynumber: 3.5 Consensus size: 90
957569 ATTTTTCCCG
* * *
957579 AAGGTCTTATGG-TTGCCTGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCGT-AGTTTCTTA
1 AAGGTCTTACGGATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGC-TCAGTTTCTTA
*
957642 AATCTCATTTGAAAACATCCTGCACTA
64 GATCTCATTTGAAAACATCCTGCACTA
* *
957669 AAGGTCTTACAGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAATTTCTTAGA
1 AAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGA
*
957734 TCTCATTTGAAAACATCCTGCACTG
66 TCTCATTTGAAAACATCCTGCACTA
957759 AAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGA
1 AAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGA
957824 TCTCATTTGAAAACATCCTGCACTA
66 TCTCATTTGAAAACATCCTGCACTA
*
957849 AAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAAC
1 AAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAAC
957891 TCTTGAAAAT
Statistics
Matches: 209, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
89 1 0.00
90 195 0.93
91 13 0.06
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (90 bp):
AAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGA
TCTCATTTGAAAACATCCTGCACTA
Found at i:957991 original size:43 final size:43
Alignment explanation
Indices: 957925--958023 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 43
957915 AAATTGTCAC
* *
957925 CAAGGAACCCCTACATATCACGATGGTCCCTCAAGTTTTTCAT
1 CAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCAT
** *
957968 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCTT
1 CAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCAT
958011 CAAGAAACCCCTA
1 CAAGAAACCCCTA
958024 AAAATCAGGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (43 bp):
CAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCAT
Found at i:958124 original size:36 final size:36
Alignment explanation
Indices: 958084--958188 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
958074 AAGCTAGACT
958084 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACC
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACC
* * * *
958120 GTCTCAAGAGAGACAAAATTTGTTTCGAGAGAAACT
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACC
*
958156 GTCTCAAGGGAGAC--AATTTATTTCAAGGGAAAC
1 GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
958189 TATCTTGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
34 16 0.26
36 45 0.74
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (36 bp):
GTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACC
Found at i:958533 original size:34 final size:34
Alignment explanation
Indices: 958493--958647 Score: 231
Period size: 34 Copynumber: 4.6 Consensus size: 34
958483 TCTTAGAGAA
*
958493 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
958527 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
*
958561 AAATGGTCTCAAGCGAGACCAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
* * *
958595 AAATTGTCTCAA-CTAAGACAAAATTTATTTTGAG
1 AAATTGTCTCAAGC-GAGACCAAATTTGTTTTGAG
* *
958629 AAATTGTCTCGAGTGAGAC
1 AAATTGTCTCAAGCGAGAC
958648 AAAAAAAATT
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
33 1 0.01
34 109 0.99
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACCAAATTTGTTTTGAG
Found at i:958664 original size:68 final size:68
Alignment explanation
Indices: 958524--958665 Score: 151
Period size: 68 Copynumber: 2.1 Consensus size: 68
958514 AATTTGTTTT
* * * * ****
958524 GAGAAATTGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATGGTCTCAAGCGAGACCAAATTTGT
1 GAGAAATTGTCTCAAGCAAGACAAAATTTATTTTGAGAAATGGTCTCAAGCGAGACAAAAAAAAT
**
958589 TTT
66 TAA
* * *
958592 GAGAAATTGTCTCAA-CTAAGACAAAATTTATTTTGAGAAATTGTCTCGAGTGAGACAAAAAAAA
1 GAGAAATTGTCTCAAGC-AAGACAAAATTTATTTTGAGAAATGGTCTCAAGCGAGACAAAAAAAA
958656 TTAA
65 TTAA
958660 GAGAAA
1 GAGAAA
958666 CAACATCAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
67 1 0.02
68 59 0.98
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (68 bp):
GAGAAATTGTCTCAAGCAAGACAAAATTTATTTTGAGAAATGGTCTCAAGCGAGACAAAAAAAAT
TAA
Found at i:958843 original size:32 final size:32
Alignment explanation
Indices: 958754--958985 Score: 338
Period size: 32 Copynumber: 7.2 Consensus size: 32
958744 AGGATATTGA
* * * *
958754 ATGCCACAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
958786 ATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
*
958819 ATGCCCCAACATTTAATGTTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
* * *
958851 ATGCCCCAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
958883 ATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
* * *
958916 AAGCCTCAACATTTGATGTTGAATCTCCAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
*
958948 ATGCCCCAACATTTGATGTTGAATCTTCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
958980 ATGCCC
1 ATGCCC
958986 TCTATTGCTT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
32 121 0.68
33 58 0.32
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCCAAAG
Found at i:958858 original size:65 final size:64
Alignment explanation
Indices: 958754--958985 Score: 338
Period size: 65 Copynumber: 3.6 Consensus size: 64
958744 AGGATATTGA
* * * *
958754 ATGCCACAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
* * * *
958819 ATGCCCCAACATTTAATGTTGAATCTCCAAAGATGCCCCAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
* * *
958883 ATGCCCCAACATTTTGATGTTGAATCTCCAAAGAAGCCTCAACATTTGATGTTGAATCTCCAAAA
1 ATGCCCCAACA-TTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
*
958948 ATGCCCCAACATTTGATGTTGAATCTTCAAAGATGCCC
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCC
958986 TCTATTGCTT
Statistics
Matches: 148, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
64 54 0.36
65 94 0.64
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (64 bp):
ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
Found at i:958926 original size:97 final size:97
Alignment explanation
Indices: 958753--958985 Score: 385
Period size: 97 Copynumber: 2.4 Consensus size: 97
958743 CAGGATATTG
*
958753 AATGCCACAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAA
1 AATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAA
*
958818 GATGCCCCAACATTTAATGTTGAATCTCCAAA
66 GAAGCCCCAACATTTAATGTTGAATCTCCAAA
*
958850 GATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAA
1 AATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAA
* *
958915 GAAGCCTCAACATTTGATGTTGAATCTCCAAA
66 GAAGCCCCAACATTTAATGTTGAATCTCCAAA
* * * *
958947 AATGCCCCAACATTTGATGTTGAATCTTCAAAGATGCCC
1 AATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCC
958986 TCTATTGCTT
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 126 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (97 bp):
AATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAA
GAAGCCCCAACATTTAATGTTGAATCTCCAAA
Found at i:959392 original size:32 final size:32
Alignment explanation
Indices: 959348--959432 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
959338 ACTCAGGTTA
*
959348 TTGTGTTTGGTCAATGGTTTGAATGTCTCAGG
1 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
959380 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
1 TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
* *
959412 TTATTTTTGGTTAATGGTTTG
1 TTGTTTTTGGTCAATGGTTTG
959433 GCCTTCTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.15, C:0.07, G:0.28, T:0.49
Consensus pattern (32 bp):
TTGTTTTTGGTCAATGGTTTGAATGTCTCAGG
Found at i:960093 original size:14 final size:13
Alignment explanation
Indices: 960062--960092 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
960052 TTATCGTCCC
960062 TTTTTCTTTACAT
1 TTTTTCTTTACAT
*
960075 TTTTTCTTTGCAT
1 TTTTTCTTTACAT
960088 TTTTT
1 TTTTT
960093 TTGCTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTCTTTACAT
Found at i:961338 original size:6 final size:6
Alignment explanation
Indices: 961321--961359 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
961311 AATTAATGTT
*
961321 ATGCATA ATGCAA ATGCAG ATGCCAA ATGCAA ATGCAA A
1 ATGCA-A ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
961360 AGGTGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:967356 original size:3 final size:3
Alignment explanation
Indices: 967343--967393 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
967333 TATTGTAAAG
* * * *
967343 TAA TTA TAA TAA TAA TAA TAA TAA TAA TCA TAC T-A TAG TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
967388 TAA TAA
1 TAA TAA
967394 ATATAATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.03
3 35 0.92
4 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:967399 original size:12 final size:11
Alignment explanation
Indices: 967347--967403 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 11
967337 GTAAAGTAAT
967347 TATAATAATAA
1 TATAATAATAA
967358 TAATAATAATAA
1 T-ATAATAATAA
* *
967370 TCATACT-ATAG
1 T-ATAATAATAA
967381 TAT-ATAATAA
1 TATAATAATAA
967391 TA-AAT-ATAA
1 TATAATAATAA
967400 TATA
1 TATA
967404 TATTTTAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
9 7 0.19
10 10 0.27
11 5 0.14
12 15 0.41
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (11 bp):
TATAATAATAA
Found at i:969720 original size:15 final size:15
Alignment explanation
Indices: 969700--969733 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
969690 TGCCCAAATC
* *
969700 CTCCCGCCTGATTTA
1 CTCCCGCCCGATATA
969715 CTCCCGCCCGATATA
1 CTCCCGCCCGATATA
969730 CTCC
1 CTCC
969734 ATCCCAGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.47, G:0.12, T:0.26
Consensus pattern (15 bp):
CTCCCGCCCGATATA
Found at i:979190 original size:60 final size:60
Alignment explanation
Indices: 979085--979202 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
979075 AATGAAGAAA
* * * *
979085 AGTTAAATTCCTAATTGTGCATATTGGTATAAAGGTGCCATTAATGTAAGTTAGATGATT
1 AGTTAAATTCCTAATTGTGCATATTAGCAGAAAGGTGCCAATAATGTAAGTTAGATGATT
*
979145 AGTTAAATGT-CTAATTGTGCATATTAGCAGAAATGG-GTCAATAATGTAAGTTAGATGA
1 AGTTAAAT-TCCTAATTGTGCATATTAGCAGAAA-GGTGCCAATAATGTAAGTTAGATGA
979203 AAGGTCTAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 48 0.94
61 3 0.06
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (60 bp):
AGTTAAATTCCTAATTGTGCATATTAGCAGAAAGGTGCCAATAATGTAAGTTAGATGATT
Found at i:979301 original size:52 final size:52
Alignment explanation
Indices: 979155--979525 Score: 377
Period size: 52 Copynumber: 6.9 Consensus size: 52
979145 AGTTAAATGT
* * * * *
979155 CTAATTGTGCATATTAGCAGAAATGG-GTCAATAATGTAAGTTAGATGAAAGGT
1 CTAACTGTGCA-ATTGGCAGAAA-GGTGCCAATAATGCAAGTTAGATGAAAGGC
* * * * *
979208 CTAACTGTGCATGTTGGAAGAAAGGTGTCAATAATTG-AAGTTATATAAAAGGC
1 CTAACTGTGCA-ATTGGCAGAAAGGTGCCAATAA-TGCAAGTTAGATGAAAGGC
* *
979261 CTAACTGTGTAATTGGGAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* * * **
979313 CTAACTGTGCATATTGGCAAAAATGTGTCAATAATATAAGTTAGATGAAAGGC
1 CTAACTGTGCA-ATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* * *
979366 CTAACTGTGCAATTGGCATAAATGTGCCAATAATACAAGTTAGATGAAAGGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
* *
979418 CTAACTGTGCATTTGGCAGAAAGGTACCAATAATGCAAGTTAGATGAAATGTTAAATGC
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA-G------GC
* * * * *
979477 CTAGCTGTGCATTTGGTAGAAAAGTGCCACTAATGCAAGTTAGATGAAA
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
979526 AACATTGTAT
Statistics
Matches: 274, Mismatches: 33, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
51 2 0.01
52 127 0.46
53 97 0.35
54 2 0.01
59 46 0.17
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (52 bp):
CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGC
Found at i:979355 original size:105 final size:105
Alignment explanation
Indices: 979155--979525 Score: 394
Period size: 105 Copynumber: 3.5 Consensus size: 105
979145 AGTTAAATGT
* * * * *
979155 CTAATTGTGCATATTAGCAGAAATGG-GTCAATAATGTAAGTTAGATGAAAGGTCTAACTGTGCA
1 CTAACTGTGCA-ATTGGCAGAAA-GGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCA
*
979219 TGTTGG-AAGAAAGGTGTCAATAATTGAAGTTATATAAAAGGC
64 T-TTGGCAAGAAAGGTGTCAATAATTGAAGTTAGATAAAAGGC
* *
979261 CTAACTGTGTAATTGGGAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATA
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCAT-
* *
979326 TTGGCAA-AAATGTGTCAATAATAT-AAGTTAGATGAAAGGC
65 TTGGCAAGAAAGGTGTCAATAAT-TGAAGTTAGATAAAAGGC
* * *
979366 CTAACTGTGCAATTGGCATAAATGTGCCAATAATACAAGTTAGATGAAAGGCCTAACTGTGCATT
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATT
** *
979431 TGGC-AGAAAGGTACCAATAA-TGCAAGTTAGATGAAATGTTAAATGC
66 TGGCAAGAAAGGTGTCAATAATTG-AAGTTAGAT---A----AAAGGC
* * * * *
979477 CTAGCTGTGCATTTGGTAGAAAAGTGCCACTAATGCAAGTTAGATGAAA
1 CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
979526 AACATTGTAT
Statistics
Matches: 224, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
102 1 0.00
103 1 0.00
104 27 0.12
105 136 0.61
106 12 0.05
111 47 0.21
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (105 bp):
CTAACTGTGCAATTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATT
TGGCAAGAAAGGTGTCAATAATTGAAGTTAGATAAAAGGC
Found at i:980954 original size:76 final size:75
Alignment explanation
Indices: 980863--981027 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
980853 TTAAACTCAA
* *
980863 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTTTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
980927 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
980939 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
981004 TTTAATTAGG
66 TTTAATTAAG
*
981014 ATTTAGAATATTAT
1 ATTTAGGATATTAT
981028 ATTGTTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.57
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:981092 original size:21 final size:21
Alignment explanation
Indices: 981060--981114 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
981050 TTTAAATAGT
981060 TTTAAG-TGTTTTAATTAGGA
1 TTTAAGATGTTTTAATTAGGA
981080 TTTAAGATGTTTTAATTAGGA
1 TTTAAGATGTTTTAATTAGGA
*
981101 TTTAAGATGCTTTA
1 TTTAAGATGTTTTA
981115 GCTTGTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.18
21 27 0.82
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (21 bp):
TTTAAGATGTTTTAATTAGGA
Found at i:981727 original size:18 final size:17
Alignment explanation
Indices: 981688--981743 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
981678 TCTTAATCTC
* *
981688 TTTAATTTGTTTATTTA
1 TTTAATTTTTTTTTTTA
*
981705 ATTAATTTTTTTCTTTTA
1 TTTAATTTTTTT-TTTTA
*
981723 TTTAATTCTTATTTTTTA
1 TTTAATT-TTTTTTTTTA
981741 TTT
1 TTT
981744 TAACCACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 10 0.31
18 18 0.56
19 4 0.12
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTAATTTTTTTTTTTA
Found at i:986988 original size:15 final size:15
Alignment explanation
Indices: 986965--986995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
986955 TATTTCATTC
*
986965 TATTTATTTTATTTT
1 TATTAATTTTATTTT
986980 TATTAATTTTATTTT
1 TATTAATTTTATTTT
986995 T
1 T
986996 TCTGAATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTAATTTTATTTT
Found at i:988835 original size:76 final size:75
Alignment explanation
Indices: 988744--988908 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
988734 TTGAACTCAA
*
988744 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
988808 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
988820 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
988885 TTTAATTAGG
66 TTTAATTAAG
*
988895 ATTTAGAATATTAT
1 ATTTAGGATATTAT
988909 ATTATTTTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:988894 original size:19 final size:19
Alignment explanation
Indices: 988866--988927 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
988856 TGTATTTTAG
*
988866 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
988885 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
988904 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
988924 TTTA
1 TTTA
988928 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:989492 original size:17 final size:17
Alignment explanation
Indices: 989470--989511 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
989460 TCTTAATCTC
989470 TTTAATTTATTTATTTA
1 TTTAATTTATTTATTTA
* *
989487 TTTAA-TTATTTTTTTC
1 TTTAATTTATTTATTTA
*
989503 TTTTATTTA
1 TTTAATTTA
989512 ATTCTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTAATTTATTTATTTA
Found at i:989507 original size:21 final size:22
Alignment explanation
Indices: 989483--989523 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
989473 AATTTATTTA
989483 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
989504 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
989524 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:989602 original size:13 final size:13
Alignment explanation
Indices: 989563--989605 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
989553 CTTTTTATAT
989563 TTATTACTA-TTA
1 TTATTACTATTTA
*
989575 CTATTACTATTTA
1 TTATTACTATTTA
989588 TTATTA-TATTATA
1 TTATTACTATT-TA
989601 TTATT
1 TTATT
989606 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTACTATTTA
Found at i:995401 original size:53 final size:53
Alignment explanation
Indices: 995334--995702 Score: 466
Period size: 52 Copynumber: 7.0 Consensus size: 53
995324 TCAGTTAAAT
* *
995334 GCCTAACTGTGCATATTGGCAAAAATGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
995387 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTAAGTT--A--AATG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
995436 GCCTAACTGTACA-AGTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * *
995488 GCCTAACTGTGCATATTGGTAGAAAAGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* * * *
995541 GCATAACTGTGCA-GTTGGTAGAAAGGTATCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
* *
995593 GCCTAACTGTGAAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAATGTTAAG
1 GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATG--A----AAG
* *
995651 TGCCTAACTGTGCAT-TTGGCAGAAAGGTGTCACTAATGCCAGTTAGATGAAA
1 -GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
995703 AAATAGTGTA
Statistics
Matches: 276, Mismatches: 27, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
48 28 0.10
49 15 0.05
50 1 0.00
51 1 0.00
52 92 0.33
53 90 0.33
54 1 0.00
57 1 0.00
58 3 0.01
59 44 0.16
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (53 bp):
GCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAG
Found at i:995501 original size:101 final size:101
Alignment explanation
Indices: 995326--995636 Score: 430
Period size: 101 Copynumber: 3.0 Consensus size: 101
995316 TTAGATAATC
* * *
995326 AGTTAAAT-GCCTAACTGTGCATATTGGCAAAAATGTGTCAATAATGCAAGTTAGATGAAAGGCC
1 AGTTAAATGGCCTAACTGTGCA-AGTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
995390 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA
65 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA
*
995427 AGTTAAATGGCCTAACTGTACAAGTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCT
1 AGTTAAATGGCCTAACTGTGCAAGTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCT
* *
995492 AACTGTGCATATTGGTAGAAAAGTGTCAATAATGTA
66 AACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA
* * * *
995528 AGTTAGATGAAAGGCATAACTGTGC-AGTTGGTAGAAAGGTATCAATAATGCAAGTTAGATGAAA
1 AGTT--A--AATGGCCTAACTGTGCAAG-TGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
* * *
995592 GGCCTAACTGTGAAT-TTGGCAGAAAGGTGCCAATAATGCA
61 GGCCTAACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA
995632 AGTTA
1 AGTTA
995637 GATGAAATGT
Statistics
Matches: 188, Mismatches: 16, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
101 86 0.46
102 13 0.07
103 1 0.01
104 27 0.14
105 61 0.32
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (101 bp):
AGTTAAATGGCCTAACTGTGCAAGTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCCT
AACTGTGCATATTGGCAGAAAGGTGTCAATAATGTA
Found at i:995556 original size:25 final size:26
Alignment explanation
Indices: 995471--995603 Score: 75
Period size: 26 Copynumber: 5.1 Consensus size: 26
995461 GTGTCAATAA
*
995471 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCATAACTG
*
995497 TGCATA-TT-GGTAGAAAAGTGTCAATAA-TG
1 TGCA-AGTTAGAT-G-AAAG-G-C-ATAACTG
995526 T--AAGTTAGATGAAAGGCATAACTG
1 TGCAAGTTAGATGAAAGGCATAACTG
* * *
995550 TGC-AGTT-GGTAGAAAGGTATCAA-TAA
1 TGCAAGTTAGAT-GAAAGGCAT-AACT-G
*
995576 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCATAACTG
995602 TG
1 TG
995604 AATTTGGCAG
Statistics
Matches: 80, Mismatches: 10, Indels: 34
0.65 0.08 0.27
Matches are distributed among these distances:
23 4 0.05
24 6 0.08
25 16 0.20
26 21 0.26
27 21 0.26
28 5 0.06
29 4 0.05
30 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (26 bp):
TGCAAGTTAGATGAAAGGCATAACTG
Found at i:1000546 original size:18 final size:18
Alignment explanation
Indices: 1000523--1000557 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1000513 AAGGGGGAAT
1000523 ATTTCTTATAATTTATTC
1 ATTTCTTATAATTTATTC
* *
1000541 ATTTCTTTTATTTTATT
1 ATTTCTTATAATTTATT
1000558 TCCTTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTCTTATAATTTATTC
Found at i:1006690 original size:203 final size:203
Alignment explanation
Indices: 1006341--1006747 Score: 814
Period size: 203 Copynumber: 2.0 Consensus size: 203
1006331 ATATAATCCT
1006341 ATAAAGCATAATAATACATAAAACTAACTTGGTAAACCAAGTTTCTTTCACATAACCTATGAAAT
1 ATAAAGCATAATAATACATAAAACTAACTTGGTAAACCAAGTTTCTTTCACATAACCTATGAAAT
1006406 AATATTTAGTATGCCCAATATACCCATCAATCATATTTTCCAAAATGTCCATTTATTGCCCAATG
66 AATATTTAGTATGCCCAATATACCCATCAATCATATTTTCCAAAATGTCCATTTATTGCCCAATG
1006471 TATGCCAAATGAGAATGCAAGGTACATGAGTTGCACATAAGTGCTAAACGAAAGCATATGTTATG
131 TATGCCAAATGAGAATGCAAGGTACATGAGTTGCACATAAGTGCTAAACGAAAGCATATGTTATG
1006536 TGATGACA
196 TGATGACA
1006544 ATAAAGCATAATAATACATAAAACTAACTTGGTAAACCAAGTTTCTTTCACATAACCTATGAAAT
1 ATAAAGCATAATAATACATAAAACTAACTTGGTAAACCAAGTTTCTTTCACATAACCTATGAAAT
1006609 AATATTTAGTATGCCCAATATACCCATCAATCATATTTTCCAAAATGTCCATTTATTGCCCAATG
66 AATATTTAGTATGCCCAATATACCCATCAATCATATTTTCCAAAATGTCCATTTATTGCCCAATG
1006674 TATGCCAAATGAGAATGCAAGGTACATGAGTTGCACATAAGTGCTAAACGAAAGCATATGTTATG
131 TATGCCAAATGAGAATGCAAGGTACATGAGTTGCACATAAGTGCTAAACGAAAGCATATGTTATG
1006739 TGATGACA
196 TGATGACA
1006747 A
1 A
1006748 CAACATTATA
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 204 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (203 bp):
ATAAAGCATAATAATACATAAAACTAACTTGGTAAACCAAGTTTCTTTCACATAACCTATGAAAT
AATATTTAGTATGCCCAATATACCCATCAATCATATTTTCCAAAATGTCCATTTATTGCCCAATG
TATGCCAAATGAGAATGCAAGGTACATGAGTTGCACATAAGTGCTAAACGAAAGCATATGTTATG
TGATGACA
Found at i:1007412 original size:46 final size:46
Alignment explanation
Indices: 1007362--1007915 Score: 669
Period size: 46 Copynumber: 12.0 Consensus size: 46
1007352 TATAGCCTCT
* * ** * * *
1007362 TTTCATGCATTAATACATCAATTCATACATTTTAGTTATGGCATTC
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
*
1007408 TTTCATGCCTTAATGCATACGTTCATGCACTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
* * *
1007454 TTTCATGCCTTAAAGCATCCGTTCATGCATTTTTATTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGTTATGGCATCC
** ** * * **
1007501 TTTCATGCCTTGGTGCATCATTTCATGCACTTTAGTTTTGACATTA
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
* * *
1007547 TTTCATGCCTTAATGCGTCCGTTCATGCATTTTTATTTAT-GCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGTTATGGCATCC
* * *
1007593 TTTCATGCCTTAGTGCATCCGTTCATGGACTTTAGTTATAGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
* *
1007639 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGTTATGGCATCC
* * *
1007686 TTTCATGCCTTAGTTCATCCGTTTATGCACTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
* * * *
1007732 TTTCATGCCTTAATTCATCCGTTCATGAATTTTTATTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGTTATGGCATCC
* *
1007779 TTTCATACCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
* ** * *
1007825 TTTCATGCCTTAATTCATATGTTCATGCATTTTTATTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGTTATGGCATCC
* *
1007872 TTTCATGCCTTAGTGCATCTGTTCATGCACTTTAGTTATGGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCAT
1007916 AATCAATACT
Statistics
Matches: 430, Mismatches: 72, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
45 8 0.02
46 255 0.59
47 167 0.39
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTATGGCATCC
Found at i:1007432 original size:20 final size:20
Alignment explanation
Indices: 1007409--1007481 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
1007399 ATGGCATTCT
*
1007409 TTCATGCCTTAATGCATACG
1 TTCATGCCTTAATGCATCCG
*
1007429 TTCATGCACTTTAGTTATGGCATCCT
1 TTCATGC-C-TTA---AT-GCATCCG
*
1007455 TTCATGCCTTAAAGCATCCG
1 TTCATGCCTTAATGCATCCG
1007475 TTCATGC
1 TTCATGC
1007482 ATTTTTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 20 0.47
21 2 0.05
22 3 0.07
24 3 0.07
25 3 0.07
26 12 0.28
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCCG
Found at i:1007504 original size:93 final size:93
Alignment explanation
Indices: 1007362--1007915 Score: 833
Period size: 93 Copynumber: 6.0 Consensus size: 93
1007352 TATAGCCTCT
* * ** * * * *
1007362 TTTCATGCATTAATACATCAATTCATACA-TTTTAGTTATGGCATTCTTTCATGCCTTAATGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
*
1007426 ACGTTCATGCACTTTAGTTATGGCATCC
66 CCGTTCATGCACTTTAGTTATGGCATCC
* *
1007454 TTTCATGCCTTAAAGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTGGTGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
** * * **
1007519 CATTTCATGCACTTTAGTTTTGACATTA
66 CCGTTCATGCACTTTAGTTATGGCATCC
*
1007547 TTTCATGCCTTAATGCGTCCGTTCATGCATTTTTATTTAT-GCATCCTTTCATGCCTTAGTGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
* *
1007611 CCGTTCATGGACTTTAGTTATAGCATCC
66 CCGTTCATGCACTTTAGTTATGGCATCC
*
1007639 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTTCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
*
1007704 CCGTTTATGCACTTTAGTTATGGCATCC
66 CCGTTCATGCACTTTAGTTATGGCATCC
* * *
1007732 TTTCATGCCTTAATTCATCCGTTCATGAATTTTTATTTATGGCATCCTTTCATACCTTAGTGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
1007797 CCGTTCATGCACTTTAGTTATGGCATCC
66 CCGTTCATGCACTTTAGTTATGGCATCC
* **
1007825 TTTCATGCCTTAATTCATATGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
*
1007890 CTGTTCATGCACTTTAGTTATGGCAT
66 CCGTTCATGCACTTTAGTTATGGCAT
1007916 AATCAATACT
Statistics
Matches: 417, Mismatches: 43, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
92 105 0.25
93 312 0.75
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (93 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCAT
CCGTTCATGCACTTTAGTTATGGCATCC
Found at i:1007570 original size:139 final size:139
Alignment explanation
Indices: 1007362--1007915 Score: 673
Period size: 139 Copynumber: 4.0 Consensus size: 139
1007352 TATAGCCTCT
* * * * * * *
1007362 TTTCATGCATTAATACATCAATTCATACATTTTAGTTATGGCATTCTTTCATGCCTTAATGCATA
1 TTTCATGCCTTAGTGCATCAGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATA
* * *
1007427 CGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAAAGCATCCGTTCATGCATTTTTATT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGT
1007491 TATGGCATCC
130 TATGGCATCC
* * * * ** * *
1007501 TTTCATGCCTTGGTGCATCATTTCATGCACTTTAGTTTTGACATTATTTCATGCCTTAATGCGTC
1 TTTCATGCCTTAGTGCATCAGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATA
* * * *
1007566 CGTTCATGCATTTTTATTTAT-GCATCCTTTCATGCCTTAGTGCATCCGTTCATGGACTTTAGTT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
*
1007630 ATAGCATCC
131 ATGGCATCC
* * * * * *
1007639 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTTCAT
1 TTTCATGCCTTAGTGCATCAGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT
* * * * * *
1007704 CCGTTTATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATTCATCCGTTCATGAATTTTTAT
65 ACGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAG
1007768 TTATGGCATCC
129 TTATGGCATCC
* * *
1007779 TTTCATACCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATTCATA
1 TTTCATGCCTTAGTGCATCAGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATA
* * * * *
1007844 TGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCTGTTCATGCACTTTAGTT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
1007909 ATGGCAT
131 ATGGCAT
1007916 AATCAATACT
Statistics
Matches: 352, Mismatches: 58, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
138 47 0.13
139 216 0.61
140 89 0.25
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (139 bp):
TTTCATGCCTTAGTGCATCAGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATA
CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
ATGGCATCC
Found at i:1007611 original size:20 final size:20
Alignment explanation
Indices: 1007586--1007666 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 20
1007576 TTTTTATTTA
*
1007586 TGCATCCTTTCATGCCTTAG
1 TGCATCCGTTCATGCCTTAG
*
1007606 TGCATCCGTTCATGGACTTTAG
1 TGCATCCGTTCAT-G-CCTTAG
* *
1007628 TTATAGCATCCTTTCATGCCTTAA
1 ---T-GCATCCGTTCATGCCTTAG
1007652 TGCATCCGTTCATGC
1 TGCATCCGTTCATGC
1007667 ATTTTTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 25 0.51
21 2 0.04
22 5 0.10
24 4 0.08
25 2 0.04
26 11 0.22
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (20 bp):
TGCATCCGTTCATGCCTTAG
Found at i:1007713 original size:20 final size:20
Alignment explanation
Indices: 1007681--1007758 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
1007671 TTATTTATGG
1007681 CATCCTTTCATGCCTTAGTT
1 CATCCTTTCATGCCTTAGTT
1007701 CATCCGTTT-ATGCACTTTAGTTAT
1 CATCC-TTTCATGC-C-TTAG-T-T
*
1007725 GGCATCCTTTCATGCCTTAATT
1 --CATCCTTTCATGCCTTAGTT
*
1007747 CATCCGTTCATG
1 CATCCTTTCATG
1007759 AATTTTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
20 20 0.42
21 4 0.08
22 5 0.10
23 2 0.04
24 4 0.08
25 4 0.08
26 9 0.19
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAGTT
Found at i:1013187 original size:15 final size:14
Alignment explanation
Indices: 1013158--1013216 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
1013148 TATCAAAAGT
1013158 AATAATAAAA-T-A
1 AATAATAAAATTAA
1013170 AATAATAATAATTAA
1 AATAATAA-AATTAA
1013185 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
1013200 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
1013215 AA
1 AA
1013217 ACTATAGGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 1 0.03
15 23 0.59
16 5 0.13
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:1014544 original size:3 final size:3
Alignment explanation
Indices: 1014536--1014601 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
1014526 ATATTTATTA
* ** **
1014536 AAT AAT AAT AAT ATAT ATAT AAT -AT AAT ATT AAT AAT TTT AAT TTT
1 AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1014582 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1014602 AATGAAATGA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 42 0.82
4 7 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:1014862 original size:76 final size:76
Alignment explanation
Indices: 1014736--1015064 Score: 516
Period size: 76 Copynumber: 4.3 Consensus size: 76
1014726 TGTTGAAAAT
** * **
1014736 ATCATGCACTAAAGGGCTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1014801 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
1014812 ATCATACACTGTAGGACTTAAAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
1014877 TTTTTGGAAAT
66 TTTTTGGAAAC
* * *
1014888 ATCATGCACTGTAGGACTTACAGATGATCCTAAGGCTTTAAAAACATCAAAAAGATCCCGAAGG-
1 ATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1014952 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
1014963 ATCATGTACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1015028 TTTTTGGAAAC
66 TTTTTGGAAAC
*
1015039 ATCATGCCCTGTAGGACTTACAGATG
1 ATCATGCACTGTAGGACTTACAGATG
1015065 TGGGAAATAG
Statistics
Matches: 231, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 69 0.30
76 162 0.70
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
ATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:1015013 original size:151 final size:152
Alignment explanation
Indices: 1014732--1015064 Score: 533
Period size: 151 Copynumber: 2.2 Consensus size: 152
1014722 AAAATGTTGA
** * * * *
1014732 AAATATCATGCACTAAAGGGCTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGATCCCGA
1014797 AGGCTTTTTGGAAACATCATACACTGTAGGACTTAAAGATGAACCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATACACTGTAGGACTTAAAGATGAACCTAAGGCTTTGAAAACATCAA
*
1014862 AAAGCTCCCGAAGGCTTTTTGG
131 AAACCTCCCGAAGGCTTTTTGG
*
1014884 AAATATCATGCACTGTAGGACTTACAGATGATCCTAAGGCTTTAAAAACATCAAAAAGATCCCGA
1 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGATCCCGA
** * *
1014949 AGG-TTTTTGGAAACATCATGTACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATACACTGTAGGACTTAAAGATGAACCTAAGGCTTTGAAAACATCAA
1015013 AAACCTCCCGAAGGCTTTTTGG
131 AAACCTCCCGAAGGCTTTTTGG
* *
1015035 AAACATCATGCCCTGTAGGACTTACAGATG
1 AAATATCATGCACTGTAGGACTTACAGATG
1015065 TGGGAAATAG
Statistics
Matches: 167, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
151 106 0.63
152 61 0.37
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (152 bp):
AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGATCCCGA
AGGCTTTTTGGAAACATCATACACTGTAGGACTTAAAGATGAACCTAAGGCTTTGAAAACATCAA
AAACCTCCCGAAGGCTTTTTGG
Found at i:1015287 original size:76 final size:76
Alignment explanation
Indices: 1015189--1015399 Score: 379
Period size: 76 Copynumber: 2.8 Consensus size: 76
1015179 TCAAAATAAC
*
1015189 AACATCAAAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1015253 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1015264 AACATCAAAAAACTCCCAAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1015329 AAGGCTTTGAA
66 AAGGCTTTGAA
*
1015340 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATTCACTGTAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1015400 TGGGAAATAG
Statistics
Matches: 129, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 13 0.10
76 116 0.90
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1015469 original size:335 final size:335
Alignment explanation
Indices: 1014854--1015524 Score: 1141
Period size: 335 Copynumber: 2.0 Consensus size: 335
1014844 AGGCTTTGAA
* * *
1014854 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGATCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCT
* *
1014919 AAGGCTTTAAAAACATCAAAAAGATCCCGAAGGTTTTTGGAAACATCATGTACTGTAGGACTTAC
66 AAGGCTTTAAAAACATCAAAAAGATCCCAAAGGTTTTTGGAAACATCATGCACTGTAGGACTTAC
*
1014984 AGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGCTTTTTGGAAACATCATGCCCT
131 AGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGCTTTTTGGAAACATCATGCACT
* *
1015049 GTAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATTGTTTTCTTACT
196 GTAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACT
* *
1015114 TTTTAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCTTTTTCTCATTATTTT
261 TTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTT
1015179 TCAAAATAAC
326 TCAAAATAAC
1015189 AACATCAAAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCT
*
1015253 AAGGCTTTGAAAACATCAAAAA-ACTCCCAAAGGCTTTTTGGAAACATCATGCACTGTAGGACTT
66 AAGGCTTTAAAAACATCAAAAAGA-TCCCAAAGG-TTTTTGGAAACATCATGCACTGTAGGACTT
* *
1015317 ACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATTCA
129 ACAGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGCTTTTTGGAAACATCATGCA
* *
1015382 CTGTAGGACTTACAGATGTGGGAAATAGTTTACTAAGT-AAGAAACTATGAAAATCGTTTTCTTA
194 CTGTAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTA
**
1015446 CTTTTCAACAATTTCATTTTTAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTAT
259 CTTTTCAACAATTTCA-TTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTAT
1015511 TTTTCAAAATAAC
323 TTTTCAAAATAAC
1015524 A
1 A
1015525 TGTTGATTGG
Statistics
Matches: 316, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
333 1 0.00
334 113 0.36
335 202 0.64
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (335 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCT
AAGGCTTTAAAAACATCAAAAAGATCCCAAAGGTTTTTGGAAACATCATGCACTGTAGGACTTAC
AGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGCTTTTTGGAAACATCATGCACT
GTAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACT
TTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTT
TCAAAATAAC
Found at i:1016100 original size:22 final size:21
Alignment explanation
Indices: 1016075--1016153 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
1016065 AATAAAGCTT
1016075 TCATCTTTGAAAATAGAACCTA
1 TCATCTTTGAAAA-AGAACCTA
* * *
1016097 TCATATTT-AAAGAGATATGCTA
1 TCATCTTTGAAAAAGA-A-CCTA
**
1016119 TCATCTTTGAAGAAAGAATATA
1 TCATCTTTGAA-AAAGAACCTA
1016141 TCATCTTTGAAAA
1 TCATCTTTGAAAA
1016154 GTGTAGATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 3 0.07
21 6 0.13
22 30 0.65
23 3 0.07
24 4 0.09
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (21 bp):
TCATCTTTGAAAAAGAACCTA
Found at i:1018413 original size:114 final size:113
Alignment explanation
Indices: 1018213--1018431 Score: 312
Period size: 114 Copynumber: 1.9 Consensus size: 113
1018203 GATCATGCAG
* * * * * * *
1018213 TTCATCTTTCAATTCCAGTGATTTGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTCGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
* * *
1018278 ACACTTCCAGAATATTCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCC-TATTTATACTATGAGCAAA
* * *
1018327 TTCATCTTTCAAATCTAATGATTGGTTTCGGGGTTTATACCAAACCAGATCAAATATCTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTCGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
1018392 ACACTTCCAGAAGATGCTATTGGGTCTCCTATTTATACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTATTTATACTA
1018432 CGAGAACGTG
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
113 10 0.11
114 82 0.89
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTGGTTTCGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTATTTATACTATGAGCAAA
Found at i:1024990 original size:28 final size:27
Alignment explanation
Indices: 1024939--1024992 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1024929 ATATTAATAA
*
1024939 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAACTATGAAAAT
* *
1024966 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAACTATGAAAA
1024993 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
AATAATATATATAAAAACTATGAAAAT
Found at i:1025922 original size:15 final size:14
Alignment explanation
Indices: 1025892--1025951 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
1025882 TATCAAATGT
1025892 AATAATAAAA-TAA
1 AATAATAAAATTAA
1025905 AATAATAATAATTAA
1 AATAATAA-AATTAA
1025920 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
1025935 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
1025950 AA
1 AA
1025952 ACTATAGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:1027351 original size:3 final size:3
Alignment explanation
Indices: 1027343--1027419 Score: 93
Period size: 3 Copynumber: 25.0 Consensus size: 3
1027333 ATATTTATTA
*
1027343 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
**
1027390 AAT TTT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1027420 GAAATGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.03
3 53 0.83
4 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:1029840 original size:46 final size:45
Alignment explanation
Indices: 1029790--1030692 Score: 738
Period size: 46 Copynumber: 19.5 Consensus size: 45
1029780 TTAGTAATTA
* * * * *
1029790 TTCATCAATTTCAGTTATAGCCTCTTTTCATGCATTAATACATTCG
1 TTCATCAATTT-AGTTATGGCATCCTTTCATGCCTTAATGCATTCG
*
1029836 TTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGCA-TCTG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTC-G
* *
1029882 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCA
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * ** * *
1029928 TTCATGTATTTTTAATTATGACATCCTTTCATGCCTTGGTGCATCCT
1 TTCAT-CA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * ** * *
1029975 TTCATGCACTTTAGTTATGACATTATTTCATGCCTTAATGCGTCCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * *
1030021 TTCATGCATTTTTATTTATGGCATCCTTTCATGACTTAGTGCATCCG
1 TTCAT-CA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
** * *
1030068 TTCATGCGCTTTAGTTATGGCATCCTTTCATGCCTTAGTGCATCCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
** *
1030114 TTCATGCGCTTTAGTTATGGCATCCTTTCATGACTTAATGCA-TCTG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTC-G
* * * * *
1030160 TTCATTCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCA
1 TTCA-TCA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
*
1030207 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCA-TCTG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTC-G
* * * * *
1030253 TTCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCATCCG
1 TTCAT-CA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * *
1030300 TTCATGCACTTTAGTAAAGGCATTCTTTCATGCCTTAATGCATCCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * * *
1030346 CTCATGCATTTTATTTATGGCATCCTTTCATGCCTTATTTCATCCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * *
1030392 TTCATGCACTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCCA
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * *
1030438 ATCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCA-TCTG
1 TTCAT-CA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTC-G
* * * *
1030485 TTCATGCACTTTAGTTATGGCATCCTTTCAAGCATTAATGCATCCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * *
1030531 TTCATGCATTTTTA-TGTATGGCATTCTTTCAAGCCTTAGTGCATTCG
1 TTCAT-CA-ATTTAGT-TATGGCATCCTTTCATGCCTTAATGCATTCG
*
1030578 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCA-TCG
1 TTCAT-CAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * * * *
1030623 TTCATGCATTTTTATTTATGGTATCCTTTCATGCCTTAGTGCATCCG
1 TTCAT-CA-ATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
* * *
1030670 TTCATGCACTATATTTATGGCAT
1 TTCAT-CAATTTAGTTATGGCAT
1030693 AGTCAATACT
Statistics
Matches: 723, Mismatches: 113, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
45 15 0.02
46 461 0.64
47 245 0.34
48 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (45 bp):
TTCATCAATTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCG
Found at i:1029979 original size:93 final size:93
Alignment explanation
Indices: 1029815--1030692 Score: 1163
Period size: 93 Copynumber: 9.5 Consensus size: 93
1029805 TATAGCCTCT
* * * * * *
1029815 TTTCATGCATTAATACATTCGTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * *
1029880 TGTTCATGCA-CTTTAGTTATGGCATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
* * * * * * * **
1029907 TTTCATGCCTTAATGCATTCATTCATGTATTTTTAATTATGACATCCTTTCATGCCTTGGTGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT
* * * * **
1029972 CCTTTCATGCA-CTTTAGTTATGACATTA
65 CCGTTCATGCATTTTTATTTATGGCATCC
* * * * * *
1030000 TTTCATGCCTTAATGCGTCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGACTTAGTGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT
** *
1030065 CCGTTCATGC-GCTTTAGTTATGGCATCC
65 CCGTTCATGCATTTTTATTTATGGCATCC
* *
1030093 TTTCATGCCTTAGTGCATCCGTTCATGCGCTTTAGTTATGGCATCCTTTCATGACTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* *
1030158 TGTTCATTCATTTTTATTTATGGCATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
*
1030186 TTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
*
1030251 TGTTCATGCATTTTTATTTATGGCATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
* * * *
1030279 TTTCATACCTTAGTGCATCCGTTCATGCACTTTAGTAAAGGCATTCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
*
1030344 CGCTCATGCA-TTTTATTTATGGCATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
* * *
1030371 TTTCATGCCTTATTTCATCCGTTCATGCACTTTAGTTATGGCATCCTTTTATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
**
1030436 CAATCATGCATTTTTATTTATGGCATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
* * * *
1030464 TTTCATACCTTAGTGCATCTGTTCATGCACTTTAGTTATGGCATCCTTTCAAGCATTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* *
1030529 CGTTCATGCATTTTTATGTATGGCATTC
66 CGTTCATGCATTTTTATTTATGGCATCC
* *
1030557 TTTCAAGCCTTAGTGCATTCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT-
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
*
1030621 CGTTCATGCATTTTTATTTATGGTATCC
66 CGTTCATGCATTTTTATTTATGGCATCC
* *
1030649 TTTCATGCCTTAGTGCATCCGTTCATGCACTATATTTATGGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCAT
1030693 AGTCAATACT
Statistics
Matches: 701, Mismatches: 81, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
92 212 0.30
93 489 0.70
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (93 bp):
TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
CGTTCATGCATTTTTATTTATGGCATCC
Found at i:1030024 original size:139 final size:139
Alignment explanation
Indices: 1029815--1030692 Score: 1073
Period size: 139 Copynumber: 6.3 Consensus size: 139
1029805 TATAGCCTCT
* * * * * *
1029815 TTTCATGCATTAATACATTCGTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * * * *
1029880 TGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCATTCATGTATTTTTAAT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-CTTTAGT
*
1029944 TATGACATCC
130 TATGGCATCC
* * * ** *
1029954 TTTCATGCCTTGGTGCATCCTTTCATGCACTTTAGTTATGACATTATTTCATGCCTTAATGCGTC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * * *
1030019 CGTTCATGCATTTTTATTTATGGCATCCTTTCATGACTTAGTGCATCCGTTCATGCGCTTTAGTT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
1030084 ATGGCATCC
131 ATGGCATCC
* *
1030093 TTTCATGCCTTAGTGCATCCGTTCATGCGCTTTAGTTATGGCATCCTTTCATGACTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * * * *
1030158 TGTTCATTCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
1030223 ATGGCATCC
131 ATGGCATCC
* * * * * *
1030232 TTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT
* * * * * *
1030297 CCGTTCATGCA-CTTTAGTAAAGGCATTCTTTCATGCCTTAATGCATCCGCTCATGCATTTTATT
65 CCGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGT
1030361 TATGGCATCC
130 TATGGCATCC
* * *
1030371 TTTCATGCCTTATTTCATCCGTTCATGCACTTTAGTTATGGCATCCTTTTATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
** * * * * *
1030436 CAATCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCATCTGTTCATGCACTTTAGTT
66 CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
1030501 ATGGCATCC
131 ATGGCATCC
* * * * * * *
1030510 TTTCAAGCATTAATGCATCCGTTCATGCATTTTTA-TGTATGGCATTCTTTCAAGCCTTAGTGCA
1 TTTCATGCCTTAGTGCATCCGTTCATGCA-CTTTAGT-TATGGCATCCTTTCATGCCTTAATGCA
* *
1030574 TTCGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT-CGTTCATGCATTTTTA
64 TCCGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA-CTTTA
* *
1030637 TTTATGGTATCC
128 GTTATGGCATCC
* *
1030649 TTTCATGCCTTAGTGCATCCGTTCATGCACTATATTTATGGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCAT
1030693 AGTCAATACT
Statistics
Matches: 629, Mismatches: 103, Indels: 15
0.84 0.14 0.02
Matches are distributed among these distances:
138 59 0.09
139 457 0.73
140 113 0.18
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (139 bp):
TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
CGTTCATGCATCTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTT
ATGGCATCC
Found at i:1030066 original size:20 final size:20
Alignment explanation
Indices: 1030041--1030157 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
1030031 TTTATTTATG
1030041 GCATCCTTTCATGACTTAGT
1 GCATCCTTTCATGACTTAGT
* *
1030061 GCATCCGTTCATGCGCTTTAGTTAT
1 GCATCCTTTCATG-AC-TTAG---T
*
1030086 GGCATCCTTTCATGCCTTAGT
1 -GCATCCTTTCATGACTTAGT
* *
1030107 GCATCCGTTCATGCGCTTTAGTTAT
1 GCATCCTTTCATG-AC-TTAG---T
*
1030132 GGCATCCTTTCATGACTTAAT
1 -GCATCCTTTCATGACTTAGT
1030153 GCATC
1 GCATC
1030158 TGTTCATTCA
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
20 29 0.38
21 4 0.05
22 8 0.11
24 7 0.09
25 4 0.05
26 24 0.32
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (20 bp):
GCATCCTTTCATGACTTAGT
Found at i:1030205 original size:20 final size:20
Alignment explanation
Indices: 1030180--1030259 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
1030170 TTTATTTATG
1030180 GCATCCTTTCATGCCTTAGT
1 GCATCCTTTCATGCCTTAGT
*
1030200 GCATCCATTCATGCACTTTAGTTAT
1 GCATCCTTTCATGC-C-TTAG---T
*
1030225 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAGT
1030246 GCAT-CTGTTCATGC
1 GCATCCT-TTCATGC
1030260 ATTTTTATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
19 2 0.04
20 24 0.48
21 2 0.04
22 4 0.08
24 3 0.06
25 2 0.04
26 13 0.26
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.39
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAGT
Found at i:1030221 original size:232 final size:232
Alignment explanation
Indices: 1029834--1030692 Score: 1165
Period size: 232 Copynumber: 3.7 Consensus size: 232
1029824 TTAATACATT
* * *
1029834 CGTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCACTTTAGTTA
1 CGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTA
* * * *
1029899 TGGCATCCTTTCATGCCTTAATGCAT-TCATTCATGTATTTTTAATTATGACATCCTTTCATGCC
66 TGGCATCCTTTCATGCCTTAATGCATCT-GTTCATGCATTTTTATTTATGGCATCCTTTCATGCC
* * * ** * *
1029963 TTGGTGCATCCTTTCATGCACTTTAGTTATGACATTATTTCATGCCTTAATGCGTCCGTTCATGC
130 TTAGTGCATCCATTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGC
1030028 ATTTTTATTTATGGCATCCTTTCATGACTTAGTGCATC
195 ATTTTTATTTATGGCATCCTTTCATGACTTAGTGCATC
* * *
1030066 CGTTCATGCGCTTTAGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCGCTTTAGTTA
1 CGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTA
* *
1030131 TGGCATCCTTTCATGACTTAATGCATCTGTTCATTCATTTTTATTTATGGCATCCTTTCATGCCT
66 TGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCT
1030196 TAGTGCATCCATTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCA
131 TAGTGCATCCATTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCA
1030261 TTTTTATTTATGGCATCCTTTCAT-ACCTTAGTGCATC
196 TTTTTATTTATGGCATCCTTTCATGA-CTTAGTGCATC
* * * * * *
1030298 CGTTCATGCACTTTAGTAAAGGCATTCTTTCATGCCTTAATGCATCCGCTCATGCATTTTATTTA
1 CGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTA
* * * * * *
1030363 TGGCATCCTTTCATGCCTTATTTCATCCGTTCATGCA-CTTTAGTTATGGCATCCTTTTATGCCT
66 TGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCT
* * * * * *
1030427 TAATGCATCCAATCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCATCTGTTCATGC
131 TAGTGCATCCATTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGC
* * * *
1030492 A-CTTTAGTTATGGCATCCTTTCAAG-CATTAATGCATC
195 ATTTTTATTTATGGCATCCTTTCATGAC-TTAGTGCATC
* * * * *
1030529 CGTTCATGCATTTTTA-TGTATGGCATTCTTTCAAGCCTTAGTGCATTCGTTCATGCACTTTAGT
1 CGTTCATGCA-CTTTAGT-TATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGT
*
1030593 TATGGCATCCTTTCATGCCTTAATGCATC-GTTCATGCATTTTTATTTATGGTATCCTTTCATGC
64 TATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATGC
* * *
1030657 CTTAGTGCATCCGTTCATGCACTATATTTATGGCAT
129 CTTAGTGCATCCATTCATGCACTTTAGTTATGGCAT
1030693 AGTCAATACT
Statistics
Matches: 553, Mismatches: 66, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
230 1 0.00
231 104 0.19
232 447 0.81
233 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (232 bp):
CGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCACTTTAGTTA
TGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCT
TAGTGCATCCATTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCA
TTTTTATTTATGGCATCCTTTCATGACTTAGTGCATC
Found at i:1030330 original size:278 final size:278
Alignment explanation
Indices: 1029815--1030692 Score: 1181
Period size: 278 Copynumber: 3.2 Consensus size: 278
1029805 TATAGCCTCT
* * * * * *
1029815 TTTCATGCATTAATACATTCGTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * * * * *
1029880 TGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCATTCATTCATGTATTTTTAAT
66 TGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCA-CTTTAGT
* ** * * * * *
1029944 TATGACATCCTTTCATGCCTTGGTGCATCCT-TTCATGCA-CTTTAGTTATGACATTATTTCATG
130 TATGGCATCCTTTCATGCCTTAATGCAT-CTGTTCATGCATTTTTATTTATGGCATTCTTTCATA
* * * * * *
1030007 CCTTAATGCGTCCGTTCATGCATTTTTATTTATGGCATCCTTTCATGACTTAGTGCATCCGTTCA
194 CCTTAGTGCATCCGTTCATGCA-CTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCA
** *
1030072 TGCGCTTTAGTTATGGCATCC
258 TGCATTTTATTTATGGCATCC
* *
1030093 TTTCATGCCTTAGTGCATCCGTTCATGCGCTTTAGTTATGGCATCCTTTCATGACTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
*
1030158 TGTTCATTCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTT
66 TGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTT
*
1030223 ATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATCCTTTCATACC
131 ATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATTCTTTCATACC
* * * *
1030288 TTAGTGCATCCGTTCATGCACTTTAGTAAAGGCATTCTTTCATGCCTTAATGCATCCGCTCATGC
196 TTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
1030353 ATTTTATTTATGGCATCC
261 ATTTTATTTATGGCATCC
* * *
1030371 TTTCATGCCTTATTTCATCCGTTCATGCACTTTAGTTATGGCATCCTTTTATGCCTTAATGCATC
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
*** * **
1030436 CAATCATGCATTTTTATTTATGGCATCCTTTCATACCTTAGTGCATCTGTTCATGCACTTTAGTT
66 TGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTT
* * * *
1030501 ATGGCATCCTTTCAAGCATTAATGCATCCGTTCATGCATTTTTATGTATGGCATTCTTTCA-AGC
131 ATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATTCTTTCATA-C
*
1030565 CTTAGTGCATTCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCAT-CGTTCATG
195 CTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATG
*
1030629 CATTTTTATTTATGGTATCC
260 CA-TTTTATTTATGGCATCC
* *
1030649 TTTCATGCCTTAGTGCATCCGTTCATGCACTATATTTATGGCAT
1 TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCAT
1030693 AGTCAATACT
Statistics
Matches: 530, Mismatches: 65, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
277 12 0.02
278 439 0.83
279 79 0.15
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (278 bp):
TTTCATGCCTTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
TGTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAGTT
ATGGCATCCTTTCATGCCTTAATGCATCTGTTCATGCATTTTTATTTATGGCATTCTTTCATACC
TTAGTGCATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
ATTTTATTTATGGCATCC
Found at i:1051947 original size:30 final size:30
Alignment explanation
Indices: 1051882--1051937 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
1051872 CAATTTAAGG
1051882 CAAAATGGTTTTGGACTTGAATTGAATTCA
1 CAAAATGGTTTTGGACTTGAATTGAATTCA
1051912 CAAAAT-GTATTT-GACTT-AATTGAATT
1 CAAAATGGT-TTTGGACTTGAATTGAATT
1051938 TATTCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 9 0.36
29 7 0.28
30 9 0.36
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (30 bp):
CAAAATGGTTTTGGACTTGAATTGAATTCA
Found at i:1052030 original size:19 final size:19
Alignment explanation
Indices: 1052006--1052048 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1051996 GTTTTATGAT
*
1052006 AGTAAATTACTATTCGAAC
1 AGTAAATCACTATTCGAAC
* *
1052025 AGTAAATCACTGTTTGAAC
1 AGTAAATCACTATTCGAAC
1052044 AGTAA
1 AGTAA
1052049 CCTGCGCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (19 bp):
AGTAAATCACTATTCGAAC
Found at i:1054420 original size:44 final size:44
Alignment explanation
Indices: 1054339--1054427 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
1054329 ACATCAATGA
*
1054339 ACATTCAAGGGCATGCATCGGTGCATCAGCTGATGTATCGATGC
1 ACATTCAAGGGCATGCATCGGTGCATCAGCTAATGTATCGATGC
* *
1054383 ACATTCCAAGGG-ATGCATCGGTGCA-CTGTTAAGTGTATCGATGC
1 ACATT-CAAGGGCATGCATCGGTGCATCAGCTAA-TGTATCGATGC
1054427 A
1 A
1054428 TTAAGCACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 4 0.10
44 30 0.75
45 6 0.15
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
ACATTCAAGGGCATGCATCGGTGCATCAGCTAATGTATCGATGC
Found at i:1060328 original size:45 final size:46
Alignment explanation
Indices: 1060240--1060330 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
1060230 TTGAAAAAGC
* *
1060240 CTAAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTAAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
*
1060286 CTAAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTAAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
1060331 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (46 bp):
CTAAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
Found at i:1065003 original size:22 final size:22
Alignment explanation
Indices: 1064977--1065023 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1064967 TAAGAAATTC
*
1064977 ATATAAAGTTATATTTTTTAAA
1 ATATAAAGTTATATTTTTAAAA
***
1064999 ATATACTTTTATATTTTTAAAA
1 ATATAAAGTTATATTTTTAAAA
1065021 ATA
1 ATA
1065024 AATTTTGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATAAAGTTATATTTTTAAAA
Found at i:1067255 original size:2 final size:2
Alignment explanation
Indices: 1067248--1067280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1067238 GATATGTGGG
1067248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1067281 ATGTTGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1070614 original size:17 final size:16
Alignment explanation
Indices: 1070578--1070618 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1070568 ATCTAGGGAT
*
1070578 TTTTTCTTTGAGAATG
1 TTTTTCCTTGAGAATG
1070594 TTTTTCCTTGAGAATG
1 TTTTTCCTTGAGAATG
1070610 TTTTTCCTT
1 TTTTTCCTT
1070619 TTAGGAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTTTCCTTGAGAATG
Found at i:1072971 original size:14 final size:15
Alignment explanation
Indices: 1072936--1072972 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1072926 TAATTTATTT
*
1072936 TTATAAT-TATATTA
1 TTATAATATATAATA
1072950 TTATAATATATAATA
1 TTATAATATATAATA
1072965 -TATAATAT
1 TTATAATAT
1072973 TATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATAATATATAATA
Found at i:1072996 original size:41 final size:40
Alignment explanation
Indices: 1072912--1073024 Score: 113
Period size: 41 Copynumber: 2.8 Consensus size: 40
1072902 GATGATTTTA
* * *
1072912 ATAATATATCATTATAAT-TTATTTTTATAATTATATTATT
1 ATAATATATAATTATAATATTATTTTTAT-TTTATAATATT
1072952 ATAATATATAATATATAATATTATTTTTATTTTAATAATA-T
1 ATAATATATAAT-TATAATATTATTTTTATTTT-ATAATATT
* * * *
1072993 ATAATAAATTATTAATAAAATTAATTTTATTT
1 ATAATATATAATT-ATAATATTATTTTTATTT
1073025 ATTATTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 12 0.19
41 35 0.56
42 15 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (40 bp):
ATAATATATAATTATAATATTATTTTTATTTTATAATATT
Found at i:1073048 original size:26 final size:28
Alignment explanation
Indices: 1073007--1073058 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1072997 TAAATTATTA
*
1073007 ATAAAATTAATTTTATTT-ATTATTTTT
1 ATAAAATTAATATTATTTAATTATTTTT
1073034 ATAAAA-TAATATTATTTAATTATTT
1 ATAAAATTAATATTATTTAATTATTT
1073059 AATATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATAAAATTAATATTATTTAATTATTTTT
Found at i:1073155 original size:25 final size:24
Alignment explanation
Indices: 1073095--1073155 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
1073085 ATAATATAAT
1073095 ATTTTTAATATTATAATTTTAAAA
1 ATTTTTAATATTATAATTTTAAAA
* * *
1073119 ATTTTATTATATTTTTATTTTAAAA
1 ATTTT-TAATATTATAATTTTAAAA
1073144 ATTATTTAATAT
1 ATT-TTTAATAT
1073156 AATTAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 5 0.16
25 24 0.77
26 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTTAATATTATAATTTTAAAA
Found at i:1073234 original size:27 final size:27
Alignment explanation
Indices: 1073175--1073236 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
1073165 TATATTACTC
1073175 TTAT-TTTTAAAAATAATTTATAATAT
1 TTATATTTTAAAAATAATTTATAATAT
* *
1073201 TTTTATTTTAATAA-AATATTATAAT-T
1 TTATATTTTAAAAATAAT-TTATAATAT
1073227 TTAATATTTT
1 TT-ATATTTT
1073237 TATTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATTTTAAAAATAATTTATAATAT
Found at i:1076383 original size:16 final size:17
Alignment explanation
Indices: 1076362--1076393 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1076352 GATACAGATC
1076362 TTTTTAAAA-CATATTT
1 TTTTTAAAACCATATTT
1076378 TTTTTAAAACCATATT
1 TTTTTAAAACCATATT
1076394 AATTCCTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAAAACCATATTT
Found at i:1076792 original size:24 final size:23
Alignment explanation
Indices: 1076739--1076831 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
1076729 AAGATATCAT
* * *
1076739 AAATCAAAACATAATTCAGGTCA
1 AAATCAAAACAGAATTCAGATCG
* *
1076762 AATATCAGAACATAATTCAGATCGG
1 AA-ATCAAAACAGAATTCAGATC-G
*
1076787 AAATCAAAATAGAATTCAGATCAG
1 AAATCAAAACAGAATTCAGATC-G
* *
1076811 AAATCATAACAGAAATCAGAT
1 AAATCAAAACAGAATTCAGAT
1076832 AAAACATTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.22
Consensus pattern (23 bp):
AAATCAAAACAGAATTCAGATCG
Found at i:1076830 original size:48 final size:48
Alignment explanation
Indices: 1076739--1076831 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
1076729 AAGATATCAT
* * * *
1076739 AAATCAAAACATAATTCAGGTCAAATATCAGAACATAATTCAGATCGG
1 AAATCAAAACAGAATTCAGATCAAATATCAGAACAGAAATCAGATCGG
* *
1076787 AAATCAAAATAGAATTCAGATCAGAA-ATCATAACAGAAATCAGAT
1 AAATCAAAACAGAATTCAGATCA-AATATCAGAACAGAAATCAGAT
1076832 AAAACATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 36 0.95
49 2 0.05
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.22
Consensus pattern (48 bp):
AAATCAAAACAGAATTCAGATCAAATATCAGAACAGAAATCAGATCGG
Found at i:1080245 original size:24 final size:24
Alignment explanation
Indices: 1080218--1080298 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
1080208 ATCAAAAGAT
* * *
1080218 AATTCAGGTC-AAATATCATAACAG
1 AATTCAGATCGAAA-ATCAGAACAA
1080242 AATTCAGATCGAAAATCAGAACAA
1 AATTCAGATCGAAAATCAGAACAA
* *
1080266 AATTCATATCGTAAATCAGAACAGA
1 AATTCAGATCGAAAATCAGAACA-A
1080291 AA-TCAGAT
1 AATTCAGAT
1080299 AAAACATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 43 0.88
25 6 0.12
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (24 bp):
AATTCAGATCGAAAATCAGAACAA
Found at i:1084004 original size:14 final size:14
Alignment explanation
Indices: 1083985--1084014 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1083975 AATTAAACTC
1083985 TTTTTATATTATTA
1 TTTTTATATTATTA
1083999 TTTTTATATTATTA
1 TTTTTATATTATTA
1084013 TT
1 TT
1084015 ATTAAGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTATATTATTA
Found at i:1091108 original size:135 final size:135
Alignment explanation
Indices: 1090864--1091147 Score: 322
Period size: 135 Copynumber: 2.1 Consensus size: 135
1090854 TGAGTCAAGA
* * * * *
1090864 TTTGGATGACTCCCCTTTGCGGTTTGAGTTTCATTGAAACTAGCTCTTCCTTACAAGTTGAGCTA
1 TTTGGATGACTCCCCTTTACGGGTTGAGTCTCATTGAAACTAGCTCTTCCTTACAAGGTAAGCTA
* * * *
1090929 GTTAAGATAAGCGCCTCCTTGTGAGTTGATCCAGGTTATGAATGACTCTTTTTTGTGAGTTGAGT
66 GTTAAGATAAGCACCTCCTTGTGAGTTGAACCAAGTTATAAATGACTCTTTTTTGTGAGTTGAGT
1090994 GAGGG
131 GAGGG
* *
1090999 TTTGTATGACTCCCCTTTACGGGTTGAGTCTCATTGAAACTAGCTCATT-CTTACCAGGTAAGCT
1 TTTGGATGACTCCCCTTTACGGGTTGAGTCTCATTGAAACTAGCTC-TTCCTTACAAGGTAAGCT
* * * *** **
1091063 AGTTAAGGT-TGACACCTCCTT-TCGAGTTGAACCAAGTTGTAAATGACTCACCTTTACGAGTTG
65 AGTTAAGATAAG-CACCTCCTTGT-GAGTTGAACCAAGTTATAAATGACTCTTTTTTGTGAGTTG
* *
1091126 AGTTAAGG
128 AGTGAGGG
*
1091134 TTTGGATAACTCCC
1 TTTGGATGACTCCC
1091148 ATTTTCCGGC
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
134 2 0.02
135 119 0.97
136 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (135 bp):
TTTGGATGACTCCCCTTTACGGGTTGAGTCTCATTGAAACTAGCTCTTCCTTACAAGGTAAGCTA
GTTAAGATAAGCACCTCCTTGTGAGTTGAACCAAGTTATAAATGACTCTTTTTTGTGAGTTGAGT
GAGGG
Found at i:1092523 original size:21 final size:20
Alignment explanation
Indices: 1092480--1092535 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1092470 CAGTAAGTTT
**
1092480 GGGATCGATCCTTTAGGCCAA
1 GGGATCGATCCTTT-TCCCAA
1092501 GGGATCGATCCTTTTCCCTAA
1 GGGATCGATCCTTTTCCC-AA
*
1092522 GGAATCGAT-CTTTT
1 GGGATCGATCCTTTT
1092536 TTCTGGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (20 bp):
GGGATCGATCCTTTTCCCAA
Found at i:1095357 original size:124 final size:124
Alignment explanation
Indices: 1095138--1095478 Score: 632
Period size: 124 Copynumber: 2.8 Consensus size: 124
1095128 AAACATACCA
1095138 CCCATACCTAGATGAAATGG--ACACCACGTGGGTTTGATTAACCCACCAATTTTAACACTAAAA
1 CCCATACCTAGATGAAATGGCTAC-CCACGTGGGTTTGATTAACCCACCAATTTTAACACTAAAA
1095201 TACTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
65 TACTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
*
1095261 CCCATACCTAGATGAAATGGCTACCCACGTGGGTTTGATTAAGCCACCAATTTTAACACTAAAAT
1 CCCATACCTAGATGAAATGGCTACCCACGTGGGTTTGATTAACCCACCAATTTTAACACTAAAAT
1095326 ACTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
66 ACTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
**
1095385 CCCATACCTAGATGAAATGGCTACCCACGTGGGTTTGATTAACCCACCAATTTTTGCACTAAAAT
1 CCCATACCTAGATGAAATGGCTACCCACGTGGGTTTGATTAACCCACCAATTTTAACACTAAAAT
1095450 ACTAAACAATTATTATCATATTACTAACC
66 ACTAAACAATTATTATCATATTACTAACC
1095479 TAATTTTAAC
Statistics
Matches: 212, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
123 20 0.09
124 190 0.90
125 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.27
Consensus pattern (124 bp):
CCCATACCTAGATGAAATGGCTACCCACGTGGGTTTGATTAACCCACCAATTTTAACACTAAAAT
ACTAAACAATTATTATCATATTACTAACCCAAATAAACTCTTATATGAAAACAAACAAC
Found at i:1096415 original size:3 final size:3
Alignment explanation
Indices: 1096399--1096457 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
1096389 AAACACATAT
1096399 ATA ATA A-A ATTA ATA ATA ATA ATA A-A TATA ATA ATA ATA ATA AT-
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
1096443 ATA AT- ATA TATA ATA
1 ATA ATA ATA -ATA ATA
1096458 TTTTTTAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 7 0.14
3 36 0.73
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1096422 original size:18 final size:19
Alignment explanation
Indices: 1096399--1096457 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 19
1096389 AAACACATAT
1096399 ATAATAAAAT-TAATAATA
1 ATAATAAAATATAATAATA
1096417 ATAATAAATATAATAATAATA
1 ATAATAAA-AT-ATAATAATA
*
1096438 ATAATATAATATATATAATA
1 ATAATAAAATATA-ATAATA
1096458 TTTTTTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 8 0.22
19 5 0.14
20 8 0.22
21 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAATAAAATATAATAATA
Found at i:1097045 original size:136 final size:136
Alignment explanation
Indices: 1096803--1097403 Score: 851
Period size: 136 Copynumber: 4.5 Consensus size: 136
1096793 AATTTGAAAG
* * * *
1096803 GAACAAGTTCTTCTCATTATAAAC-T-TTCT-CCT-T-TAGGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
1096863 CTCCATTAGAAATTTCAATCCCTCAAGCGAGG-AGTCACTGATTCGAAATGCCATGAATCGAGTG
66 CTCCATTGGAAATTTCAATCCCTCAAGCGAGGTA-TCACTGATTCGAAATGCCATGAATCGAGTG
1096927 ATAGGTC
130 ATAGGTC
* * * *
1096934 GAACAAGCTCTTCTCATTATGAACTTATTCTCTCTATGTTGGATGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * * * *
1096999 CTCCATTGGAAATTTTAATCCCTCAAGCGAGGTGTCATTAAATCGAAATGCCGTGAATCAAGTGA
66 CTCCATTGGAAATTTCAATCCCTCAAGCGAGGTATCACTGATTCGAAATGCCATGAATCGAGTGA
1097064 TA-GTC
131 TAGGTC
* * *
1097069 GAACAAGCTCTTCTTATTATGAACTTATTCT-CTTCCGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* ***
1097133 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCGAAATGTTGTGAATCGAGTGA
66 CTCCATTGGAAATTTCAATCCCTCAAGCGAGGTATCACTGATTCGAAATGCCATGAATCGAGTGA
1097198 TAGGTC
131 TAGGTC
* * *
1097204 GAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTTTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
1097269 CTCAATTGGAAATATCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCATGAATGGAGTGA
66 CTCCATTGGAAATTTCAATCCCTCAAGCGAGGTATCACTGATTCGAAATGCCATGAATCGAGTGA
1097334 TAGGTC
131 TAGGTC
1097340 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1097404 TGTTCTGAAA
Statistics
Matches: 417, Mismatches: 45, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
131 22 0.05
132 1 0.00
133 4 0.01
134 87 0.21
135 90 0.22
136 213 0.51
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATTTCAATCCCTCAAGCGAGGTATCACTGATTCGAAATGCCATGAATCGAGTGA
TAGGTC
Found at i:1097335 original size:270 final size:271
Alignment explanation
Indices: 1096842--1097403 Score: 851
Period size: 270 Copynumber: 2.1 Consensus size: 271
1096832 CCTTTAGGAC
*
1096842 GAGTTCTTCTCATTATGAACTCTCCATTAGAAATTTCAATCCCTCAAGCGAGGAGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTAGAAATGTCAATCCCTCAAGCGAGGAGTCACTGATTC
*
1096907 GAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCTCTATG
66 GAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTATG
* * * * ** *
1096972 TTGGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATTTTAATCCCTCAAGCGAGGTGTCAT
131 TCGGATGAGTTATTCTCATTATGAACTCTCAATTGGAAATATCAATCCCTCAAGCGAGGCATCAC
* *
1097037 TAAATCGAAATGCCGTGAATCAAGTGATA-GTCGAACAAGCTCTTCTTATTATGAACTTATTCT-
196 TAAATCGAAATGCCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTC
*
1097100 CTTCCGTCGGAT
261 CCTCCGT-GGAT
*
1097112 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTA-TCACTGATT
1 GAGTTCTTCTCATTATGAACTCTCCATTAGAAATGTCAATCCCTCAAGCGAGG-AGTCACTGATT
*** * * *
1097176 CGAAATGTTGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTTT
65 CGAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTAT
*
1097241 GTCGGATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATATCAATCCCTCAAGCGAGGCATCA
130 GTCGGATGAGTTATTCTCATTATGAACTCTCAATTGGAAATATCAATCCCTCAAGCGAGGCATCA
* * * **
1097306 CTGATTCGAAATGTCATGAATGGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCT
195 CTAAATCGAAATGCCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCT
*
1097371 CCCTCTGTGGAT
260 CCCTCCGTGGAT
1097383 GAGTTCTTCTCATTATGAACT
1 GAGTTCTTCTCATTATGAACT
1097404 TGTTCTGAAA
Statistics
Matches: 263, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
270 199 0.76
271 59 0.22
272 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (271 bp):
GAGTTCTTCTCATTATGAACTCTCCATTAGAAATGTCAATCCCTCAAGCGAGGAGTCACTGATTC
GAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTATG
TCGGATGAGTTATTCTCATTATGAACTCTCAATTGGAAATATCAATCCCTCAAGCGAGGCATCAC
TAAATCGAAATGCCATGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTC
CCTCCGTGGAT
Found at i:1097756 original size:36 final size:36
Alignment explanation
Indices: 1097716--1097834 Score: 94
Period size: 36 Copynumber: 3.2 Consensus size: 36
1097706 AGGAAAACTG
1097716 TCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCA
* ** * * * * * **
1097752 TCTCAAGTAAGATTCAATTTATTGTTTCGAGGGAAAACTG
1 TCTCAAGCAAGA-AGAA-GTA-GGTTT-TAAGAAAAACCA
*
1097792 TCTAAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCA
*
1097828 TATCAAG
1 TCTCAAG
1097835 TGAGATACAT
Statistics
Matches: 56, Mismatches: 23, Indels: 8
0.64 0.26 0.09
Matches are distributed among these distances:
36 23 0.41
37 6 0.11
38 4 0.07
39 6 0.11
40 17 0.30
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (36 bp):
TCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCA
Found at i:1097865 original size:73 final size:73
Alignment explanation
Indices: 1097684--1097901 Score: 319
Period size: 76 Copynumber: 2.9 Consensus size: 73
1097674 AGCTCTCTCG
* *
1097684 AGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAA
1 AGTGAGATACATTTTGTTTCAAGGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAA
*
1097749 CCATCTCA
66 CCATATCA
* * * *
1097757 AGTAAGATTCAATTTATTGTTTCGAGGGAAAACTGTCTAAAGCAAGAAGAAGTAGGTTTTAAGAA
1 AGTGAGATAC-A-TT-TTGTTTCAAGGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAA
1097822 AAACCATATCA
63 AAACCATATCA
* * *
1097833 AGTGAGATACATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAGAAAAA
1 AGTGAGATACATTTTGTTTCAAGGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAA
1097898 CCAT
66 CCAT
1097902 CTTAAGGGAA
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
73 58 0.45
74 3 0.02
75 3 0.02
76 64 0.50
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (73 bp):
AGTGAGATACATTTTGTTTCAAGGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAA
CCATATCA
Found at i:1097940 original size:73 final size:73
Alignment explanation
Indices: 1097692--1097943 Score: 285
Period size: 73 Copynumber: 3.4 Consensus size: 73
1097682 CGAGTGAGAT
1097692 AAATTTTGTTTCAA-AGGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTC
1 AAATTTTGTTTCAAGA-GAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTC
*
1097756 AA-GTAAGATTC
65 AAGGGAA-A--C
* * * * *
1097767 AATTTATTGTTTCGAGGGAAAACTGTCTAAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATATC
1 AAATT-TTGTTTCAAGAGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTC
* * *
1097832 AAGTGAGAT
65 AAGGGAAAC
* * * * * *
1097841 ACATTTTGTTTCAAGGGAAAACTGTCTCAAGCGAGACGAAGTTGGTTTTAAGAAAAACCATCTTA
1 AAATTTTGTTTCAAGAGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTCA
1097906 AGGGAAAC
66 AGGGAAAC
*
1097914 AAAACTTTGTTTCAAGAGAAAA-TGTCTCAA
1 -AAATTTTGTTTCAAGAGAAAACTGTCTCAA
1097944 AAACTTGTTT
Statistics
Matches: 149, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
73 66 0.44
74 21 0.14
75 4 0.03
76 57 0.38
77 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (73 bp):
AAATTTTGTTTCAAGAGAAAACTGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTCA
AGGGAAAC
Found at i:1097953 original size:28 final size:29
Alignment explanation
Indices: 1097914--1097971 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
1097904 TAAGGGAAAC
1097914 AAAACTTTGTTTCAAGAGAAAATGTCTCA
1 AAAACTTTGTTTCAAGAGAAAATGTCTCA
*
1097943 AAAAC-TTGTTTCAAGAGAAACTGTCTCA
1 AAAACTTTGTTTCAAGAGAAAATGTCTCA
1097971 A
1 A
1097972 GAAAGACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (29 bp):
AAAACTTTGTTTCAAGAGAAAATGTCTCA
Found at i:1097973 original size:15 final size:15
Alignment explanation
Indices: 1097925--1097973 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1097915 AAACTTTGTT
*
1097925 TCAAGAGAAAATGTC
1 TCAAGAGAAACTGTC
*
1097940 TC-A-A-AAACTTGTT
1 TCAAGAGAAAC-TGTC
1097953 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
1097968 TCAAGA
1 TCAAGA
1097974 AAGACAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 3 0.11
13 6 0.22
14 2 0.07
15 12 0.44
16 4 0.15
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:1098072 original size:92 final size:90
Alignment explanation
Indices: 1097951--1098118 Score: 248
Period size: 92 Copynumber: 1.8 Consensus size: 90
1097941 CAAAAACTTG
*
1097951 TTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTAGTTTCAAGGGAAACGTTCTCAAAGTTATGT
1 TTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTAGTCTCAAGGGAAACGTTCTCAAAGTTA--T
1098016 GTTTCAAGAGAAATGGGAGACAATTTT
64 GTTTCAAGAGAAATGGGAGACAATTTT
* * * * *
1098043 TTTCAAGGGAAACTGTCTCAA-ATGAGACAAAATTTGTCTCAAGGGAAATGTTTTCAAAGTTATG
1 TTTCAAGAGAAACTGTCTCAAGA-AAGACAAAATTAGTCTCAAGGGAAACGTTCTCAAAGTTATG
1098107 TTTCAAGAGAAA
65 TTTCAAGAGAAA
1098119 CTATCTCAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
90 14 0.20
91 1 0.01
92 54 0.78
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (90 bp):
TTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTAGTCTCAAGGGAAACGTTCTCAAAGTTATGT
TTCAAGAGAAATGGGAGACAATTTT
Found at i:1098162 original size:21 final size:22
Alignment explanation
Indices: 1098124--1098174 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
1098114 AGAAACTATC
**
1098124 TCAAGGGAGACAAAAATTTGTT
1 TCAAGGGAGACAAAAATTCATT
1098146 TCAAGGGAGAC-AAAATTCATT
1 TCAAGGGAGACAAAAATTCATT
1098167 TCAAGGGA
1 TCAAGGGA
1098175 AACGTTCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (22 bp):
TCAAGGGAGACAAAAATTCATT
Found at i:1098186 original size:86 final size:87
Alignment explanation
Indices: 1098066--1098225 Score: 234
Period size: 86 Copynumber: 1.9 Consensus size: 87
1098056 TGTCTCAAAT
** * *
1098066 GAGACAAAATTTGTCTCAAGGGAAATGTTTTCAAAG-T-TATGTTTCAAGAGAAACTATCTCAAG
1 GAGACAAAATTCATCTCAAGGGAAACGTTCTCAAAGTTCTATGTTTCAAGAGAAA-TATCTCAAG
1098129 GGAGACAAAAATTTGTTTCAAGG
65 GGAGACAAAAATTTGTTTCAAGG
* * *
1098152 GAGACAAAATTCATTTCAAGGGAAACGTTCTCAAAGTTCTGTGTTTGAAGAGAAATATCTCAAGG
1 GAGACAAAATTCATCTCAAGGGAAACGTTCTCAAAGTTCTATGTTTCAAGAGAAATATCTCAAGG
1098217 GAGACAAAA
66 GAGACAAAA
1098226 TTTATTTTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 31 0.48
87 20 0.31
88 14 0.22
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (87 bp):
GAGACAAAATTCATCTCAAGGGAAACGTTCTCAAAGTTCTATGTTTCAAGAGAAATATCTCAAGG
GAGACAAAAATTTGTTTCAAGG
Found at i:1099589 original size:12 final size:12
Alignment explanation
Indices: 1099550--1099599 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1099540 ATTCTCGTCC
1099550 CTTTTTCTTTGCT
1 CTTTTTCTTT-CT
* *
1099563 -TTTTTGTTTAT
1 CTTTTTCTTTCT
*
1099574 -TTTTTCTTTTT
1 CTTTTTCTTTCT
1099585 CTTTTTCTTTCT
1 CTTTTTCTTTCT
1099597 CTT
1 CTT
1099600 GTTGCTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (12 bp):
CTTTTTCTTTCT
Found at i:1100844 original size:19 final size:18
Alignment explanation
Indices: 1100810--1100851 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1100800 TGCTTAAATG
*
1100810 AATGCTATGCAGAATGTA
1 AATGCTATGCAGAATGCA
1100828 AATGCATATGCCA-AATGCA
1 AATGC-TATG-CAGAATGCA
1100847 AATGC
1 AATGC
1100852 GAAAGGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 14 0.67
20 2 0.10
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (18 bp):
AATGCTATGCAGAATGCA
Found at i:1102928 original size:18 final size:16
Alignment explanation
Indices: 1102905--1102939 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1102895 CAACTTTAAA
1102905 CTTCTTCATTCATCGGAT
1 CTTCTTC-TTCAT-GGAT
1102923 CTTCTTCTTCATGGAT
1 CTTCTTCTTCATGGAT
1102939 C
1 C
1102940 GTTTGAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.14, C:0.29, G:0.11, T:0.46
Consensus pattern (16 bp):
CTTCTTCTTCATGGAT
Found at i:1105763 original size:3 final size:3
Alignment explanation
Indices: 1105747--1105822 Score: 90
Period size: 3 Copynumber: 26.0 Consensus size: 3
1105737 AAACACATAT
1105747 ATA ATA A-A ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1105792 A-A TATA ATA AT- ATA AT- ATA AT- ATA TATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
1105823 TTTTTTAAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
2 9 0.14
3 50 0.77
4 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1112194 original size:6 final size:6
Alignment explanation
Indices: 1112151--1112209 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
1112141 TCTGAGTGAT
* * *
1112151 ATATTA ATA-TA TTATT- ATATAA ATATAA ATATAATA ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA ATATTA
*
1112199 ATATTA TTATT
1 ATATTA ATATT
1112210 TATAAAGCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 7 0.16
6 32 0.73
8 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:1120555 original size:20 final size:19
Alignment explanation
Indices: 1120530--1120831 Score: 352
Period size: 20 Copynumber: 15.1 Consensus size: 19
1120520 TTTCTCATGA
1120530 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCT-TGGGTC
*
1120550 ATTTGTAAAGCCTTCAGGTC
1 ATTTGTAAAGCCTT-GGGTC
*
1120570 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCT-TGGGTC
** *
1120590 ATTTGTAAAGCCTCCAGATC
1 ATTTGTAAAGCCT-TGGGTC
*
1120610 ATTTGTAAATCCTTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
*
1120630 ATTTATAAAGCCTCTGGGTC
1 ATTTGTAAAGCCT-TGGGTC
*
1120650 ATTTGTAAAGCATTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
1120670 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
1120690 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
*
1120710 ATTTGTAAAGCCTATGGATC
1 ATTTGTAAAGCCT-TGGGTC
* *
1120730 ATTTATAAATCCTTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
*
1120750 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCT-TGGGTC
1120770 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTT-GGGTC
*
1120790 ATTTGTAAAGCCTTTGAGTC
1 ATTTGTAAAGCC-TTGGGTC
1120810 ATTTGTAAAGCCTTTGGGTC
1 ATTTGTAAAGCC-TTGGGTC
1120830 AT
1 AT
1120832 CTATAAGTCT
Statistics
Matches: 248, Mismatches: 24, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
19 3 0.01
20 241 0.97
21 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTTGTAAAGCCTTGGGTC
Found at i:1120574 original size:40 final size:40
Alignment explanation
Indices: 1120530--1120831 Score: 398
Period size: 40 Copynumber: 7.5 Consensus size: 40
1120520 TTTCTCATGA
1120530 ATTTGTAAAGCC-TCTGGGTCATTTGTAAAGCCTTCAGGTC
1 ATTTGTAAAGCCTTC-GGGTCATTTGTAAAGCCTTCAGGTC
* * *
1120570 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTCCAGATC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCAGGTC
* * *
1120610 ATTTGTAAATCCTTCGGGTCATTTATAAAGCC-TCTGGGTC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTC-AGGTC
* *
1120650 ATTTGTAAAGCATTCGGGTCATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCAGGTC
1120690 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCC-T-ATGGATC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCA-GG-TC
* * * *
1120730 ATTTATAAATCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCAGGTC
*
1120770 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTT-TGAGTC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCAG-GTC
*
1120810 ATTTGTAAAGCCTTTGGGTCAT
1 ATTTGTAAAGCCTTCGGGTCAT
1120832 CTATAAGTCT
Statistics
Matches: 231, Mismatches: 23, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
39 5 0.02
40 221 0.96
41 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (40 bp):
ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCAGGTC
Found at i:1120624 original size:60 final size:60
Alignment explanation
Indices: 1120530--1120831 Score: 424
Period size: 60 Copynumber: 5.0 Consensus size: 60
1120520 TTTCTCATGA
* *
1120530 ATTTGTAAAGCCTCTGGGTCATTTGTAAAGCCTTCAGGTCATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
* * * * *
1120590 ATTTGTAAAGCCTCCAGATCATTTGTAAATCCTTCGGGTCATTTATAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
* * *
1120650 ATTTGTAAAGCATTCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
** * * *
1120710 ATTTGTAAAGCCTATGGATCATTTATAAATCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
* * * **
1120770 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGAGTCATTTGTAAAGCCTTTGGGTC
1 ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
1120830 AT
1 AT
1120832 CTATAAGTCT
Statistics
Matches: 211, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 211 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (60 bp):
ATTTGTAAAGCCTCCGGGTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCCGGGTC
Found at i:1121033 original size:89 final size:87
Alignment explanation
Indices: 1120890--1121219 Score: 244
Period size: 89 Copynumber: 3.6 Consensus size: 87
1120880 ATCTTCACGG
* * * *
1120890 AAGAGTAGTGAAGTATTTCAACTTCG-GATCTAATCTTCACGAAAGAGTAGTGAAATTGGATTCT
1 AAGAGTAGTGAAGTAATCCAACCTCGAG-TCTGATCTTCACGAAAGAGTAGTGAAA-T-GATTCT
1120954 TCTCAAGTCAATTCAACCTTCACAT
63 TCTCAAGTCAATTCAACCTTCACAT
*
1120979 AAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCAAGAAAGAGTAGTGAAACAT-ATTCCT
1 AAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTG-AA-ATGATT-CT
*
1121043 TCTATTCAAGTCATTCAAATCAAGCCTTCACAT
63 TC---TCAAG----TCAATTCAA-CCTTCACAT
* * ** * * * * * *
1121076 AAGAGTAGTGAAGCTGGA-GCAAGATCAAAAT-TCGCTCTCCACGGAAGAGTAGTGAAACAGATT
1 AAGAGTAGTGAAG-T-AATCCAACCTC-GAGTCT-GATCTTCACGAAAGAGTAGTGAAA-TGATT
*
1121139 -TT-TC-AG-CAAAGTATCAACCTTCACAG
61 CTTCTCAAGTC-AA-T-TCAACCTTCACAT
*
1121165 AAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAATGAAA
1 AAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTGAAA
1121220 CAGATTCCTT
Statistics
Matches: 189, Mismatches: 29, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
87 24 0.13
88 12 0.06
89 70 0.37
90 8 0.04
91 1 0.01
92 7 0.04
93 2 0.01
96 8 0.04
97 25 0.13
98 9 0.05
99 23 0.12
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (87 bp):
AAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTGAAATGATTCTTCT
CAAGTCAATTCAACCTTCACAT
Found at i:1121211 original size:186 final size:186
Alignment explanation
Indices: 1120966--1121456 Score: 701
Period size: 186 Copynumber: 2.7 Consensus size: 186
1120956 TCAAGTCAAT
* *
1120966 TCAACCTTCACATAAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCAAGAAAGAGTAGTG
1 TCAACCTTCACAGAAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTG
* * *
1121031 AAACATATTCCTTCTATTCAAGTCATTCAAATCAAGCCTTCACATAAGAGTAGTGAAGCTGGAGC
66 AAACAGATTCCTTCTATTCAAGTCATTCAAATCAAGCCTTCACAGAAGAGTAGTGAAGCAGGAGC
* *
1121096 AAGATCAAAATTCGCTCTCCACGGAAGAGTAGTGAAACAGATTTTTCAGCAAAGTA
131 AAGATAAAAATTCGCTCTCCACGAAAGAGTAGTGAAACAGATTTTTCAGCAAAGTA
*
1121152 TCAACCTTCACAGAAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAATG
1 TCAACCTTCACAGAAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTG
* *
1121217 AAACAGATTCCTTCTATTCAAGTCATTCAAATCGAGCCTTCACAGAAGAGTAATGAAGCAGGAGC
66 AAACAGATTCCTTCTATTCAAGTCATTCAAATCAAGCCTTCACAGAAGAGTAGTGAAGCAGGAGC
* *
1121282 AAGATAAAAATTGGCTCTCCACGAAAGAGTAGTGGAACAGATTTTTCAGCAAAGTA
131 AAGATAAAAATTCGCTCTCCACGAAAGAGTAGTGAAACAGATTTTTCAGCAAAGTA
* * * * * * *
1121338 TGAA-GTATCACGGAA-ACGTAGTGAAGTAACCCAACATTGAGTCTGATCTTCACGGAAGAGTAG
1 TCAACCT-TCACAGAAGA-GTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAG
* *
1121401 TGAAACAGATTCTGTTCT-TCTCAAGT-A---AACTCAA-CCTTCACAGAAGAGTAGTGAAG
64 TGAAACAGATTC-CTTCTAT-TCAAGTCATTCAAATCAAGCCTTCACAGAAGAGTAGTGAAG
1121457 TATTCCAACC
Statistics
Matches: 277, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
182 21 0.08
183 5 0.02
185 2 0.01
186 239 0.86
187 10 0.04
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (186 bp):
TCAACCTTCACAGAAGAGTAGTGAAGTAATCCAACCTCGAGTCTGATCTTCACGAAAGAGTAGTG
AAACAGATTCCTTCTATTCAAGTCATTCAAATCAAGCCTTCACAGAAGAGTAGTGAAGCAGGAGC
AAGATAAAAATTCGCTCTCCACGAAAGAGTAGTGAAACAGATTTTTCAGCAAAGTA
Found at i:1121818 original size:12 final size:12
Alignment explanation
Indices: 1121774--1121825 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1121764 CCGAGTGATA
1121774 TATTAATA-TAT
1 TATTAATATTAT
*
1121785 TATT-ATATATAA
1 TATTAATAT-TAT
*
1121797 TAATATATATTAT
1 TATTA-ATATTAT
1121810 TATTAATATTAT
1 TATTAATATTAT
1121822 TATT
1 TATT
1121826 TACAAAGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 16 0.48
13 6 0.18
14 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:1125074 original size:36 final size:34
Alignment explanation
Indices: 1125026--1125191 Score: 162
Period size: 34 Copynumber: 4.8 Consensus size: 34
1125016 CGATGGTTTG
*
1125026 GTGTTTCAAGAGAAATGTTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAATGATTTCAAAGG--TTTTTTT
* **
1125062 TTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAATGATTTCAAA-GG--TTTTTTT
1125099 GTGTTTCAAGAGAAACTG-TCTT--AAGGATTTTTTT
1 GTGTTTCAAGAGAAA-TGAT-TTCAAAGG-TTTTTTT
*
1125133 -TGTTTCAAGAAAAACTG-TTTCAAAGGTTTTTTT
1 GTGTTTCAAGAGAAA-TGATTTCAAAGGTTTTTTT
*
1125166 GTGTTTCAAGAGAAATAATTTCAAAG
1 GTGTTTCAAGAGAAATGATTTCAAAG
1125192 ATTGGTGCTT
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
32 2 0.02
33 25 0.22
34 32 0.29
35 2 0.02
36 23 0.21
37 26 0.23
38 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (34 bp):
GTGTTTCAAGAGAAATGATTTCAAAGGTTTTTTT
Found at i:1125137 original size:33 final size:33
Alignment explanation
Indices: 1125026--1125180 Score: 129
Period size: 37 Copynumber: 4.5 Consensus size: 33
1125016 CGATGGTTTG
*
1125026 GTGTTTCAAGAGAAA-TGTTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACTGTCTT--AAGG--TTTTTTT
* * *
1125062 TTGTTTCAAGAGAAACAATTTC-AAAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAAC--TGTCTTAA-GG--TTTTTTT
1125099 GTGTTTCAAGAGAAACTGTCTTAAGGATTTTTTT
1 GTGTTTCAAGAGAAACTGTCTTAAGG-TTTTTTT
*
1125133 -TGTTTCAAGAAAAACTGT-TTCAAAGGTTTTTTT
1 GTGTTTCAAGAGAAACTGTCTT--AAGGTTTTTTT
1125166 GTGTTTCAAGAGAAA
1 GTGTTTCAAGAGAAA
1125181 TAATTTCAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.02
33 24 0.24
34 24 0.24
35 5 0.05
36 18 0.18
37 26 0.26
39 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.45
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACTGTCTTAAGGTTTTTTT
Found at i:1125329 original size:102 final size:101
Alignment explanation
Indices: 1125167--1125382 Score: 269
Period size: 102 Copynumber: 2.1 Consensus size: 101
1125157 GGTTTTTTTG
*
1125167 TGTTTCAAGAGAAATA-A-TTTCAAAGATTGGTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAA-ACAGATTCAAAGATTGGTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAA
* *
1125230 ACTTTGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATT
65 A-TTTGTTCCAAAA-AAA-TATCTCAAGAGAGACAAAATT
* * * *
1125270 TGTTTCAAG-GAAAACAGATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAA
1 TGTTTCAAGAGAAAACAGATTCAAAGATTGGTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1125333 TTTGTTTCTAAAAAATGTCTCAAGAGAGACAAAATT
66 TTTGTTCCAAAAAAATATCTCAAGAGAGACAAAATT
*
1125369 TGTTTTAAGAGAAA
1 TGTTTCAAGAGAAA
1125383 CTGTCTCAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
99 26 0.26
100 7 0.07
101 11 0.11
102 36 0.36
103 19 0.19
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (101 bp):
TGTTTCAAGAGAAAACAGATTCAAAGATTGGTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
TTTGTTCCAAAAAAATATCTCAAGAGAGACAAAATT
Found at i:1125393 original size:172 final size:172
Alignment explanation
Indices: 1125203--1125583 Score: 656
Period size: 172 Copynumber: 2.2 Consensus size: 172
1125193 TTGGTGCTTC
1125203 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTATCTCAAGGGAGACGAAA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTATCTCAAGGGAGACGAAA
* * *
1125268 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAA
66 TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1125333 TTTGTTTCT-AAAAAATGTCTCAAGAGAGACAAAATTTGTTTT
131 TTTGTTT-TAAAAAAATGTCTCAAGAGAGACAAAATTTGTTTT
* *
1125375 AAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTATCTCAAGGGAGACGAAA
*
1125440 TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGATACAAAA
66 TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1125505 TTTGTTTTAAGAAAAAATGTCTCAAGAGAGACAAAATTTGTTTT
131 TTTGTTTT-A-AAAAAATGTCTCAAGAGAGACAAAATTTGTTTT
* *
1125549 AAGAGAAACTGTATTAAGAGAGACAAAACTTTGTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
1125584 TTGAGTAAAT
Statistics
Matches: 197, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
171 1 0.01
172 131 0.66
174 65 0.33
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (172 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAAACTATCTCAAGGGAGACGAAA
TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
TTTGTTTTAAAAAAATGTCTCAAGAGAGACAAAATTTGTTTT
Found at i:1125395 original size:36 final size:36
Alignment explanation
Indices: 1125297--1125585 Score: 260
Period size: 36 Copynumber: 8.2 Consensus size: 36
1125287 ATTCAAAGAT
* * *
1125297 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1125333 TTTGTTTCTAA-A-AAA-TGTCTCAAGAGAGACAAAA
1 TTTGTTT-TAAGAGAAACTGTCTCAAGAGAGACAAAA
1125367 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* ** * * *
1125403 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* ** *
1125440 TTTGTTTCAAG-GAAAACAAAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
* * * *
1125469 TTTGTTTCAAGGGAAACTATCTCAAGAGATACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1125505 TTTGTTTTAAGAAAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1125541 TTTGTTTTAAGAGAAACTGTATTAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1125577 CTTTGTTTT
1 -TTTGTTTT
1125586 GAGTAAATTA
Statistics
Matches: 207, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
31 1 0.00
32 1 0.00
33 5 0.02
34 26 0.13
35 8 0.04
36 103 0.50
37 41 0.20
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1125493 original size:29 final size:30
Alignment explanation
Indices: 1125440--1125498 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1125430 GGAGACGAAA
1125440 TTTGTTTCAAGGAAAACAAATTCAA-AGAT
1 TTTGTTTCAAGGAAAACAAATTCAAGAGAT
* *
1125469 TTTGTTTCAAGGGAAAC-TATCTCAAGAGAT
1 TTTGTTTCAAGGAAAACAAAT-TCAAGAGAT
1125499 ACAAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 20 0.77
30 4 0.15
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (30 bp):
TTTGTTTCAAGGAAAACAAATTCAAGAGAT
Found at i:1125503 original size:102 final size:102
Alignment explanation
Indices: 1125367--1125556 Score: 249
Period size: 102 Copynumber: 1.9 Consensus size: 102
1125357 AGAGACAAAA
* * * *
1125367 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AAGAAACTGTCTCAAGG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTAGTTCCAAGAA-AAAATGTCTCAAGA
*
1125431 GAGACGAAATTTGTTTCAAG-GAAAACAAATTCAAAGAT
64 GAGACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
* * * **
1125469 TTTGTTTCAAGGGAAACTATCTCAAGAGATACAAAATTTGTTTTAAGAAAAAATGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTCCAAGAAAAAATGTCTCAAGAGA
*
1125534 GACAAAATTTGTTTTAAGAGAAA
66 GACAAAATTTGTTTCAAGAGAAA
1125557 CTGTATTAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
101 37 0.49
102 38 0.51
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTAGTTCCAAGAAAAAATGTCTCAAGAGA
GACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
Found at i:1125552 original size:21 final size:20
Alignment explanation
Indices: 1125492--1125555 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
1125482 AAACTATCTC
1125492 AAGAGATACAAAATTTGTTTT
1 AAGAGA-ACAAAATTTGTTTT
* *
1125513 -A-AGAA-AAAA--TGTCTC
1 AAGAGAACAAAATTTGTTTT
1125528 AAGAGAGACAAAATTTGTTTT
1 AAGAGA-ACAAAATTTGTTTT
1125549 AAGAGAA
1 AAGAGAA
1125556 ACTGTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 13
0.66 0.08 0.26
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 7 0.21
18 2 0.06
19 7 0.21
20 2 0.06
21 10 0.30
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (20 bp):
AAGAGAACAAAATTTGTTTT
Found at i:1131374 original size:3 final size:3
Alignment explanation
Indices: 1131366--1131449 Score: 98
Period size: 3 Copynumber: 28.0 Consensus size: 3
1131356 AAAACCATAG
* * *
1131366 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1131414 TAA TAA TATA TAC TAA TAT TAA TAT TAA TAA -AA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1131450 ATAAGAAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.93
4 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1131591 original size:16 final size:16
Alignment explanation
Indices: 1131566--1131620 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
1131556 ACATATAATT
*
1131566 AAATATTAGAGGAAA-A
1 AAATAATAGA-GAAATA
1131582 AAATAATAGAGAAATA
1 AAATAATAGAGAAATA
* *
1131598 TAATAATA-AAAAATA
1 AAATAATAGAGAAATA
*
1131613 TAATAATA
1 AAATAATA
1131621 ATAAAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
AAATAATAGAGAAATA
Found at i:1131611 original size:15 final size:15
Alignment explanation
Indices: 1131583--1131627 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
1131573 AGAGGAAAAA
*
1131583 AATAATAGAGAAATAT
1 AATAATA-AAAAATAT
1131599 AATAATAAAAAATAT
1 AATAATAAAAAATAT
1131614 AATAATAATAAAAT
1 AATAATAA-AAAAT
1131628 GAAATAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAAAAAATAT
Found at i:1132877 original size:14 final size:14
Alignment explanation
Indices: 1132836--1132883 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1132826 AAGTATTTTC
1132836 CTTAAATTTTAAAT
1 CTTAAATTTTAAAT
*
1132850 -TTCAAGTTTTAAAT
1 CTT-AAATTTTAAAT
*
1132864 CTTAAATTTAAAAT
1 CTTAAATTTTAAAT
*
1132878 CCTAAA
1 CTTAAA
1132884 ACTTAGACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (14 bp):
CTTAAATTTTAAAT
Found at i:1147841 original size:33 final size:33
Alignment explanation
Indices: 1147799--1147865 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
1147789 AAGGCTGCCA
1147799 GTGGAGGAGTCCTCCGAGATACCAACT-GAGAGT
1 GTGGAGGAGTCCTCCGAGATACCAA-TGGAGAGT
1147832 GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
1 GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
1147865 G
1 G
1147866 AGTAGCGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.27, C:0.19, G:0.36, T:0.18
Consensus pattern (33 bp):
GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
Found at i:1149552 original size:39 final size:40
Alignment explanation
Indices: 1149495--1149586 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
1149485 ATATCTCGGG
* * *
1149495 GTCTTCAACATAATTTGCATGCAAA-ATCGAATCTCTAGGC
1 GTCTTTAACACAATTTGCATGCAAACAT-GAAGCTCTAGGC
* * *
1149535 GTCTTTAACACAA-TTGCATTCAAACATGGAGGTCTAGGC
1 GTCTTTAACACAATTTGCATGCAAACATGAAGCTCTAGGC
1149574 GTCTTTAACACAA
1 GTCTTTAACACAA
1149587 AACATGGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 32 0.71
40 13 0.29
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (40 bp):
GTCTTTAACACAATTTGCATGCAAACATGAAGCTCTAGGC
Found at i:1149590 original size:30 final size:30
Alignment explanation
Indices: 1149556--1149675 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 30
1149546 AATTGCATTC
1149556 AAACATGGAGGTCTAGGCGTCTTTAACACA
1 AAACATGGAGGTCTAGGCGTCTTTAACACA
*
1149586 AAACATGGAGGTCTAGACGTCTTTAACACA
1 AAACATGGAGGTCTAGGCGTCTTTAACACA
** * * *
1149616 ATTCAAGGAGGTCTCGGTGTCTTTAA-ATTC-
1 AAACATGGAGGTCTAGGCGTCTTTAACA--CA
* * * *
1149646 AAACTTGGAGGGCTTGGCGTCTTCAACACA
1 AAACATGGAGGTCTAGGCGTCTTTAACACA
1149676 GTTTCCATGC
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
29 2 0.03
30 67 0.94
31 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (30 bp):
AAACATGGAGGTCTAGGCGTCTTTAACACA
Found at i:1151190 original size:3 final size:3
Alignment explanation
Indices: 1151182--1151338 Score: 226
Period size: 3 Copynumber: 51.7 Consensus size: 3
1151172 TTTATCCATT
* * *
1151182 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1151230 ATA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1151278 TTA TTA TTA TTA GTA TTTA TTA TTA TTA -TA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
1151324 TATA TTA TTA TTA TT
1 T-TA TTA TTA TTA TT
1151339 TAATAAATAA
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.01
3 128 0.93
4 8 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1152047 original size:13 final size:13
Alignment explanation
Indices: 1152029--1152057 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1152019 ACCACCGTTA
1152029 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1152042 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1152055 CGG
1 CGG
1152058 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1152647 original size:19 final size:19
Alignment explanation
Indices: 1152609--1152644 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1152599 CAATTTAGTC
1152609 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
1152628 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
1152645 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:1152709 original size:19 final size:20
Alignment explanation
Indices: 1152673--1152712 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1152663 AGAATTATTC
**
1152673 TTTTATTATATTGTTAAATA
1 TTTTATTATATTCATAAATA
1152693 TTTTA-TATATTCATAAATA
1 TTTTATTATATTCATAAATA
1152712 T
1 T
1152713 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATTATATTCATAAATA
Done.