Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 26
Found at i:1572031 original size:71 final size:73
Alignment explanation
Indices: 1571905--1572043 Score: 203
Period size: 71 Copynumber: 1.9 Consensus size: 73
1571895 GCGAAATTAG
* * *
1571905 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGCTTTACATTT-CGCATTGC
1 TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATGTACATTTCCGCATTGC
1571969 GATTTTCA
66 GATTTTCA
* *
1571977 TTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGT-CATTTCCGCGTTG
1 TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGAT-GTACATTTCCGCATTG
1572040 CGAT
65 CGAT
1572044 AGTCAATTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 31 0.52
72 29 0.48
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (73 bp):
TTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATGTACATTTCCGCATTGC
GATTTTCA
Found at i:1572040 original size:20 final size:20
Alignment explanation
Indices: 1572015--1572103 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
1572005 GCGATTCTCT
1572015 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1572035 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1572055 CGTTGCGATAGTCTTTTCCA
1 CGTTGCGATAGTCATTTCCG
* *
1572075 TGTTGCGATAGTCATATCCG
1 CGTTGCGATAGTCATTTCCG
1572095 CGTTGCGAT
1 CGTTGCGAT
1572104 TTCCGCATTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1573439 original size:15 final size:15
Alignment explanation
Indices: 1573419--1573448 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1573409 AACCCCGTAA
1573419 GCTAATAAGTTTACT
1 GCTAATAAGTTTACT
1573434 GCTAATAAGTTTACT
1 GCTAATAAGTTTACT
1573449 CCAAGGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
GCTAATAAGTTTACT
Found at i:1575427 original size:20 final size:20
Alignment explanation
Indices: 1575404--1575462 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1575394 TTGCGATAGT
* *
1575404 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
1575424 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
1575444 C-GTAATCGCATTGCGATTT
1 CAG-AATCGCATTGCGATTT
1575463 TCCAAATTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:1575483 original size:41 final size:40
Alignment explanation
Indices: 1575414--1575500 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 40
1575404 CAGAATCTCG
*
1575414 TTGCGATTTACAGATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACAAATTCGCATTGCGATTTACGTAATCGCA
* * * *
1575454 TTGCGATTTTCCAAATTCGCGTTGTGATTTACGTATTCGCA
1 TTGCGA-TTTACAAATTCGCATTGCGATTTACGTAATCGCA
1575495 TTGCGA
1 TTGCGA
1575501 ATTAGGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 6 0.15
41 35 0.85
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACAAATTCGCATTGCGATTTACGTAATCGCA
Found at i:1575493 original size:20 final size:20
Alignment explanation
Indices: 1575414--1575500 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
1575404 CAGAATCTCG
1575414 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
1575434 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
1575454 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
1575475 TTGTGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1575495 TTGCGA
1 TTGCGA
1575501 ATTAGGAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.02
20 38 0.72
21 14 0.26
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1575523 original size:21 final size:21
Alignment explanation
Indices: 1575497--1575542 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1575487 TATTCGCATT
*
1575497 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1575518 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1575539 GCGA
1 GCGA
1575543 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1580815 original size:27 final size:29
Alignment explanation
Indices: 1580780--1580838 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 29
1580770 TCACTTTGGC
*
1580780 TTCATTTTTCTATTTTTTTC-TTTTTCTT
1 TTCATTTTTCTATATTTTTCATTTTTCTT
1580808 TTCA-TTTTCTATATTTTTCATTTTTTCTT
1 TTCATTTTTCTATATTTTTCA-TTTTTCTT
1580837 TT
1 TT
1580839 TTTTTCAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 14 0.50
28 4 0.14
29 10 0.36
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (29 bp):
TTCATTTTTCTATATTTTTCATTTTTCTT
Found at i:1581497 original size:4 final size:4
Alignment explanation
Indices: 1581490--1581524 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1581480 GAACCTTCCT
*
1581490 TTTC TTTC TTTC TTTC TTTC TTTC TTTT TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1581525 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:1581525 original size:8 final size:8
Alignment explanation
Indices: 1581488--1581534 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
1581478 TTGAACCTTC
1581488 CTTTTCTTT
1 CTTTT-TTT
*
1581497 CTTTCTTT
1 CTTTTTTT
*
1581505 CTTTCTTT
1 CTTTTTTT
1581513 CTTTTTTT
1 CTTTTTTT
1581521 CTTTTTTT
1 CTTTTTTT
*
1581529 ATTTTT
1 CTTTTT
1581535 AATTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
8 31 0.89
9 4 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTT
Found at i:1581542 original size:17 final size:18
Alignment explanation
Indices: 1581522--1581561 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1581512 TCTTTTTTTC
1581522 TTTTTTTATTTTT-AATT
1 TTTTTTTATTTTTAAATT
*
1581539 TTTTATTATTTTTAAATT
1 TTTTTTTATTTTTAAATT
1581557 TTTTT
1 TTTTT
1581562 CTTCAAGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTATTTTTAAATT
Found at i:1583423 original size:16 final size:16
Alignment explanation
Indices: 1583402--1583439 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1583392 TTAGTGAATT
1583402 TGTGGAAAATCCTCAG
1 TGTGGAAAATCCTCAG
*
1583418 TGTGGAAAATCCTTAG
1 TGTGGAAAATCCTCAG
1583434 TGTGGA
1 TGTGGA
1583440 TAGCTAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTGGAAAATCCTCAG
Found at i:1588195 original size:20 final size:21
Alignment explanation
Indices: 1588150--1588207 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
1588140 CTTCAACGTA
*
1588150 TATCGATACCCTCTTTGAATGTG
1 TATCGATACCC-C-TTGAATGGG
1588173 TATCGATACCCCTT-AATGGG
1 TATCGATACCCCTTGAATGGG
*
1588193 TATTGATACCCCTTG
1 TATCGATACCCCTTG
1588208 TCGGGTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 1 0.03
23 11 0.34
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (21 bp):
TATCGATACCCCTTGAATGGG
Found at i:1597388 original size:17 final size:18
Alignment explanation
Indices: 1597355--1597388 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1597345 TGGCTTGACT
1597355 TTTACTTCTTCCAACATA
1 TTTACTTCTTCCAACATA
*
1597373 TTTATTTCTT-CAACAT
1 TTTACTTCTTCCAACAT
1597389 CTCTTGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTACTTCTTCCAACATA
Found at i:1619737 original size:22 final size:21
Alignment explanation
Indices: 1619695--1619734 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1619685 GAGTTTGTTT
*
1619695 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1619716 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1619735 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1623054 original size:96 final size:95
Alignment explanation
Indices: 1622929--1623152 Score: 290
Period size: 96 Copynumber: 2.3 Consensus size: 95
1622919 TACCGAAGAG
*** *
1622929 GTAGTATCGATACCATGGTAAGGGTATCGATACC-AGTCTTTATCGAATCTAAAATGGGTATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAG-CAAAATCGAATCAAAAATGGGTATCGA
* **
1622993 TA-CTGGTAGGGGTATCGGTACCATAATATTTA
65 TATCAGAAAGGGGTATCGGTACCATAATA--TA
* * *
1623025 GTTGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAAATCGAATCAAAAATTGGTATTGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAAATCGAATCAAAAATGGGTATCGAT
* *
1623090 ATCAGAAAGGGGTATTGGTACCATAGTATA
66 ATCAGAAAGGGGTATCGGTACCATAATATA
*
1623120 GTAGTATAGATACCATGGTAAGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
1623153 TATAGAGCCA
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
95 33 0.29
96 56 0.50
97 23 0.21
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAAATCGAATCAAAAATGGGTATCGAT
ATCAGAAAGGGGTATCGGTACCATAATATA
Found at i:1623825 original size:58 final size:58
Alignment explanation
Indices: 1623489--1624175 Score: 954
Period size: 58 Copynumber: 11.8 Consensus size: 58
1623479 CACTTCGTGT
* **
1623489 GCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT-GTGT
1 GCTAAAATGTG-AA-GAAATCATACTAAGTGTATGAATTTCCATATAGGGCA-TTTCGTAC
* * * **
1623548 GCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTCCGTGT
1 GCTAAAATGTG-AA-GAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
* * * * * **
1623607 GATGAAATG-GTAAGAAAATCATACTAAGTGTATGAATTTCCAAATAAGGCACTTCGTGT
1 GCTAAAATGTG-AAG-AAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
* * * **
1623666 GCTAAAAGGAT-AAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCGTGT
1 GCTAAAATG-TGAA-GAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
** *
1623725 GCTAAAATG-GTAAGGAAATCATACTAAGTGTATGAATTTCCATATAGGGTGTTTCATAC
1 GCTAAAATGTG-AA-GAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
* *
1623784 GCTAAAATGTGAAGGAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTAC
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1623842 GCTAAAATGTTAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1623900 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAT
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1623958 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTAC
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1624016 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTAC
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1624074 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCGTTTCGTAC
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
*
1624132 GCTAAAATGTTAAGAAATCATACTAAGTGTATGAATTTCCATAT
1 GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATAT
1624176 TGGAAATATA
Statistics
Matches: 589, Mismatches: 31, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
58 370 0.63
59 217 0.37
60 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (58 bp):
GCTAAAATGTGAAGAAATCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTAC
Found at i:1626295 original size:21 final size:21
Alignment explanation
Indices: 1626269--1626316 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1626259 TTGAATCGTT
*
1626269 GATGGTCCCGATAGTCCATTG
1 GATGGTCCCAATAGTCCATTG
1626290 GATGGTCCCAATAGTCCATTG
1 GATGGTCCCAATAGTCCATTG
*
1626311 GGTGGT
1 GATGGT
1626317 TCTTCTCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (21 bp):
GATGGTCCCAATAGTCCATTG
Found at i:1626828 original size:31 final size:31
Alignment explanation
Indices: 1626766--1626837 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
1626756 ATAAAATAAA
* *
1626766 AAAATAAATTTGAAAGTTAGAGTGATTAAATT
1 AAAA-AAATTTCAAAGTTAGAGTAATTAAATT
*
1626798 AGAAACAATTTCAAAGTTA-AGTAATTAAATT
1 A-AAAAAATTTCAAAGTTAGAGTAATTAAATT
1626829 AAAAAAATT
1 AAAAAAATT
1626838 AAACTTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 7 0.20
31 12 0.34
32 13 0.37
33 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (31 bp):
AAAAAAATTTCAAAGTTAGAGTAATTAAATT
Found at i:1632426 original size:30 final size:30
Alignment explanation
Indices: 1632392--1632451 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1632382 ATGTAAAATT
* *
1632392 GATTTTGGACTTAATTGAATTTATCAAAAA
1 GATTTTAGACTTAATCGAATTTATCAAAAA
*
1632422 GATTTTAGACTTAATCGAATTTATTAAAAA
1 GATTTTAGACTTAATCGAATTTATCAAAAA
1632452 TAATTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (30 bp):
GATTTTAGACTTAATCGAATTTATCAAAAA
Found at i:1634944 original size:10 final size:10
Alignment explanation
Indices: 1634929--1634958 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1634919 TAGGTGTGTT
1634929 GGAGCAATGG
1 GGAGCAATGG
1634939 GGAGCAATGG
1 GGAGCAATGG
*
1634949 TGAGCAATGG
1 GGAGCAATGG
1634959 CATTGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.47, T:0.13
Consensus pattern (10 bp):
GGAGCAATGG
Found at i:1638064 original size:22 final size:22
Alignment explanation
Indices: 1637998--1638099 Score: 129
Period size: 22 Copynumber: 4.7 Consensus size: 22
1637988 TAGAACCCGT
*
1637998 GGGGGGATCGATT-CCCTT-AA
1 GGGGGAATCGATTCCCCTTCAA
*
1638018 GGGGGAATC-AGTTCCCATTCAAA
1 GGGGGAATCGA-TTCCCCTTC-AA
1638041 GGGGGAATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1638063 GGGGGTATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
1638085 GGGGGTATCGATTCC
1 GGGGGAATCGATTCC
1638100 TCCTACACTA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.01
20 10 0.14
21 4 0.05
22 38 0.52
23 19 0.26
24 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:1639029 original size:21 final size:21
Alignment explanation
Indices: 1639003--1639044 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1638993 AGTAAAGAGC
1639003 CAATCATTGACCTATATAATT
1 CAATCATTGACCTATATAATT
1639024 CAATCATTGACCTATATAATT
1 CAATCATTGACCTATATAATT
1639045 TAACATCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (21 bp):
CAATCATTGACCTATATAATT
Found at i:1642202 original size:117 final size:118
Alignment explanation
Indices: 1641982--1642202 Score: 270
Period size: 117 Copynumber: 1.9 Consensus size: 118
1641972 CTTTCAAATC
*
1641982 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * *
1642047 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCCAATTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
1642100 AAAA-TTTCTTTTTCAA-AGTTTTCATATTTTATTTTTGAAAGCTCTAACTCATT-TCTCAACAT
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
1642162 TTCATTTTGATTTTCCAAGTGTAATTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCAATTTAG-TTTCTAAAAGAA
1642203 TATCATTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 2 0.02
117 77 0.89
118 8 0.09
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCAATTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:1642227 original size:12 final size:12
Alignment explanation
Indices: 1642210--1642237 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1642200 GAATATCATT
1642210 TTTAGAAATAAA
1 TTTAGAAATAAA
1642222 TTTAGAAATAAA
1 TTTAGAAATAAA
1642234 TTTA
1 TTTA
1642238 TTGTATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
TTTAGAAATAAA
Found at i:1648137 original size:18 final size:18
Alignment explanation
Indices: 1648114--1648152 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1648104 GTTAGGGTGT
1648114 TACATAATTGGTATTTGG
1 TACATAATTGGTATTTGG
* *
1648132 TACATATTTTGTATTTGG
1 TACATAATTGGTATTTGG
1648150 TAC
1 TAC
1648153 TTGAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.49
Consensus pattern (18 bp):
TACATAATTGGTATTTGG
Found at i:1648184 original size:20 final size:20
Alignment explanation
Indices: 1648143--1648185 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1648133 ACATATTTTG
*
1648143 TATTTGGTACTTGAATATTT
1 TATTTGGTACTTGAATAGTT
*
1648163 TATTTGGTTATTTGAAT-GTT
1 TATTTGG-TACTTGAATAGTT
1648183 TAT
1 TAT
1648186 GACTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.58
Consensus pattern (20 bp):
TATTTGGTACTTGAATAGTT
Found at i:1650709 original size:94 final size:96
Alignment explanation
Indices: 1650597--1650772 Score: 241
Period size: 94 Copynumber: 1.9 Consensus size: 96
1650587 GAAGGTATCA
* * * * *
1650597 ATACCATTGATTTACAGAATGCAGAAATGGTATCGATACTGTAA-TATAGTATCGGTACCATATT
1 ATACCATAGATTTACAGAATACAGAAATGGTATCGATACTG-AAGGAGAGTATCGGTACCACATT
* *
1650661 ATAGACGTATCGGTACTAAGAGACAAATACTG
65 ATAGAAGTATCGATACTAAGAGACAAATACTG
* *
1650693 ATACCATAGA-TT-CAGAATATAGAAATGGTATCGATACTGAAGGGGAGTATCGGTACCACATTA
1 ATACCATAGATTTACAGAATACAGAAATGGTATCGATACTGAAGGAGAGTATCGGTACCACATTA
1650756 TAGAAGTATCGATACTA
66 TAGAAGTATCGATACTA
1650773 TTGAACTAGA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.03
94 57 0.81
95 2 0.03
96 9 0.13
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (96 bp):
ATACCATAGATTTACAGAATACAGAAATGGTATCGATACTGAAGGAGAGTATCGGTACCACATTA
TAGAAGTATCGATACTAAGAGACAAATACTG
Found at i:1651182 original size:55 final size:55
Alignment explanation
Indices: 1651098--1651413 Score: 515
Period size: 55 Copynumber: 5.7 Consensus size: 55
1651088 ACTATTCGTG
*
1651098 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAAAGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTGC
** * *
1651153 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGGCATTGTGTGTGAA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTG-C
* *
1651209 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCAATGTGTGTGT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTGC
*
1651264 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTGC
* * * *
1651319 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTGTGAGTGT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTGC
1651374 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1651414 TGGTAGTGGG
Statistics
Matches: 244, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 194 0.80
56 50 0.20
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATGTGTGTGC
Found at i:1651430 original size:110 final size:109
Alignment explanation
Indices: 1651098--1651413 Score: 524
Period size: 111 Copynumber: 2.9 Consensus size: 109
1651088 ACTATTCGTG
* *
1651098 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAAAGTGTGTGCAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCAATGTGTGTGTAAAACTAAGA
** * *
1651163 AATTCATAATAAGTTTATGAATTTTTGTATGGGCATTGTGTGTGAA
65 AATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTG-C
1651209 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGTCAATGTGTGTGTAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG-CAATGTGTGTGTAAAACTAAGA
1651274 AATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
65 AATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
* *
1651319 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTGTGAGTGTAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG-GCAATGTGTGTGTAAAACTAAGA
1651384 AATTCATAATAAGTTTATGAATTTCCGTAT
65 AATTCATAATAAGTTTATGAATTTCCGTAT
1651414 TGGTAGTGGG
Statistics
Matches: 195, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
110 93 0.48
111 102 0.52
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (109 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGCAATGTGTGTGTAAAACTAAGAA
ATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGC
Found at i:1655068 original size:26 final size:26
Alignment explanation
Indices: 1655032--1655082 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1655022 CATGCTAACT
1655032 TGTTTCATTGTATTAAAATTAGGTCC
1 TGTTTCATTGTATTAAAATTAGGTCC
*
1655058 TGTTTCATTGTATTAAAATTTGGTC
1 TGTTTCATTGTATTAAAATTAGGTC
1655083 ACCATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (26 bp):
TGTTTCATTGTATTAAAATTAGGTCC
Found at i:1655308 original size:16 final size:16
Alignment explanation
Indices: 1655268--1655316 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
1655258 GATTACTTAA
*
1655268 TCTTTTAGATTTAG--
1 TCTTTTACATTTAGTT
1655282 TC-TTTACATTTAGATT
1 TCTTTTACATTTAG-TT
1655298 TCTTTTA-ATTTAGTT
1 TCTTTTACATTTAGTT
1655313 TCTT
1 TCTT
1655317 GTTAGGTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 6 0.20
16 8 0.27
17 4 0.13
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (16 bp):
TCTTTTACATTTAGTT
Found at i:1664363 original size:41 final size:42
Alignment explanation
Indices: 1664284--1664363 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
1664274 GCCATTAGTA
* * ** *
1664284 AGTCTTTCGAGCATGATGATTAAATTTTTCGGGTCATCTGTC
1 AGTCTTTCAAGCAAGATGATTAAATCCTTCGGGCCATCTGTC
*
1664326 AGTCTTTCAAGCAAGATG-TTAAGTCCTTCGGGCCATCT
1 AGTCTTTCAAGCAAGATGATTAAATCCTTCGGGCCATCT
1664364 ATAATACCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 16 0.50
42 16 0.50
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
AGTCTTTCAAGCAAGATGATTAAATCCTTCGGGCCATCTGTC
Found at i:1665061 original size:42 final size:41
Alignment explanation
Indices: 1665001--1665099 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
1664991 TCGTAAGTCC
* *
1665001 TTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCAT
1 TTGGGCCATCTGTAAGTCTTTCGAGCAAGATGA-TAAATCAT
* * * *
1665043 TTGGGACATCTGTCAGTCTTTCGAGTAAGATGATAAGTCAT
1 TTGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAATCAT
*
1665084 TTGGGCCATCTATAAG
1 TTGGGCCATCTGTAAG
1665100 ACCTTTAAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
41 20 0.42
42 28 0.58
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (41 bp):
TTGGGCCATCTGTAAGTCTTTCGAGCAAGATGATAAATCAT
Found at i:1665075 original size:260 final size:257
Alignment explanation
Indices: 1664573--1665169 Score: 723
Period size: 259 Copynumber: 2.3 Consensus size: 257
1664563 TCTTTCAGCT
** * * * *
1664573 ATCTATAAGACCTTTGGGCAACATGATTTCATATGATAATTTGAAAAATGAGAAGACAATTTTTA
1 ATCTATAAGACCTTTAAGCAAGAT-TTTTCATATGATAATTTGAAAAATGAGAAAACAATTTTCA
* * *
1664638 AAGTTTCTCATTTAGTATTTTAGAAAAAGAAATATTTGAAAAGTAAGAAAGTGATTACCAAAGTT
65 AAGTTTCTCATTAAGTATTTCAGAAAAAGAAATATTTGAAAAGTAAGAAAGCGATTACCAAAGTT
* *
1664703 TCTTACATAATAAACTATTTCCAAAATTGGTAAGTCCTTCGGGTCATCACTAAGTCTTTCAAGAA
130 TCTTACATAATAAACTATTTCCAAAATTCGTAAGTCCTTCGGGCCATCACTAAGTCTTTCAAGAA
* * * *
1664768 TGATGATTAAATCCTTCGGGCCATCTGTCATTCTTTCGAGCAAGATGATAAGTTCCTTCGGGCC
195 TGATGATTAAATCATTCGGGACATCTGTCAGTCTTTCGAGCAAGATGATAAG-TCATTCGGGCC
* ** *
1664832 ATCTATAAGACCTTTACGCAAGATTCTTTCATATGATGTTTGTGAAAAATGAGAAAAGTAATTTT
1 ATCTATAAGACCTTTAAGCAAGATT-TTTCATATGATAATT-TGAAAAATGAGAAAA-CAATTTT
* * * *
1664897 CAAAGTTTCTCATTAATGT-TTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCCTAA
63 CAAAGTTTCTCATTAA-GTATTTCAGAAAAAGAAATATTTGAAAAGTAAGAAAGCGATTACCAAA
* * * * *
1664961 TTTTCTTATC-TAGTAGACTATTTCCAAAATTCGTAAGTCCTT-GGGCCATCAGTAAGTCTTTCG
127 GTTTCTTA-CATAATAAACTATTTCCAAAATTCGTAAGTCCTTCGGGCCATCACTAAGTCTTTCA
* * * *
1665024 AGCATGATGATTAAATCATTTGGGACATCTGTCAGTCTTTCGAGTAAGATGATAAGTCATTTGGG
191 AGAATGATGATTAAATCATTCGGGACATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGG
1665089 CC
256 CC
* ** * * *
1665091 ATCTATAAGACCTTTAAGCATGATGTTTTCATACAATATTTTTAAAAGAACGAGAAAACAATTTT
1 ATCTATAAGACCTTTAAGCAAGAT-TTTTCATATGATA-ATTTGAAA-AATGAGAAAACAATTTT
**
1665156 TGAAGTTTCTCATT
63 CAAAGTTTCTCATT
1665170 TAAAATAAAA
Statistics
Matches: 289, Mismatches: 41, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
259 96 0.33
260 95 0.33
261 95 0.33
262 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (257 bp):
ATCTATAAGACCTTTAAGCAAGATTTTTCATATGATAATTTGAAAAATGAGAAAACAATTTTCAA
AGTTTCTCATTAAGTATTTCAGAAAAAGAAATATTTGAAAAGTAAGAAAGCGATTACCAAAGTTT
CTTACATAATAAACTATTTCCAAAATTCGTAAGTCCTTCGGGCCATCACTAAGTCTTTCAAGAAT
GATGATTAAATCATTCGGGACATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCC
Found at i:1665212 original size:18 final size:18
Alignment explanation
Indices: 1665181--1665233 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1665171 AAAATAAAAA
1665181 AATAAAAAAG--AAAATG
1 AATAAAAAAGAAAAAATG
* *
1665197 ATTAAAAAAGAAAAAAAG
1 AATAAAAAAGAAAAAATG
*
1665215 AAGAAAAAAGAAGAAAATG
1 AATAAAAAAGAA-AAAATG
1665234 TGAGAAAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.31
18 15 0.52
19 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AATAAAAAAGAAAAAATG
Found at i:1674986 original size:144 final size:145
Alignment explanation
Indices: 1674749--1675016 Score: 441
Period size: 144 Copynumber: 1.9 Consensus size: 145
1674739 AATATATAAA
* * *
1674749 AAAATATTAGCTCCACTAAGCTTCTAACTTGTTCCTTTTTATAAACGATTAGTTCCGAACACGAA
1 AAAATATTAGCCCCACTAAGCTTCTAACTTGTACCTTTTTATAAACGATTAGTTCCGAACACAAA
* * **
1674814 ACAAGTCGCGATATGTACAAAGTTACAAATTATATTGATACATATGTTAGTATTGTACTCACCTT
66 ACAAGTCACGATATGTACAAAGTCACAAATTATATCAATACATATGTTAGTATTGTACTCACCTT
1674879 GACACTTTATATAGC
131 GACACTTTATATAGC
*
1674894 AAAATATTAGCCCCACTAAGCTTCTAACTTGTACC-TTTTATAAACGATTAGTTTCGAACACAAA
1 AAAATATTAGCCCCACTAAGCTTCTAACTTGTACCTTTTTATAAACGATTAGTTCCGAACACAAA
1674958 ATC-AGTCACGATATGTACAAAGTCACAAATTATATCAATACATATGTTAGTATTGTACT
66 A-CAAGTCACGATATGTACAAAGTCACAAATTATATCAATACATATGTTAGTATTGTACT
1675017 AACATTAATA
Statistics
Matches: 114, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
144 80 0.70
145 34 0.30
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (145 bp):
AAAATATTAGCCCCACTAAGCTTCTAACTTGTACCTTTTTATAAACGATTAGTTCCGAACACAAA
ACAAGTCACGATATGTACAAAGTCACAAATTATATCAATACATATGTTAGTATTGTACTCACCTT
GACACTTTATATAGC
Found at i:1694973 original size:18 final size:18
Alignment explanation
Indices: 1694950--1694987 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1694940 AAGGAGTAAG
*
1694950 AAGATAAAAATATAAGAC
1 AAGATAAAAAGATAAGAC
1694968 AAGATAAAAAGATAAGAC
1 AAGATAAAAAGATAAGAC
1694986 AA
1 AA
1694988 TTGACACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.13, T:0.13
Consensus pattern (18 bp):
AAGATAAAAAGATAAGAC
Found at i:1697637 original size:29 final size:29
Alignment explanation
Indices: 1697595--1697662 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
1697585 ACCTTATTAT
1697595 TCTTCTTCTTGTTTTGCTTCTCTTCATCG
1 TCTTCTTCTTGTTTTGCTTCTCTTCATCG
*
1697624 TCTTCTTCTTGTTTTGCTTCTCTTCATCT
1 TCTTCTTCTTGTTTTGCTTCTCTTCATCG
*
1697653 TCTTCCTCTT
1 TCTTCTTCTT
1697663 CTTTCACCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.03, C:0.29, G:0.07, T:0.60
Consensus pattern (29 bp):
TCTTCTTCTTGTTTTGCTTCTCTTCATCG
Found at i:1703761 original size:18 final size:18
Alignment explanation
Indices: 1703738--1703774 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1703728 CTTTTTCTTT
1703738 TCATTTCTTCA-TTCCTTC
1 TCATTT-TTCATTTCCTTC
1703756 TCATTTTTCATTTCCTTC
1 TCATTTTTCATTTCCTTC
1703774 T
1 T
1703775 TCCTCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTTTTCATTTCCTTC
Found at i:1703763 original size:25 final size:24
Alignment explanation
Indices: 1703735--1703782 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1703725 CTCCTTTTTC
1703735 TTTTCATTT-CTTCATTCCTTCTCAT
1 TTTTCATTTCCTTC-TTCC-TCTCAT
1703760 TTTTCATTTCCTTCTTCCTCTCA
1 TTTTCATTTCCTTCTTCCTCTCA
1703783 AAGCTCCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 13 0.59
26 4 0.18
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTCATTTCCTTCTTCCTCTCAT
Found at i:1704150 original size:20 final size:20
Alignment explanation
Indices: 1704121--1704158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1704111 TATAAGTTCA
*
1704121 AGTATCGATATTGGATGAAT
1 AGTATCGATATTAGATGAAT
*
1704141 AGTATTGATATTAGATGA
1 AGTATCGATATTAGATGA
1704159 TCTGGGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (20 bp):
AGTATCGATATTAGATGAAT
Found at i:1704774 original size:164 final size:164
Alignment explanation
Indices: 1704568--1705040 Score: 630
Period size: 164 Copynumber: 2.9 Consensus size: 164
1704558 GTAGTCCCGG
** * * *
1704568 TACGGTCGTTCATAAACATATTATGAATTTTGTGG-GTTGCACACTTAATACTGATATGGTCGTT
1 TACGGTCGTTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGT-CTGATACGGTCGTT
** * *
1704632 CATAAACATATTATGAATTATATGGTTTTGCACACTTAGTGTTGATACGGTCATTCATAAGCATA
65 CATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGTCGATACGGTCATTCATAAACATA
*
1704697 TTATGAATTCCATAGTT-TTGCTCACTTAGTGCTGA
130 TTATGAATTCCAT-GTTCTTGCACACTTAGTGCTGA
*
1704732 TACGGTCGTTCAT-AACATATTATGAATTTCATGGTTTTGCACACTTAGTGTCGATACGGTCGTT
1 TACGGTCGTTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTCT-GATACGGTCGTT
* *
1704796 CATAAACATATTATGAATTCCATGGTTTTGCACACTTGGTGTCGATACGGTCGTTCATAAACATA
65 CATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGTCGATACGGTCATTCATAAACATA
* ***
1704861 TCATGAATTTTGTGTTCTTGCACACTTAGTGCTGA
130 TTATGAATTCCATGTTCTTGCACACTTAGTGCTGA
* * * * *
1704896 TATGGTCGTTCATAAACATATTAT-AAATTCGTTGGTTTTGCACACTTAGTGTTGATACGGTCGC
1 TACGGTCGTTCATAAACATATTATGAATTTC-ATGGTTTTGCACACTTAGT-CTGATACGGTCGT
* * * * *
1704960 TCATGAACATATTATGAATTCCGTGGTTTTTCACACTTAGTGCCGATACGGTTATTCATAAACAT
64 TCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGTCGATACGGTCATTCATAAACAT
1705025 ATTATGAATTCCATGT
129 ATTATGAATTCCATGT
1705041 CAGCAATAGT
Statistics
Matches: 270, Mismatches: 33, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
163 23 0.09
164 138 0.51
165 108 0.40
166 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (164 bp):
TACGGTCGTTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTCTGATACGGTCGTTC
ATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGTCGATACGGTCATTCATAAACATAT
TATGAATTCCATGTTCTTGCACACTTAGTGCTGA
Found at i:1705036 original size:55 final size:55
Alignment explanation
Indices: 1704568--1705039 Score: 596
Period size: 55 Copynumber: 8.6 Consensus size: 55
1704558 GTAGTCCCGG
*** * * *
1704568 TACGGTCGTTCATAAACATATTATGAATTTTGTGG-GTTGCACACTTAATACTGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
* ** *
1704622 TATGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTAGTGTTGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
* * * *
1704677 TACGGTCATTCATAAGCATATTATGAATTCCATAGTTTTGCTCACTTAGTGCTGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
*
1704732 TACGGTCGTTCAT-AACATATTATGAATTTCATGGTTTTGCACACTTAGTG-TCGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCT-GA
*
1704786 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTGGTG-TCGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCT-GA
* *
1704841 TACGGTCGTTCATAAACATATCATGAATT--TTGTGTTCTTGCACACTTAGTGCTGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATG-GTT-TTGCACACTTAGTGCTGA
* * ** *
1704896 TATGGTCGTTCATAAACATATTATAAATTCGTTGGTTTTGCACACTTAGTGTTGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
* * * * *
1704951 TACGGTCGCTCATGAACATATTATGAATTCCGTGGTTTTTCACACTTAGTGCCGA
1 TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
**
1705006 TACGGTTATTCATAAACATATTATGAATTCCATG
1 TACGGTCGTTCATAAACATATTATGAATTCCATG
1705040 TCAGCAATAG
Statistics
Matches: 367, Mismatches: 43, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.01
54 83 0.23
55 274 0.75
56 4 0.01
57 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (55 bp):
TACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTAGTGCTGA
Found at i:1711507 original size:55 final size:55
Alignment explanation
Indices: 1711446--1711659 Score: 261
Period size: 55 Copynumber: 3.9 Consensus size: 55
1711436 GATATGGTCC
* * *
1711446 TTCATAAACATTTTATGAATTTTATGGTTTTGCACACTTAGTGTCGATACAGTCG
1 TTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTGCCGATACAGTCG
* * * * *
1711501 TTCATAAACGTATTATAAATTTCATGGTTTTGCACACTTAGTACCGGTACAGTCA
1 TTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTGCCGATACAGTCG
* ** *
1711556 TTTATAAATGTATTATGAATTAT-GTGGTTTTGCACACTTAGTGCCGATAC-GATCG
1 TTCATAAACATATTATGAATT-TCATGGTTTTGCACACTTAGTGCCGATACAG-TCG
* * *
1711611 TTCATAAACATACTATGAATTTCGTGGTTTTGTACACTTAGTGCCGATA
1 TTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTGCCGATA
1711660 GTACACATAG
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
54 2 0.01
55 133 0.98
56 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (55 bp):
TTCATAAACATATTATGAATTTCATGGTTTTGCACACTTAGTGCCGATACAGTCG
Found at i:1713906 original size:18 final size:19
Alignment explanation
Indices: 1713869--1713907 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1713859 TTAATAATGG
1713869 AATAAGAAATGATTAAATAAA
1 AATAAGAAATG--TAAATAAA
1713890 AATAAGAAATG-AAATAAA
1 AATAAGAAATGTAAATAAA
1713908 GATAGAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
21 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
AATAAGAAATGTAAATAAA
Found at i:1715684 original size:18 final size:17
Alignment explanation
Indices: 1715661--1715695 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1715651 AATCATGAAA
1715661 GGTGATGACTCTTGTAAT
1 GGTGATG-CTCTTGTAAT
*
1715679 GGTGATGTTCTTGTAAT
1 GGTGATGCTCTTGTAAT
1715696 CCTCATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.43
Consensus pattern (17 bp):
GGTGATGCTCTTGTAAT
Found at i:1718181 original size:29 final size:29
Alignment explanation
Indices: 1718140--1718201 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
1718130 TTTCCTTGGC
1718140 TTTTCTTTCTTTT-TGAAATTCTCTTT-TTCT
1 TTTTCTTTCTTTTCTG-AATT-T-TTTCTTCT
1718170 TTTTC-TTCTTTTCTGAATTTTTTCTTCT
1 TTTTCTTTCTTTTCTGAATTTTTTCTTCT
1718198 TTTT
1 TTTT
1718202 GTCTTTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.10
28 9 0.30
29 11 0.37
30 7 0.23
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTTCTTTCTTTTCTGAATTTTTTCTTCT
Found at i:1721391 original size:2 final size:2
Alignment explanation
Indices: 1721384--1721416 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1721374 TATAGATGTA
1721384 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
1721417 GCTATGTTAT
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:1728894 original size:26 final size:26
Alignment explanation
Indices: 1728855--1728905 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1728845 ACTAAGTGTG
1728855 TATGATGGGCACGACCTTATGTGTAT
1 TATGATGGGCACGACCTTATGTGTAT
* *
1728881 TATGGTGGGTACGACCTTATGTGTA
1 TATGATGGGCACGACCTTATGTGTA
1728906 GCACTTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (26 bp):
TATGATGGGCACGACCTTATGTGTAT
Found at i:1730436 original size:25 final size:25
Alignment explanation
Indices: 1730399--1730451 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1730389 ATGGGTTAAT
*
1730399 TGGGTGTTGTCCAATACAGAGATTC
1 TGGGTGTTATCCAATACAGAGATTC
1730424 TGGGTGTTATCCAATACAGAGATTC
1 TGGGTGTTATCCAATACAGAGATTC
1730449 TGG
1 TGG
1730452 ATCTTGCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (25 bp):
TGGGTGTTATCCAATACAGAGATTC
Found at i:1735194 original size:23 final size:23
Alignment explanation
Indices: 1735139--1735195 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1735129 TATAGATCGA
1735139 TCTAGTTTAGTGTATTCATGCAC
1 TCTAGTTTAGTGTATTCATGCAC
* *
1735162 TCCAATTTAGTGCT-TT-ATGCAC
1 TCTAGTTTAGTG-TATTCATGCAC
1735184 TCTAGTATTAGT
1 TCTAGT-TTAGT
1735196 CCCTTTGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 10 0.36
23 17 0.61
24 1 0.04
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.44
Consensus pattern (23 bp):
TCTAGTTTAGTGTATTCATGCAC
Found at i:1748933 original size:27 final size:30
Alignment explanation
Indices: 1748874--1748934 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1748864 ATTTTGTCCT
* *
1748874 TTTGGATGCTTTTATTTGAGATTTATGTTA
1 TTTGGATGCTTTTATATGAGATTTATGATA
1748904 TTTGGATGCTTTT-TATG-G-TTTATGATA
1 TTTGGATGCTTTTATATGAGATTTATGATA
1748931 TTTG
1 TTTG
1748935 ATATTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 1 0.03
29 3 0.10
30 13 0.45
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.57
Consensus pattern (30 bp):
TTTGGATGCTTTTATATGAGATTTATGATA
Found at i:1753100 original size:16 final size:16
Alignment explanation
Indices: 1753079--1753110 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1753069 GATATTACCC
1753079 CAATACTACAACACTA
1 CAATACTACAACACTA
*
1753095 CAATACTACGACACTA
1 CAATACTACAACACTA
1753111 GTTGCGGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (16 bp):
CAATACTACAACACTA
Found at i:1754410 original size:31 final size:32
Alignment explanation
Indices: 1754366--1754436 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1754356 ACTGTTTTTT
*
1754366 GTAAACTTGAACATGTTG-TCATCTTTTGTAA
1 GTAAACTTGAACATGGTGCTCATCTTTTGTAA
* * * *
1754397 GTAAATTTTAACATGGTGCTCATTTTTTGTAG
1 GTAAACTTGAACATGGTGCTCATCTTTTGTAA
*
1754429 GCAAACTT
1 GTAAACTT
1754437 AGACATATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (32 bp):
GTAAACTTGAACATGGTGCTCATCTTTTGTAA
Found at i:1754582 original size:36 final size:33
Alignment explanation
Indices: 1754522--1754605 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
1754512 TTGCTGCTAC
* * *
1754522 TTTTTGTAAGTAGA-TTGAAGATGTTACTGTCA
1 TTTTTGTAAGTAAATTTGAACATGTTACTATCA
* *
1754554 TTTCTTTTGTAAGTAAATTTTAACATGTTGCTATCA
1 --T-TTTTGTAAGTAAATTTGAACATGTTACTATCA
1754590 TTTTTGTAAGTAAATT
1 TTTTTGTAAGTAAATT
1754606 AGATATATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 15 0.35
34 2 0.05
35 12 0.28
36 14 0.33
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (33 bp):
TTTTTGTAAGTAAATTTGAACATGTTACTATCA
Found at i:1754600 original size:33 final size:32
Alignment explanation
Indices: 1754389--1754605 Score: 100
Period size: 34 Copynumber: 6.5 Consensus size: 32
1754379 TGTTGTCATC
* *
1754389 TTTTGTAAGTAAATTTTAACATGGTGC-TCATT
1 TTTTGTAAGTAAA-TTTAACATGTTGCTTCACT
* * * * *
1754421 TTTTGTAGGCAAACTTAGACATATTACTATCA-T
1 TTTTGTAAGTAAATTTA-ACATGTTGCT-TCACT
* * *
1754454 CTTTTGCAAGTAAACTTAGACATGTTGTTGTCACCT
1 -TTTTGTAAGTAAATTTA-ACATGTTGCT-TCA-CT
* * * * *
1754490 TTTT-CAGGTAAACTTGAAAATGTTGCTGCTACT
1 TTTTGTAAGTAAA-TTTAACATGTTGCTTC-ACT
* * * * *
1754523 TTTTGTAAGTAGATTGAAGATGTTACTGTCATTT
1 TTTTGTAAGTAAATTTAACATGTTGCT-TCA-CT
1754557 CTTTTGTAAGTAAATTTTAACATGTTGCTATCA-T
1 -TTTTGTAAGTAAA-TTTAACATGTTGCT-TCACT
1754591 TTTTGTAAGTAAATT
1 TTTTGTAAGTAAATT
1754606 AGATATATTA
Statistics
Matches: 141, Mismatches: 31, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
31 3 0.02
32 19 0.13
33 34 0.24
34 52 0.37
35 18 0.13
36 15 0.11
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.44
Consensus pattern (32 bp):
TTTTGTAAGTAAATTTAACATGTTGCTTCACT
Found at i:1757624 original size:21 final size:21
Alignment explanation
Indices: 1757600--1757645 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1757590 AATATGTTTA
1757600 TTAAACTTTTAAAACTCAAAT
1 TTAAACTTTTAAAACTCAAAT
1757621 TTAAACTTTTAAAACTCAAAT
1 TTAAACTTTTAAAACTCAAAT
1757642 TTAA
1 TTAA
1757646 TATAACTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAACTTTTAAAACTCAAAT
Found at i:1758061 original size:2 final size:2
Alignment explanation
Indices: 1758050--1758078 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1758040 TATAGTAAAA
1758050 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1758079 GCTGATCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1763122 original size:11 final size:11
Alignment explanation
Indices: 1763106--1763130 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1763096 AATGTAAACA
1763106 TTAATATATTT
1 TTAATATATTT
1763117 TTAATATATTT
1 TTAATATATTT
1763128 TTA
1 TTA
1763131 TCATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATATATTT
Found at i:1763240 original size:15 final size:15
Alignment explanation
Indices: 1763220--1763250 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1763210 CAACGGATAG
1763220 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1763235 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1763250 A
1 A
1763251 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1763505 original size:27 final size:27
Alignment explanation
Indices: 1763475--1763530 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1763465 CTTTTCTTCC
*
1763475 CATTTGATTTGACTCTTTACAAGTGTA
1 CATTTGATTTGACTCTTTACAAGTATA
1763502 CATTTGATTTGACTCTTTACAAGTATA
1 CATTTGATTTGACTCTTTACAAGTATA
1763529 CA
1 CA
1763531 GCTACACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (27 bp):
CATTTGATTTGACTCTTTACAAGTATA
Found at i:1764735 original size:226 final size:225
Alignment explanation
Indices: 1764330--1764794 Score: 598
Period size: 226 Copynumber: 2.1 Consensus size: 225
1764320 ATTATAACAA
* * * *
1764330 AATTTATTATAAATATTATCAACATATTAGGTAGCGCCTAAATTGTTACCAAAGTTTAAGTTGAT
1 AATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGAT
** ** * *
1764395 GGAGCCATAGAAATTCGACGATAACAAAACAAATTAATTATTGGAAACATTATAAACTATAATAA
66 AAAGCCATAGAAATAAGACGATAACAAAACAAATTAATTATTAGAAACATTATAAACCATAATAA
*
1764460 CATAACAGATAGACTTTATTTAACGTAATAGATAGTGGTTTTTTAAAGCTGATGGGGCCTTAGAA
131 CATAACAGATAGACTTTATTTAACGTAATA-ATAGTGGTTGTTTAAAGCTGATGGGGCCTTAGAA
* *
1764525 ATCCGACGAGAACAAAATAAGTTAATTATTT
195 ATCCGACAAGAACAAAATAAGTTAATTACTT
*
1764556 AATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAACGTTTAAGCTGAT
1 AATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGAT
* * * ** *
1764621 AAAGCCTTTA-AAATAAGACTATAACAAAATATGTTAATTATTAGAAACATTATCAACCATAATA
66 AAAGCC-ATAGAAATAAGACGATAACAAAACAAATTAATTATTAGAAACATTATAAACCATAATA
* *
1764685 ACATAACA-AGTAATAC-TTATTTAATGTAAT-AT-GCTGCGTCTGTTTAAAGCTGATGGGGCCT
130 ACATAACAGA-T-AGACTTTATTTAACGTAATAATAG-TG-GT-TGTTTAAAGCTGATGGGGCCT
* * *
1764746 TAGAAATTCGACAATAACAAAATATGTTAATTACTT
190 TAGAAATCCGACAAGAACAAAATAAGTTAATTACTT
*
1764782 AATTTGTTTTCAA
1 AATTTGTTATCAA
1764795 AGAAATCAAT
Statistics
Matches: 207, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
223 1 0.00
224 4 0.02
225 3 0.01
226 194 0.94
227 5 0.02
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (225 bp):
AATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGAT
AAAGCCATAGAAATAAGACGATAACAAAACAAATTAATTATTAGAAACATTATAAACCATAATAA
CATAACAGATAGACTTTATTTAACGTAATAATAGTGGTTGTTTAAAGCTGATGGGGCCTTAGAAA
TCCGACAAGAACAAAATAAGTTAATTACTT
Found at i:1765502 original size:19 final size:20
Alignment explanation
Indices: 1765466--1765504 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1765456 ATATTGGAAT
1765466 AAAAGTATTCATACCTTTTA
1 AAAAGTATTCATACCTTTTA
*
1765486 AAAAGTATTGATA-CTTTTA
1 AAAAGTATTCATACCTTTTA
1765505 TATAGGCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (20 bp):
AAAAGTATTCATACCTTTTA
Found at i:1765557 original size:198 final size:198
Alignment explanation
Indices: 1764937--1765672 Score: 856
Period size: 202 Copynumber: 3.7 Consensus size: 198
1764927 GATAAAAACA
* * * * *
1764937 TTTACCATGTACATTGTTAATTTACCTATTACTTTATTGTAATCGATTTCGAAAA-TCCAAGTAT
1 TTTACCGTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTC-AAAATTCCAAGTAT
* * * *
1765001 TGATATTCTATACATATGTATCGATACATTTTGCGTGTAAACTGTTTGAGAAGA-ATACTAGAAT
65 CGATACTCTATACATATGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGACATACTAGAAT
*
1765065 AAAAGTATCCATACCAATATAAAAGTATCGATA-TTTGGTACTTATACCTATTATCATTATACCG
130 AAAAGTATCCATACCTATATAAAAGTATCGATACTTT--TAC-TATACCTATTATCATTATACCG
* *
1765129 GTAAAAG
192 GTAGACG
* * * *
1765136 TTTACCGTTTACATTGTTGATTTACCTATTACTTTATAATAATAGGTTTTAAAATTTCAAGTATC
1 TTTACCGTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTCAAAATTCCAAGTATC
* * * * * * * *
1765201 GATACTTTATACATGTGTATCAATACTTTTTTCATGTAAATTGTTTGAGAAGTACTATAATAGAA
66 GATACTCTATACATATGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAG-AC-ATACTAGAA
* * *
1765266 TAAAAGTATCCATATCTATATAAAAGTATCGATACTTGGTACTTATACCTATTATCATTATACTG
129 TAAAAGTATCCATACCTATATAAAAGTATCGATACTT-TTAC-TATACCTATTATCATTATACCG
1765331 GTAGACG
192 GTAGACG
* * * * ** *
1765338 TTTACCGTTTACATTGTTAATTTACCTATTACCTTATAGTAATAAGTTTCGAACTTAAAAGTATT
1 TTTACCGTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTCAAAATTCCAAGTATC
* * * * *
1765403 GATACTCTATATATGTGTATCGATACATTTGGCGTGCAAATTGTTTGAGAA-ACATATTGGAATA
66 GATACTCTATACATATGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGACATACTAGAATA
* * *
1765467 AAAGTATTCATACCT-TTTAAAAAGTATTGATACTTTTA-TATAGGCCTATTATCATTATACCGG
131 AAAGTATCCATACCTATAT-AAAAGTATCGATACTTTTACTATA--CCTATTATCATTATACCGG
*
1765530 TAGACT
193 TAGACG
* *
1765536 TTTACCGTTTACATTGTTAATTAACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGTATC
1 TTTACCGTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTCAAAATTCCAAGTATC
* * * * * * *
1765601 AATATTTTATATATATGTATCGATACATTTTGTGTGCAAATTGTTTGAGAAG-CGTACTGGAATA
66 GATACTCTATACATATGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGACATACTAGAATA
1765665 AAAGTATC
131 AAAGTATC
1765673 GGTACGGGCA
Statistics
Matches: 457, Mismatches: 70, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
196 4 0.01
198 149 0.33
199 131 0.29
200 3 0.01
202 168 0.37
203 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (198 bp):
TTTACCGTTTACATTGTTAATTTACCTATTACTTTATAGTAATAGGTTTCAAAATTCCAAGTATC
GATACTCTATACATATGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGACATACTAGAATA
AAAGTATCCATACCTATATAAAAGTATCGATACTTTTACTATACCTATTATCATTATACCGGTAG
ACG
Found at i:1765835 original size:21 final size:23
Alignment explanation
Indices: 1765792--1765836 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1765782 GCGCCTATTT
1765792 TATTTTAACTGGTTAAGTTTATA
1 TATTTTAACTGGTTAAGTTTATA
*
1765815 TATTTT-ACTGTTTAA-TTTATA
1 TATTTTAACTGGTTAAGTTTATA
1765836 T
1 T
1765837 TTCAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (23 bp):
TATTTTAACTGGTTAAGTTTATA
Found at i:1766155 original size:17 final size:18
Alignment explanation
Indices: 1766133--1766166 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1766123 AGCTGAGTTG
1766133 AGTCACA-AAAAGAAAGC
1 AGTCACACAAAAGAAAGC
*
1766150 AGTCACACAAATGAAAG
1 AGTCACACAAAAGAAAG
1766167 ACAAGACGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (18 bp):
AGTCACACAAAAGAAAGC
Found at i:1766894 original size:20 final size:20
Alignment explanation
Indices: 1766871--1766928 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1766861 TCTCTTTACT
1766871 AGTTTTGTCAAATTGAAACA
1 AGTTTTGTCAAATTGAAACA
* * *
1766891 AGTTTTGTCATATTTAAACC
1 AGTTTTGTCAAATTGAAACA
*
1766911 GGTTTTGTCAAATTGAAA
1 AGTTTTGTCAAATTGAAA
1766929 TCTGATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (20 bp):
AGTTTTGTCAAATTGAAACA
Found at i:1766937 original size:20 final size:19
Alignment explanation
Indices: 1766871--1766944 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1766861 TCTCTTTACT
1766871 AGTTTTGTCAAATTGAAAC
1 AGTTTTGTCAAATTGAAAC
* *
1766890 AAGTTTTGTCATATTTAAACC
1 -AGTTTTGTCAAATTGAAA-C
*
1766911 GGTTTTGTCAAATTGAAATC
1 AGTTTTGTCAAATTGAAA-C
* *
1766931 TGATTTGTCAAATT
1 AGTTTTGTCAAATT
1766945 TCAACCTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (19 bp):
AGTTTTGTCAAATTGAAAC
Found at i:1766938 original size:40 final size:40
Alignment explanation
Indices: 1766872--1766950 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1766862 CTCTTTACTA
* *
1766872 GTTTTGTCAAATTGAAACAAGTTTTGTCATATTTAAACCG
1 GTTTTGTCAAATTGAAACAAGATTTGTCAAATTTAAACCG
* *
1766912 GTTTTGTCAAATTGAAATC-TGATTTGTCAAATTTCAACC
1 GTTTTGTCAAATTGAAA-CAAGATTTGTCAAATTTAAACC
1766951 TATTATACTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (40 bp):
GTTTTGTCAAATTGAAACAAGATTTGTCAAATTTAAACCG
Found at i:1767526 original size:82 final size:83
Alignment explanation
Indices: 1767371--1767531 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 83
1767361 AAGGGTGAGC
** * *
1767371 TTTTTCTCCCTTTTGGGTGGTTTAGTTTATTGGGTATTATTTTCTAGTTTTCTAATCTTCTTCTT
1 TTTTTCTCCCTTTTCAGTGGTTTAGCTTATTGGGTATCATTTTCTAGTTTTCTAATCTTCTTCTT
*
1767436 TGCAAAATGCCAAGCCTT
66 TACAAAATGCCAAGCCTT
*
1767454 TTTTTCTCCCTTTTCAGTGGTTTAGCTTATTGGG-ATCATTTTCTAGTTTTCTTATCTTCTTCTT
1 TTTTTCTCCCTTTTCAGTGGTTTAGCTTATTGGGTATCATTTTCTAGTTTTCTAATCTTCTTCTT
* *
1767518 TACTAAATGTCAAG
66 TACAAAATGCCAAG
1767532 ATTTATGGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 39 0.56
83 31 0.44
ACGTcount: A:0.16, C:0.17, G:0.14, T:0.52
Consensus pattern (83 bp):
TTTTTCTCCCTTTTCAGTGGTTTAGCTTATTGGGTATCATTTTCTAGTTTTCTAATCTTCTTCTT
TACAAAATGCCAAGCCTT
Found at i:1768055 original size:17 final size:17
Alignment explanation
Indices: 1768035--1768068 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1768025 CTGACACCTC
1768035 GGAGCGAGGGTGAGATA
1 GGAGCGAGGGTGAGATA
1768052 GGAGCGAGGGTGAGATA
1 GGAGCGAGGGTGAGATA
1768069 TTACAGTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.53, T:0.12
Consensus pattern (17 bp):
GGAGCGAGGGTGAGATA
Found at i:1769906 original size:20 final size:19
Alignment explanation
Indices: 1769873--1769940 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
1769863 TTTTTTAAAG
*
1769873 AAACATTTACCAAACTTTGA
1 AAACATTT-TCAAACTTTGA
1769893 AAACCATTTTCAAA----GA
1 AAA-CATTTTCAAACTTTGA
*
1769909 AAA-ATTTACAAACTTTGA
1 AAACATTTTCAAACTTTGA
1769927 AAATCATTTTCAAA
1 AAA-CATTTTCAAA
1769941 GTTGGTTGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
14 8 0.21
16 5 0.13
18 5 0.13
20 15 0.39
21 5 0.13
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (19 bp):
AAACATTTTCAAACTTTGA
Found at i:1769926 original size:34 final size:35
Alignment explanation
Indices: 1769842--1769941 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 35
1769832 TCTACCAAAC
* * *
1769842 TTTATCAAACTTTGAAAAACATTTTTTAAAGAAACA
1 TTTACCAAACTTTGAAAAACA-TTTTCAAAGAAAAA
*
1769878 TTTACCAAACTTTGAAAACCATTTTCAAAGAAAAA
1 TTTACCAAACTTTGAAAAACATTTTCAAAGAAAAA
*
1769913 TTTA-CAAACTTTGAAAATCATTTTCAAAG
1 TTTACCAAACTTTGAAAAACATTTTCAAAG
1769942 TTGGTTGACA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 24 0.41
35 16 0.27
36 19 0.32
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (35 bp):
TTTACCAAACTTTGAAAAACATTTTCAAAGAAAAA
Found at i:1772320 original size:22 final size:22
Alignment explanation
Indices: 1772292--1772338 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1772282 TTCCATTATT
*
1772292 AGACCTCAACTGCATGACTATC
1 AGACCTCAACCGCATGACTATC
* *
1772314 AGACCTCAACCGCTTGACTTTC
1 AGACCTCAACCGCATGACTATC
1772336 AGA
1 AGA
1772339 TCAGTCTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (22 bp):
AGACCTCAACCGCATGACTATC
Found at i:1774521 original size:35 final size:35
Alignment explanation
Indices: 1774453--1774567 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
1774443 ACCCATTCCT
* * *
1774453 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1774487 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
* *
1774523 ATTTTCAAATAAACATTTACCAAACTTTAAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1774558 ATTTTCAAAG
1 ATTTTCAAAG
1774568 TTGGTTGTCA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.01
35 46 0.63
36 26 0.36
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:1774525 original size:21 final size:20
Alignment explanation
Indices: 1774501--1774561 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
1774491 TTCAAAGAAA
1774501 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTT-AAAAC
*
1774522 CATTT-TCAAA---T-AAA-
1 CATTTACCAAACTTTAAAAC
1774536 CATTTACCAAACTTTAAAAAC
1 CATTTACCAAACTTT-AAAAC
1774557 CATTT
1 CATTT
1774562 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 1 0.03
18 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (20 bp):
CATTTACCAAACTTTAAAAC
Found at i:1782279 original size:20 final size:19
Alignment explanation
Indices: 1782247--1782289 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1782237 CAAGAAGCTT
* *
1782247 TAAC-AACTTTTAACCACC
1 TAACTAACTCTTAACAACC
1782265 TCAACTAACTCTTAACAACC
1 T-AACTAACTCTTAACAACC
1782285 TAACT
1 TAACT
1782290 GCTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 7 0.33
20 13 0.62
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (19 bp):
TAACTAACTCTTAACAACC
Found at i:1788894 original size:20 final size:20
Alignment explanation
Indices: 1788869--1788906 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1788859 AATGCAATTA
*
1788869 GTGCATCGATGCACCCTGTT
1 GTGCATCCATGCACCCTGTT
1788889 GTGCATCCATGCACCCTG
1 GTGCATCCATGCACCCTG
1788907 GCTGCAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (20 bp):
GTGCATCCATGCACCCTGTT
Found at i:1800215 original size:11 final size:11
Alignment explanation
Indices: 1800199--1800223 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1800189 TTTTTATTCT
1800199 TTCACTTGCAC
1 TTCACTTGCAC
1800210 TTCACTTGCAC
1 TTCACTTGCAC
1800221 TTC
1 TTC
1800224 TTCTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:1801779 original size:19 final size:20
Alignment explanation
Indices: 1801752--1801799 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1801742 CCATTCGGCC
*
1801752 AAAAGCATGCACTTTCATT-
1 AAAATCATGCACTTTCATTA
* * *
1801771 AAAATCATGTATTTTTATTA
1 AAAATCATGCACTTTCATTA
1801791 AAAATCATG
1 AAAATCATG
1801800 TATTTTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (20 bp):
AAAATCATGCACTTTCATTA
Found at i:1802684 original size:34 final size:34
Alignment explanation
Indices: 1802641--1802710 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1802631 AAGGATTTAT
1802641 ATAATAAAATTTAAATAAAATAAATTCTTTGTAG
1 ATAATAAAATTTAAATAAAATAAATTCTTTGTAG
1802675 ATAATAAAATTTAAATAAAATAAATTCTTTGTAG
1 ATAATAAAATTTAAATAAAATAAATTCTTTGTAG
1802709 AT
1 AT
1802711 TACATCTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (34 bp):
ATAATAAAATTTAAATAAAATAAATTCTTTGTAG
Found at i:1804279 original size:4 final size:4
Alignment explanation
Indices: 1804270--1804294 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1804260 TTAATCAGTA
1804270 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1804295 GTTTCTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1804505 original size:138 final size:138
Alignment explanation
Indices: 1804257--1804781 Score: 673
Period size: 138 Copynumber: 3.8 Consensus size: 138
1804247 TGTAATTTGG
* * * * * *
1804257 ACTTTAATCAGTATTATTTATTTATTTATTTATTTATTGTTTCTAATATTCGATTTGGCCTTGTG
1 ACTTTAATCATTGTTATTTATTTATTTATGTATTTATTGATTCTAATATTCGATTCGACCTTGTG
* * * *
1804322 GTGATCCGATCTAGGGTATGATCCGTATTATTATGGTTCGGACTCTGCTAATTACTAACTTTTAT
66 GTGATCCGATCCAGGGTATGATCCGTATTATTATGGTTCAGACTCTGCTAAATATTAACTTTTAT
1804387 TTTATTGC
131 TTTATTGC
* *
1804395 ACTTTAATCATTGTTATTTATTTATTTATGTATTTATTGATTCTAATATTCGATTTGGCCTTGTG
1 ACTTTAATCATTGTTATTTATTTATTTATGTATTTATTGATTCTAATATTCGATTCGACCTTGTG
* * *
1804460 GTGATTCGATCCAGGGTATGATCC-TCATTATTATGGTTCAGACTCTTCTAACTATTAACTTTTA
66 GTGATCCGATCCAGGGTATGATCCGT-ATTATTATGGTTCAGACTCTGCTAAATATTAACTTTTA
*
1804524 TTTTATTAC
130 TTTTATTGC
* *
1804533 ACATTAATCATTGTTATTTATTTATTTATGTATTTATTGTTTCTAATATTCGATTCGACCTTGTG
1 ACTTTAATCATTGTTATTTATTTATTTATGTATTTATTGATTCTAATATTCGATTCGACCTTGTG
* * * * * * * *
1804598 GTAACCCGATCCGGGGTATGATCTGCATTATTATGGTTCGGACTCTGCGAAATATTGACTTTTAT
66 GTGATCCGATCCAGGGTATGATCCGTATTATTATGGTTCAGACTCTGCTAAATATTAACTTTTAT
1804663 TTTATTGC
131 TTTATTGC
* * * * *
1804671 A-TTCTAACCATTGTTTATTTATTTAGTTATTTATTTATT-ATTTCTAATATTTGATTCGATCTT
1 ACTT-TAATCATTG-TTATTTATTTATTTATGTATTTATTGA-TTCTAATATTCGATTCGACCTT
* *
1804734 GTGGTGA-CCTACTCC-TGGTATGATCCGTATTATTATGGTTCAGACTCT
63 GTGGTGATCCGA-TCCAGGGTATGATCCGTATTATTATGGTTCAGACTCT
1804782 ACAAACCGCT
Statistics
Matches: 341, Mismatches: 40, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
137 2 0.01
138 287 0.84
139 52 0.15
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (138 bp):
ACTTTAATCATTGTTATTTATTTATTTATGTATTTATTGATTCTAATATTCGATTCGACCTTGTG
GTGATCCGATCCAGGGTATGATCCGTATTATTATGGTTCAGACTCTGCTAAATATTAACTTTTAT
TTTATTGC
Found at i:1805027 original size:19 final size:18
Alignment explanation
Indices: 1804999--1805042 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1804989 TATTTTAAGT
* *
1804999 TTTTTATTTATTTTTTTAC
1 TTTTT-TTTATTATTGTAC
1805018 TATTTTTTTATTATTGTAC
1 T-TTTTTTTATTATTGTAC
1805037 TTTTTT
1 TTTTTT
1805043 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTTTATTATTGTAC
Found at i:1808923 original size:10 final size:9
Alignment explanation
Indices: 1808908--1809010 Score: 73
Period size: 10 Copynumber: 10.3 Consensus size: 9
1808898 AAAGAAAGAT
1808908 AGAAAAAAG
1 AGAAAAAAG
1808917 AGTAAAAAAG
1 AG-AAAAAAG
*
1808927 AGGAAAAAAT
1 A-GAAAAAAG
1808937 AGAAAAAAG
1 AGAAAAAAG
1808946 -GAAAAAAG
1 AGAAAAAAG
1808954 AAGAGAGAAAGAG
1 -AGA-A-AAA-AG
*
1808967 AGAAAAGTAAA
1 AGAAAA--AAG
1808978 AGAAAAAAG
1 AGAAAAAAG
*
1808987 AAAGAAAAAAAA
1 --AG-AAAAAAG
1808999 AGAAAAAAG
1 AGAAAAAAG
1809008 AGA
1 AGA
1809011 TCAAAGAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
8 8 0.11
9 20 0.26
10 21 0.28
11 12 0.16
12 13 0.17
13 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:1808987 original size:7 final size:7
Alignment explanation
Indices: 1808931--1809036 Score: 67
Period size: 7 Copynumber: 14.9 Consensus size: 7
1808921 AAAAAGAGGA
1808931 AAAAATAG
1 AAAAA-AG
1808939 AAAAAAGG
1 AAAAAA-G
1808947 AAAAAAG
1 AAAAAAG
* *
1808954 AAGAGAG
1 AAAAAAG
*
1808961 -AAAGAG
1 AAAAAAG
*
1808967 AGAAAAG
1 AAAAAAG
*
1808974 -TAAAAG
1 AAAAAAG
1808980 AAAAAAG
1 AAAAAAG
1808987 AAAGAAA-
1 AAA-AAAG
1808994 AAAAAAG
1 AAAAAAG
1809001 AAAAAAG
1 AAAAAAG
*
1809008 AGATCAAAG
1 A-A-AAAAG
1809017 -AAAAAG
1 AAAAAAG
*
1809023 AAGAAAG
1 AAAAAAG
1809030 AAGAAAA
1 AA-AAAA
1809037 TAGACAGATC
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
6 17 0.22
7 38 0.49
8 19 0.24
9 4 0.05
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:1808998 original size:26 final size:26
Alignment explanation
Indices: 1808949--1808998 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1808939 AAAAAAGGAA
* * * *
1808949 AAAAGAAGAGAGAAAGAGAGAAAAGT
1 AAAAGAAAAAAGAAAGAAAAAAAAGT
1808975 AAAAGAAAAAAGAAAGAAAAAAAA
1 AAAAGAAAAAAGAAAGAAAAAAAA
1808999 AGAAAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAAAGAAAGAAAAAAAAGT
Found at i:1809007 original size:34 final size:34
Alignment explanation
Indices: 1808941--1809007 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1808931 AAAAATAGAA
* * * *
1808941 AAAAGGAAAAAAGAAGAGAGAAAGAGAGAAAAGT
1 AAAAGGAAAAAAGAAGAAAAAAAAAGAAAAAAGT
1808975 AAAA-GAAAAAAGAAAGAAAAAAAAAGAAAAAAG
1 AAAAGGAAAAAAG-AAGAAAAAAAAAGAAAAAAG
1809008 AGATCAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (34 bp):
AAAAGGAAAAAAGAAGAAAAAAAAAGAAAAAAGT
Found at i:1809696 original size:28 final size:28
Alignment explanation
Indices: 1809653--1809733 Score: 153
Period size: 28 Copynumber: 2.9 Consensus size: 28
1809643 GCAAGAAGCC
*
1809653 AACCTGAAACACATTACCTCCCCAAATT
1 AACCTGAAACAAATTACCTCCCCAAATT
1809681 AACCTGAAACAAATTACCTCCCCAAATT
1 AACCTGAAACAAATTACCTCCCCAAATT
1809709 AACCTGAAACAAATTACCTCCCCAA
1 AACCTGAAACAAATTACCTCCCCAA
1809734 GTCAGCCTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.20
Consensus pattern (28 bp):
AACCTGAAACAAATTACCTCCCCAAATT
Found at i:1809727 original size:14 final size:15
Alignment explanation
Indices: 1809675--1809724 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1809665 ATTACCTCCC
1809675 CAAATTAACCTGAAA
1 CAAATTAACCTGAAA
***
1809690 CAAATT-ACCT-CCC
1 CAAATTAACCTGAAA
1809703 CAAATTAACCTGAAA
1 CAAATTAACCTGAAA
1809718 CAAATTA
1 CAAATTA
1809725 CCTCCCCAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 6 0.22
14 8 0.30
15 13 0.48
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (15 bp):
CAAATTAACCTGAAA
Found at i:1810138 original size:3 final size:3
Alignment explanation
Indices: 1810130--1810209 Score: 106
Period size: 3 Copynumber: 26.3 Consensus size: 3
1810120 CAATTTTAAA
* * *
1810130 ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT ATA ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1810178 ATT AAT ATT AAT ATT ATTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
1810210 AATAAATATA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1812552 original size:66 final size:66
Alignment explanation
Indices: 1812446--1812613 Score: 264
Period size: 66 Copynumber: 2.5 Consensus size: 66
1812436 TGAAAGCGAC
* * * *
1812446 GTCTTCGTGAGAATTTATTCTCCATGTCAGACCTAACAAGTAGCTTTAGGGGTTCATTTATACTA
1 GTCTTCGTGAGAATTTATTCTCCATGTCAGGCATAGCAAGTAGCTTTAGGGGTTCATATATACTA
1812511 T
66 T
1812512 GTCTTCGTGAGAATTTATTCTCCATGTCAGGCATAGCAAGTAGCTTTAGGGGTTCATATATACTA
1 GTCTTCGTGAGAATTTATTCTCCATGTCAGGCATAGCAAGTAGCTTTAGGGGTTCATATATACTA
1812577 T
66 T
* ** *
1812578 ATCTTCGTGAGAATTTATTCTCTGTGTGAGGCATAG
1 GTCTTCGTGAGAATTTATTCTCCATGTCAGGCATAG
1812614 GGAAATGTGT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 94 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (66 bp):
GTCTTCGTGAGAATTTATTCTCCATGTCAGGCATAGCAAGTAGCTTTAGGGGTTCATATATACTA
T
Found at i:1814765 original size:14 final size:14
Alignment explanation
Indices: 1814748--1814783 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1814738 TTCATTTTTT
*
1814748 ATTTTTGTATTTGC
1 ATTTTTATATTTGC
*
1814762 ATTTTTATATTTTC
1 ATTTTTATATTTGC
1814776 ATTTTTAT
1 ATTTTTAT
1814784 TTTATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (14 bp):
ATTTTTATATTTGC
Found at i:1816954 original size:72 final size:73
Alignment explanation
Indices: 1816837--1816981 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 73
1816827 ATACAATAAA
* * * *
1816837 GCTTGAGTTGTCCCCCTAAAGCAATTTGTTAATAGCCTCGGCTTTATGGAT-AATATTCAGCTAG
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAAATATTCAGCTAG
1816901 CCTGTTAT
66 CCTGTTAT
* * *
1816909 GCTTGAGTTATTCCCCTTAAGCAATTGGTTGATAGCCCCGACTTTATGGATAAATATTCAGCTAG
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAAATATTCAGCTAG
1816974 CCTGTTAT
66 CCTGTTAT
1816982 ACTATTATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 44 0.68
73 21 0.32
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (73 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAAATATTCAGCTAG
CCTGTTAT
Found at i:1820020 original size:54 final size:54
Alignment explanation
Indices: 1819938--1820099 Score: 261
Period size: 54 Copynumber: 3.0 Consensus size: 54
1819928 TGATTGAAGA
*
1819938 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
1 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
*
1819992 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * * *
1820046 ATCTGTGTAGAAGACACAGGAAAGGATGAATGTGTTGTCAAATGTTTTATGAAC
1 ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1820100 CAGTGATTAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:1820493 original size:22 final size:22
Alignment explanation
Indices: 1820467--1820675 Score: 339
Period size: 22 Copynumber: 9.5 Consensus size: 22
1820457 ACATCTAAAT
*
1820467 TCTTCAAAGATGATAGATTCAT-
1 TCTTCAAAGATGATAGA-TCCTC
*
1820489 TCTTCAAAGATGATAGATCCTA
1 TCTTCAAAGATGATAGATCCTC
1820511 TCTTCAAAGATGATAGATCCTC
1 TCTTCAAAGATGATAGATCCTC
1820533 TCTTCAAAGATGATAGATCCTC
1 TCTTCAAAGATGATAGATCCTC
1820555 TCTTCAAAGATGATAGATCCTC
1 TCTTCAAAGATGATAGATCCTC
*
1820577 TCTTCAAAGATGATAGATCATC
1 TCTTCAAAGATGATAGATCCTC
*
1820599 TCTTCAAAGATTATAGATCCTC
1 TCTTCAAAGATGATAGATCCTC
*
1820621 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATCCTC
*
1820643 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATCCTC
*
1820665 TTTTCAAAGAT
1 TCTTCAAAGAT
1820676 AAAAGCTTTA
Statistics
Matches: 178, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
21 3 0.02
22 175 0.98
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATCCTC
Found at i:1821303 original size:32 final size:32
Alignment explanation
Indices: 1821262--1821369 Score: 216
Period size: 32 Copynumber: 3.4 Consensus size: 32
1821252 AAATAAAATA
1821262 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1821294 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1821326 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1 AAACTTTTTGAAATGGGGCATGTTACCTAATG
1821358 AAACTTTTTGAA
1 AAACTTTTTGAA
1821370 GAACCTAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (32 bp):
AAACTTTTTGAAATGGGGCATGTTACCTAATG
Found at i:1822591 original size:2 final size:2
Alignment explanation
Indices: 1822584--1822610 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1822574 AAATACGTAC
1822584 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 A
1822611 ATCATCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1822915 original size:23 final size:23
Alignment explanation
Indices: 1822862--1822927 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
1822852 CTCTAGGGGT
* * *
1822862 ACATAGAATTTGTCTTGAAAGACC
1 ACATAGAA-ATGTCTCGAAGGACC
* *
1822886 GCGTAGAAATGTCTCGAAGGACC
1 ACATAGAAATGTCTCGAAGGACC
*
1822909 ACATAG--ATGTCCCGAAGGA
1 ACATAGAAATGTCTCGAAGGA
1822928 ACACTCCTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 12 0.35
23 16 0.47
24 6 0.18
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (23 bp):
ACATAGAAATGTCTCGAAGGACC
Found at i:1822970 original size:21 final size:21
Alignment explanation
Indices: 1822937--1823029 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
1822927 AACACTCCTT
*
1822937 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
* *
1822958 AAGGACCA-A-ATATGTGTCTCG
1 AAGGACCACATATATAT-TC-CA
* * *
1822979 AAGAACCACATATATGTTCTA
1 AAGGACCACATATATATTCCA
** *
1823000 AAGGATTACATATATATCCCA
1 AAGGACCACATATATATTCCA
1823021 AAGGACCAC
1 AAGGACCAC
1823030 GTAGAATCCT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.09
20 3 0.06
21 37 0.69
22 3 0.06
23 6 0.11
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:1828127 original size:23 final size:23
Alignment explanation
Indices: 1828100--1828158 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1828090 ACATAGAATT
* *
1828100 TGTCCCGAAGGATAGTGTAGAAA
1 TGTCCCGAAGGACAGCGTAGAAA
* *
1828123 TGTCCCAAAGGACCGCGTAGAAA
1 TGTCCCGAAGGACAGCGTAGAAA
*
1828146 TTTCCCGAAGGAC
1 TGTCCCGAAGGAC
1828159 CACATACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (23 bp):
TGTCCCGAAGGACAGCGTAGAAA
Found at i:1828159 original size:23 final size:23
Alignment explanation
Indices: 1828093--1828159 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1828083 TAGGGGCACA
* ** *
1828093 TAGAATTTGTCCCGAAGGATAGTG
1 TAGAAATT-TCCCGAAGGACCGCG
* *
1828117 TAGAAATGTCCCAAAGGACCGCG
1 TAGAAATTTCCCGAAGGACCGCG
1828140 TAGAAATTTCCCGAAGGACC
1 TAGAAATTTCCCGAAGGACC
1828160 ACATACATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 29 0.83
24 6 0.17
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (23 bp):
TAGAAATTTCCCGAAGGACCGCG
Found at i:1830150 original size:19 final size:19
Alignment explanation
Indices: 1830126--1830174 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1830116 AGCTAATTTT
* *
1830126 GGTATCGATATTGGAATAG
1 GGTATCGATACTGGAAGAG
*
1830145 GGTATCAATACTGGAAGAG
1 GGTATCGATACTGGAAGAG
1830164 GGTATCGATAC
1 GGTATCGATAC
1830175 CATAATAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (19 bp):
GGTATCGATACTGGAAGAG
Found at i:1830212 original size:20 final size:20
Alignment explanation
Indices: 1830163--1830216 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 20
1830153 TACTGGAAGA
1830163 GGGTATCGATACCATAATAG
1 GGGTATCGATACCATAATAG
*
1830183 GGTAGTATCGATACCATAGTAG
1 GG--GTATCGATACCATAATAG
1830205 GGGTATCGATAC
1 GGGTATCGATAC
1830217 TGAAGGGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.39
22 19 0.61
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATAATAG
Found at i:1830684 original size:45 final size:45
Alignment explanation
Indices: 1830633--1830827 Score: 174
Period size: 45 Copynumber: 4.3 Consensus size: 45
1830623 ATACTAAAGC
* *
1830633 ATATGAGTGCATTATTGGCATGAAAGGATGCCATAGTTTAAATGT
1 ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
1830678 ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
1 ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
* * *** ** * * * *
1830723 ATATGGGTACATTATCAACAAAAAAGCATGCTAGAGTTGAAATGA
1 ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
* *** * * * * *
1830768 ATATGGGTGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGC
1 ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
* *
1830813 ATATGGGTACATTAT
1 ATATGAGTGCATTAT
1830828 CAACATAACA
Statistics
Matches: 132, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 132 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (45 bp):
ATATGAGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGT
Found at i:1830806 original size:90 final size:90
Alignment explanation
Indices: 1830667--1830995 Score: 351
Period size: 90 Copynumber: 3.7 Consensus size: 90
1830657 AGGATGCCAT
* * *** * * *
1830667 AGTTTAAATGTATATGAGTGCATTATTGGCATG-AAAGAATGCCATAGTTGAAATGTATATGGGT
1 AGTTGAAATGTATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGTATATGGGT
*
1830731 ACATTATCAACAAAAAAGCATGCTAG
65 ACATTATCAACAAAAAAGCATACTAG
* * *
1830757 AGTTGAAATGAATATGGGTGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTA
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTA
* *
1830822 CATTATCAACATAACAA-CATCCTAG
66 CATTATCAACA-AAAAAGCATACTAG
* * * * *
1830847 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATACTATG-GTTGAAATATATATGGGC
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTA-GAGTTGAAATGTATATGGGT
* * * *
1830911 ACATTATCAACAGAAACGTATACTAT
65 ACATTATCAACAAAAAAGCATACTAG
* * * *
1830937 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAA-TATGTTATAGTTTAAAGTGTATA
1 AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAA-TGTATA
1830996 ATGGTGTATT
Statistics
Matches: 198, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
89 13 0.07
90 180 0.91
91 5 0.03
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.30
Consensus pattern (90 bp):
AGTTGAAATGTATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTA
CATTATCAACAAAAAAGCATACTAG
Found at i:1830828 original size:45 final size:45
Alignment explanation
Indices: 1830712--1830995 Score: 331
Period size: 45 Copynumber: 6.3 Consensus size: 45
1830702 AGAATGCCAT
* *
1830712 AGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATGCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAG
* * *
1830757 AGTTGAAATGAATATGGGTGCATTATCAACATAAAAGTATGCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAG
* * * *
1830802 AGTTGAAATGCATATGGGTACATTATCAACATAACAA-CATCCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAA-AAGTATGCTAG
* *
1830847 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATACTATG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTA-G
* * * * *
1830893 -GTTGAAATATATATGGGCACATTATCAACAGAAACGTATACTAT
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAG
* * * *
1830937 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAA-TATGTTAT
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAG
*
1830981 AGTTTAAAGTGTATA
1 AGTTGAAA-TGTATA
1830996 ATGGTGTATT
Statistics
Matches: 207, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
44 15 0.07
45 189 0.91
46 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (45 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTAG
Found at i:1830875 original size:135 final size:135
Alignment explanation
Indices: 1830712--1830967 Score: 381
Period size: 135 Copynumber: 1.9 Consensus size: 135
1830702 AGAATGCCAT
*
1830712 AGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATGCTA-GAGTTGAAATGA-ATATGGG
1 AGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATACTATG-GTTGAAAT-ATATATGGG
** * *
1830775 TGCATTATCAACATAAAAGTATGCTAGAGTTGAAATGCATATGGGTACATTATCAACATAACAAC
64 CACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTACATTATCAACATAACAAC
1830840 ATCCTAG
129 ATCCTAG
* * *
1830847 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAGTATACTATGGTTGAAATATATATGGGCA
1 AGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATACTATGGTTGAAATATATATGGGCA
* * *
1830912 CATTATCAACAGAAACGTATACTATAGTTGAAATGCATATGGGTGCATTATCAACA
66 CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTACATTATCAACA
1830968 GAAAATATGT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
134 1 0.01
135 106 0.98
136 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (135 bp):
AGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATACTATGGTTGAAATATATATGGGCA
CATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTACATTATCAACATAACAACAT
CCTAG
Found at i:1832836 original size:13 final size:13
Alignment explanation
Indices: 1832818--1832843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1832808 GTTTGATATC
1832818 AATAATAATAAAA
1 AATAATAATAAAA
1832831 AATAATAATAAAA
1 AATAATAATAAAA
1832844 CTTAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:1834002 original size:2 final size:2
Alignment explanation
Indices: 1833965--1833992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1833955 TGTGACCGAA
1833965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1833993 GAGTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1834491 original size:2 final size:2
Alignment explanation
Indices: 1834484--1834554 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
1834474 TATAAATAAT
1834484 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1834525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1834555 AATAAAAAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1835185 original size:13 final size:13
Alignment explanation
Indices: 1835164--1835221 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
1835154 TGTCTTTTTA
*
1835164 TTTTTTATTAAAG
1 TTTTCTATTAAAG
*
1835177 TTTTCTATTAAGGTAT
1 TTTTCTATTAA---AG
1835193 TTTTCATTATTAAAG
1 TTTTC--TATTAAAG
1835208 TTTTCTATTAAAG
1 TTTTCTATTAAAG
1835221 T
1 T
1835222 ATTTTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 19 0.51
15 6 0.16
16 6 0.16
18 6 0.16
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (13 bp):
TTTTCTATTAAAG
Found at i:1835206 original size:31 final size:31
Alignment explanation
Indices: 1835168--1835227 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1835158 TTTTTATTTT
*
1835168 TTATTAAAGTTTTCTATTAAGGTATTTTTCA
1 TTATTAAAGTTTTCTATTAAAGTATTTTTCA
1835199 TTATTAAAGTTTTCTATTAAAGTATTTTT
1 TTATTAAAGTTTTCTATTAAAGTATTTTT
1835228 TTATTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (31 bp):
TTATTAAAGTTTTCTATTAAAGTATTTTTCA
Found at i:1836324 original size:5 final size:5
Alignment explanation
Indices: 1836300--1836367 Score: 84
Period size: 5 Copynumber: 13.8 Consensus size: 5
1836290 TTCCTGGAAC
* * * *
1836300 AAAAT AAAA- AAGAT AGAAT AAAAT AAAAT TATAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
1836349 AATAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
1836368 AATCAGACCC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
4 3 0.06
5 49 0.94
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1836341 original size:20 final size:20
Alignment explanation
Indices: 1836300--1836367 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
1836290 TTCCTGGAAC
* *
1836300 AAAATAAAA-AAGATAGAAT
1 AAAATAAAATAATATAAAAT
*
1836319 AAAATAAAATTATATAAAAT
1 AAAATAAAATAATATAAAAT
1836339 AAAATAAAATAATATAAAAT
1 AAAATAAAATAATATAAAAT
1836359 AAAATAAAA
1 AAAATAAAA
1836368 AATCAGACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 9 0.20
20 35 0.80
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAATAAAATAATATAAAAT
Found at i:1837117 original size:28 final size:28
Alignment explanation
Indices: 1837012--1837105 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 28
1837002 TGCAGTGCCC
* *
1837012 TATTTTAATTTAT-AAAAGTTTTATACTT
1 TATTGTAATTTATAAAAAG-TTTGTACTT
* * *
1837040 AATTGTAATTTATAAAAAATATGTACTT
1 TATTGTAATTTATAAAAAGTTTGTACTT
*
1837068 TTTTGTAATTTATAAAAAGTTTGTACTT
1 TATTGTAATTTATAAAAAGTTTGTACTT
1837096 TATTGTAATT
1 TATTGTAATT
1837106 AAAAATTAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 51 0.93
29 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.52
Consensus pattern (28 bp):
TATTGTAATTTATAAAAAGTTTGTACTT
Found at i:1850591 original size:21 final size:21
Alignment explanation
Indices: 1850550--1850594 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1850540 ATTAGAGTGC
* *
1850550 AAAAAGAAGAGAAAATCAGAA
1 AAAAAGAAAAGAAAATAAGAA
1850571 AAAAAGAAAAGAAGAA-AAGAA
1 AAAAAGAAAAGAA-AATAAGAA
1850592 AAA
1 AAA
1850595 GAAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAGAAAAGAAAATAAGAA
Found at i:1855213 original size:91 final size:90
Alignment explanation
Indices: 1855082--1855420 Score: 473
Period size: 91 Copynumber: 3.7 Consensus size: 90
1855072 GTGAAAAATC
* *
1855082 CATAATGAGAATAACTCATCCAACGTGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
1855147 TGAATCAACATTTCCAGGGGAGAGTT
66 TGAATCAACATTTCCAGGGG-GAGTT
* * *
1855173 CATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCC
1 CATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
* * **
1855238 TGCATTAACATTTCCAACTGGGAGTT
66 TGAATCAACATTTCC-AGGGGGAGTT
* *
1855264 CATAATAAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAA-AACTTGTTCAACC
1 CATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA-AAAGAACTTGTTCAACC
* * *
1855328 TTGCATCAACATTTCTAGCGGGGAGCT
65 TTGAATCAACATTTCCAG-GGGGAGTT
* * * *
1855355 CATAATGAGAATAACTCATCCGACGAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
1855420 T
66 T
1855421 AGTTCGATTT
Statistics
Matches: 221, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
90 3 0.01
91 213 0.96
92 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (90 bp):
CATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
TGAATCAACATTTCCAGGGGGAGTT
Found at i:1855373 original size:182 final size:182
Alignment explanation
Indices: 1855082--1855418 Score: 543
Period size: 182 Copynumber: 1.9 Consensus size: 182
1855072 GTGAAAAATC
* * *
1855082 CATAATGAGAATAACTCATCCAACGTGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
1 CATAATAAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
*
1855147 TGAATCAACATTTCCAGGGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTT
66 TGAATCAACATTTCCAGGGGAGAGCTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTT
1855212 CATAATGAGAAGAACTTGTTCAACCCTGCATTAACATTTCCAACTGGGAGTT
131 CATAATGAGAAGAACTTGTTCAACCCTGCATTAACATTTCCAACTGGGAGTT
*
1855264 CATAATAAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAA-AACTTGTTCAACC
1 CATAATAAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA-AAAGAACTTGTTCAACC
* * * * * *
1855328 TTGCATCAACATTTCTAGCGGG-GAGCTCATAATGAGAATAACTCATCCGACGAGGGATAAGAAG
65 TTGAATCAACATTTCCAG-GGGAGAGCTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAG
1855392 TTCATAATGAGAAGAACTTGTTCAACC
129 TTCATAATGAGAAGAACTTGTTCAACC
1855419 TTAGTTCGAT
Statistics
Matches: 142, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
182 136 0.96
183 6 0.04
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (182 bp):
CATAATAAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAACCT
TGAATCAACATTTCCAGGGGAGAGCTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCCTGCATTAACATTTCCAACTGGGAGTT
Done.