Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008594.1 Hibiscus syriacus cultivar Beakdansim tig00111543_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: 1173925
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1142271 original size:91 final size:91
Alignment explanation
Indices: 1142096--1142361 Score: 419
Period size: 91 Copynumber: 2.9 Consensus size: 91
1142086 CGTTATTGGA
* * ** * *
1142096 TTGAACAAGATCTTCTCATTATGAACTTCTTC-T-CTCTTGTACATGATTTATTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTT-TGGATGAGTTCTTCTCATTATGAA
* *
1142159 CTCTTCACTGAAAATAATGATGCAAGG
65 CTCTTCACTGGAAATACTGATGCAAGG
1142186 TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* *
1142251 TCTTCACTGGAAACACTGATGTAAGG
66 TCTTCACTGGAAATACTGATGCAAGG
1142277 TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1142342 TCTTCACTGGAAATACTGAT
66 TCTTCACTGGAAATACTGAT
1142362 CCCCCTCATT
Statistics
Matches: 163, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
90 30 0.18
91 128 0.79
92 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
TCTTCACTGGAAATACTGATGCAAGG
Found at i:1142858 original size:136 final size:136
Alignment explanation
Indices: 1142429--1142870 Score: 728
Period size: 136 Copynumber: 3.3 Consensus size: 136
1142419 CCTTTAAGAC
* *
1142429 GAGTTCTTCTCATTATGAACTCTTC--TGGAAATGT-TAATCCCTCAAGCGAGGCGTTACTGATT
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCT-ATCCCTCAAGCGAGGCGTCACTGATT
* *
1142491 CGAAATGCCGTGAATCAAGTGATAGGTCGAACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCT
65 CGAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT
*
1142556 GTCAGAT
130 GTCGGAT
** * *
1142563 GAGTTCTTCTCATTATGAACTCTGTACTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCTATCCCTCAAGCGAGGCGTCACTGATTC
* * *
1142628 GAAATGCCGTGAATCGAGTGATAGGTCGATCAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTT
66 GAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
*
1142693 TTGGAT
131 TCGGAT
*
1142699 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCTATTCCTCAAGCGAGGCGTCACTGATTC
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCTATCCCTCAAGCGAGGCGTCACTGATTC
1142764 GAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
66 GAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
1142829 TCGGAT
131 TCGGAT
1142835 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
1 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGT
1142871 TGATCTGTTT
Statistics
Matches: 285, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
134 23 0.08
136 262 0.92
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (136 bp):
GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCTATCCCTCAAGCGAGGCGTCACTGATTC
GAAATGCCGTGAATCGAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTG
TCGGAT
Found at i:1143354 original size:40 final size:40
Alignment explanation
Indices: 1143310--1143644 Score: 607
Period size: 40 Copynumber: 8.4 Consensus size: 40
1143300 TATCTCAAGC
*
1143310 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143350 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143390 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143430 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143470 GAGATAAAATCTTCTGTTTCCAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143510 GAGATAAAATTTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
*
1143550 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTTAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1143590 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1143630 GAGATAAAATCTTCT
1 GAGATAAAATCTTCT
1143645 TTAAGAGACG
Statistics
Matches: 288, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 288 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
Found at i:1143583 original size:23 final size:23
Alignment explanation
Indices: 1143557--1143625 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
1143547 AATGAGATAA
1143557 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
* *
1143580 AA---TC--TTT-AATGAGATAA-
1 AATCTTCTGTTTCAAGGA-AAAAC
1143597 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
1143620 AATCTT
1 AATCTT
1143626 GAATGAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
20 4 0.12
22 6 0.18
23 12 0.35
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:1143852 original size:21 final size:21
Alignment explanation
Indices: 1143827--1143877 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1143817 AAAAAACTCA
*
1143827 TTTGAAACTCATCAAGAAACT
1 TTTGAAAATCATCAAGAAACT
1143848 TTTGAAAATCATCAAGAAACT
1 TTTGAAAATCATCAAGAAACT
*
1143869 TCTGAAAAT
1 TTTGAAAAT
1143878 AAGACTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (21 bp):
TTTGAAAATCATCAAGAAACT
Found at i:1145347 original size:35 final size:35
Alignment explanation
Indices: 1145294--1145389 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
1145284 CTTGCTAAGA
*
1145294 TGAGCCTCCAAGAATGCCCAAATATTCATATTGTTG
1 TGAGCCTTCAA-AATGCCCAAATATTCATATTGTTG
1145330 TGAGCCTTCAAAATGCCCAAATATTCATATTGTTG
1 TGAGCCTTCAAAATGCCCAAATATTCATATTGTTG
* *
1145365 TGAGCCTTCAAAATACCCCAATATT
1 TGAGCCTTCAAAATGCCCAAATATT
1145390 AAATTTTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 47 0.82
36 10 0.18
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (35 bp):
TGAGCCTTCAAAATGCCCAAATATTCATATTGTTG
Found at i:1152879 original size:10 final size:10
Alignment explanation
Indices: 1152864--1152899 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1152854 ATTCGCTAAT
1152864 TTTGGATTAA
1 TTTGGATTAA
1152874 TTTGGATTAA
1 TTTGGATTAA
1152884 TTTGGATTAA
1 TTTGGATTAA
*
1152894 CTTGGA
1 TTTGGA
1152900 AAGAGTCGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (10 bp):
TTTGGATTAA
Found at i:1155634 original size:3 final size:3
Alignment explanation
Indices: 1155628--1155683 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
1155618 ATATTATTAT
* * * * *
1155628 TAA TAA TAC TAA TAA TAC TAT TAC TAA TAA TAA TAA TAA T-T TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1155674 TAA TAA TAA T
1 TAA TAA TAA T
1155684 TGTAGACACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 3 0.07
3 40 0.93
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1155770 original size:38 final size:36
Alignment explanation
Indices: 1155718--1156034 Score: 240
Period size: 38 Copynumber: 8.7 Consensus size: 36
1155708 TTATATATCT
* * * *
1155718 ATATATATATTATATGGTTTTAAAAAACTTTTTTAAA
1 ATATATATAATATATAGTTTT-AAAAACATTTTGAAA
*
1155755 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATAATATATAGTTTTAAAAACAT-TTTGAAA
* * *
1155793 ATATTTATACATTATATAATTTTTAAAACATTTTGAAA
1 ATATATATA-A-TATATAGTTTTAAAAACATTTTGAAA
* *
1155831 ATAAATATAATATATAGTTTTTAAAAACATTTTTGAAT
1 ATATATATAATATATAG-TTTTAAAAACA-TTTTGAAA
* * *
1155869 ATATATATATTATATAGTTTT-TAACCATTTTGAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * *
1155904 ATATGTATAGT-T-T--TTTAAAAAAACCATTTTGAAAAA
1 ATATATATAATATATAGTTT-TAAAAA-CATTTTG--AAA
* *
1155940 CATATATATATTATATAGTTTTAAAAATATTTTG-AA
1 -ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * *
1155976 A-A-A-A-ACTATATAGCTTTAAAAACATTTTTAAGAA
1 ATATATATAATATATAGTTTTAAAAACA-TTTTGA-AA
*
1156010 ATATATATAATATATAATTTTAAAA
1 ATATATATAATATATAGTTTTAAAA
1156035 TGTTTTTTTA
Statistics
Matches: 223, Mismatches: 34, Indels: 44
0.74 0.11 0.15
Matches are distributed among these distances:
31 20 0.09
32 5 0.02
33 4 0.02
34 12 0.05
35 18 0.08
36 16 0.07
37 39 0.17
38 77 0.35
39 24 0.11
40 5 0.02
41 3 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAAACATTTTGAAA
Found at i:1155997 original size:72 final size:69
Alignment explanation
Indices: 1155839--1156034 Score: 179
Period size: 69 Copynumber: 2.8 Consensus size: 69
1155829 AAATAAATAT
* * * *
1155839 AATATATAGT-TTTTAAAAACATTTTTG--AATATATATATATTATATAGTTTT-TAACCATTTT
1 AATATATAGTCTTTAAAAAACA-TTTTGAAAAAATATATATATTATATAGTTTTAAAAACATTTT
1155900 GAAAA
65 GAAAA
* * * *
1155905 TATGTATAGTTTTTTAAAAAAACCATTTTGAAAAACATATATATATTATATAGTTTTAAAAATAT
1 AATATATAG-TCTTT-AAAAAA-CATTTTGAAAAA-ATATATATATTATATAGTTTTAAAAACAT
1155970 TTTGAAAAA
62 TTTG-AAAA
* * * *
1155979 AACTATATAG-CTTT-AAAAACATTTTTAAGAAATATATATAATATATAATTTTAAAA
1 AA-TATATAGTCTTTAAAAAACATTTTGAAAAAATATATATATTATATAGTTTTAAAA
1156035 TGTTTTTTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
66 7 0.07
67 1 0.01
68 3 0.03
69 33 0.31
70 12 0.11
71 7 0.07
72 21 0.20
73 11 0.10
74 5 0.05
75 6 0.06
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (69 bp):
AATATATAGTCTTTAAAAAACATTTTGAAAAAATATATATATTATATAGTTTTAAAAACATTTTG
AAAA
Found at i:1157513 original size:24 final size:26
Alignment explanation
Indices: 1157460--1157518 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1157450 TATTTAGTAC
**
1157460 CATTTTTTTTATATTTTTTATCTTTT
1 CATTTTTTTTATATTTTTTATCTTAA
1157486 CATTTTTTATT-TATTTTTT-TC-TAA
1 CATTTTTT-TTATATTTTTTATCTTAA
1157510 CATTTTTTT
1 CATTTTTTT
1157519 GCCTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 2 0.07
26 16 0.53
27 2 0.07
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
CATTTTTTTTATATTTTTTATCTTAA
Found at i:1158568 original size:17 final size:17
Alignment explanation
Indices: 1158546--1158578 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1158536 CTCACTAACC
*
1158546 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
1158563 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
1158579 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:1158969 original size:43 final size:43
Alignment explanation
Indices: 1158908--1158991 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
1158898 AAACAAGCTC
1158908 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
1 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
*
1158951 GGTAGAAAGTGAAAGTCGGAGATGCAGTCCTTCGAGATCTT
1 GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTT
1158992 CTTTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (43 bp):
GGTAGAAAGTGAAAGTCGGAGATGCAGTCATTCGAGATCTTTT
Found at i:1159287 original size:19 final size:19
Alignment explanation
Indices: 1159249--1159293 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1159239 ATTTAGACAT
1159249 TTTGCA-TTTCTTATTCTC
1 TTTGCATTTTCTTATTCTC
* *
1159267 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTCTC
1159286 TTTGCATT
1 TTTGCATT
1159294 CACATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.11, C:0.16, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTGCATTTTCTTATTCTC
Found at i:1162884 original size:84 final size:81
Alignment explanation
Indices: 1162694--1163572 Score: 946
Period size: 84 Copynumber: 10.7 Consensus size: 81
1162684 ACCTGCCACC
* *
1162694 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
1162759 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * * * * * * * * *
1162774 AAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCT
1 AAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCG
*
1162838 AGAAGGGTTATCTGTTAGCA
64 AGAAGGGTTATCTG--ACCA
* * * *
1162858 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
1162923 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * * * * * * * * *
1162938 AAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAACTTAAGTCGA
*
1163003 GAAGGGTTATCTGTCAACA
65 GAAGGGTTATCTG--ACCA
* *
1163022 CAAGACCGTCGAGTTCGACTACGCTCAG-TTCAACGGCACATCATTTGCAGCATAACTTAAGTCG
1 -AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCG
1163086 AGAAGGGTTATCTGCCAACCA
64 AGAAGGGTTATCTG---ACCA
* * * * *
1163107 AAGGCCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* *
1163172 AAGGGTTGTCTGCCAACAA
66 AAGGGTTATCTG---ACCA
* *
1163191 AAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGA
*
1163255 GAAGGGCTATCTG-CCA
65 GAAGGGTTATCTGACCA
** * * * * *
1163271 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
1163336 GAAGGGTTATCTGTCAACCA
65 GAAGGGTTATCTG---ACCA
* * *
1163356 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATA-CTATTTGCAGCACAACTTAAGTCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC-ATTTGCAGCATAACTTAAGTCGA
* *
1163420 GAAGGGTTGTCTGCCAACAA
65 GAAGGGTTATCTG---ACCA
* *
1163440 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
1163505 AAGGGCTATCTG-CCA
66 AAGGGTTATCTGACCA
* * *
1163520 AAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAGCATA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
1163573 GCTCAAGGCA
Statistics
Matches: 668, Mismatches: 108, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
80 133 0.20
81 114 0.17
82 1 0.00
83 42 0.06
84 317 0.47
85 61 0.09
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGTTATCTGACCA
Found at i:1163134 original size:249 final size:247
Alignment explanation
Indices: 1162675--1163597 Score: 1151
Period size: 249 Copynumber: 3.7 Consensus size: 247
1162665 GCTCAAGGCC
* *
1162675 AGAAGGGCTACCTGCCAC-CAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* ** *
1162739 GCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTT
66 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTT
* * * * * ** * *
1162804 CAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGA
131 CAAGGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTGCAACCAAAGACCTTCGA
* * * * * *
1162869 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCG
196 GTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
* * * * * *
1162921 AGAAGGGCTATCTG-C-C-AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATT
1 AGAAGGGCTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATT
* * * * * * * *
1162983 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACACAAGACCGTCGAGTTCGACTACGCTC
65 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CA-AAGACCCTCGAGTTCGACTACACTC
* * * *
1163048 AG-TTCAACGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGC
126 AGCTTCAAGGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG-CAACCAAAGAC
*
1163112 CTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
190 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
* * *
1163170 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCAT
1 AGAAGGGCTATCTGCC-ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* *
1163234 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
64 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGC
* *
1163299 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGTCAACCAAAGACCTT
129 TTCAAGGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTG-CAACCAAAGACCTT
1163364 CGAGTTCGACTACGCTCAGCTCCAAGGCATA-CTATTTGCAGCACAACTTAAGTCT
193 CGAGTTCGACTACGCTCAGCTCCAAGGCATATC-ATTTGCAGCACAACTTAAGTCT
* * *
1163419 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTGCC-ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
1163484 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGCTCAACT
65 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCT
* * * * *
1163549 CCAA-GGCACATCATTTACAGCATAGCTCAAGGCAAAGAAGGGCTATCTG
130 TCAAGGGCACATCATTTACAGCATAACTTAAGTC-AAGAAGGGTTATCTG
1163598 TCAATAAAAT
Statistics
Matches: 586, Mismatches: 76, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
244 31 0.05
245 35 0.06
246 14 0.02
248 94 0.16
249 341 0.58
250 4 0.01
251 1 0.00
252 38 0.06
253 28 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (247 bp):
AGAAGGGCTATCTGCCACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTT
CAAGGGCACATCATTTACAGCATAACTTAAGTCAAGAAGGGTTATCTGCAACCAAAGACCTTCGA
GTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCT
Found at i:1163300 original size:333 final size:327
Alignment explanation
Indices: 1162666--1163597 Score: 1223
Period size: 333 Copynumber: 2.8 Consensus size: 327
1162656 TGCAGCTTAG
* * * *
1162666 CTCAAGGCCAGAAGGGCTACCTG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
* * * * *
1162730 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTTAAGTTCGAT
66 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGA-CCTTGAGTTCGAC
* * * * * * *
1162792 TACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGC
130 TACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-CA-C
* *
1162857 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCGA
192 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
* ** *
1162922 GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAGAGCATAACATTTACA
257 GAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCTTCGAGAGCACAACATTTACA
1162987 GCATAA
322 GCATAA
* * *
1162993 CTCAAGGCTAGAAGGGTTATCTGTCAACACAAGACCGTCGAGTTCGACTACGCTCAG-TTCAACG
1 CTCAAGGCAAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-G
*
1163057 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTC
64 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAAGACCTT-GAGTTC
* * *
1163122 GACTATGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCA
127 GACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTG-C-
1163187 ACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGGCACATCATTTGCAGCATAGCTTAAG
190 AC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAG
* * *
1163251 TCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
253 TCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCTTCGAGAGCACAACATT
*
1163316 TGCAGCATAA
318 TACAGCATAA
* *
1163326 CTTAAGTCAAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCAAGAAGGGTTATCTGTCAACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* * * *
1163391 CATA-CTATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTC
65 CACATC-ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAAGACC-TTGAGTTC
* * * *
1163455 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC-C
127 GACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCAC
* * * * *
1163519 AAAGACCTTTGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAA
192 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC-G
1163584 AGAAGGGCTATCTG
256 AGAAGGGCTATCTG
1163598 TCAATAAAAT
Statistics
Matches: 532, Mismatches: 55, Indels: 33
0.86 0.09 0.05
Matches are distributed among these distances:
327 20 0.04
328 7 0.01
329 123 0.23
330 19 0.04
332 50 0.09
333 307 0.58
334 6 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (327 bp):
CTCAAGGCAAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAGACCTTGAGTTCGACT
ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCACAAAG
ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
GGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCTTCGAGAGCACAACATTTACAGCAT
AA
Found at i:1164204 original size:38 final size:36
Alignment explanation
Indices: 1164152--1164461 Score: 218
Period size: 38 Copynumber: 8.7 Consensus size: 36
1164142 ATATATCTAT
* * * *
1164152 ATATATATATTATATGGTTTTAAAAAACTTTTTTAAA
1 ATATATATAATATATAGTTTT-AAAAACATTTTGAAA
*
1164189 CATATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 -ATATATATAATATATAGTTTTAAAAACAT-TTTGAAA
* * *
1164227 ATATTTATACATTATATAATTTTTAAAACATTTTGAAA
1 ATATATATA-A-TATATAGTTTTAAAAACATTTTGAAA
*
1164265 ATAAATATAATATATAGTTTTTAAAAACATTTTTG--A
1 ATATATATAATATATAG-TTTTAAAAACA-TTTTGAAA
* *
1164301 ATATATAT-AT-TATAGTTTT-TAACCATTTTGAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * * *
1164334 ATATGTAT-A-GT-T--TTTAAAAAAAATTTTGAAAAA
1 ATATATATAATATATAGTTTTAAAAACATTTTG--AAA
* *
1164367 CATATATATATTATATAGTTTTAAAAATATTTTG-AA
1 -ATATATATAATATATAGTTTTAAAAACATTTTGAAA
* * *
1164403 A-A-A-A-ACTATATAGCTTTAAAAACATTTTTAAGAA
1 ATATATATAATATATAGTTTTAAAAACA-TTTTGA-AA
*
1164437 ATATATATAATATATAATTTTAAAA
1 ATATATATAATATATAGTTTTAAAA
1164462 TGTTTTTTTA
Statistics
Matches: 216, Mismatches: 32, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
30 3 0.01
31 30 0.14
32 10 0.05
33 18 0.08
34 16 0.07
35 4 0.02
36 18 0.08
37 27 0.12
38 59 0.27
39 31 0.14
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAAACATTTTGAAA
Found at i:1164330 original size:31 final size:31
Alignment explanation
Indices: 1164268--1164351 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 31
1164258 TTTGAAAATA
1164268 AATATA-ATATATAGTTTTTAAAAACATTTTTG
1 AATATATATATATAGTTTTT--AAACATTTTTG
*
1164300 AATATATATATTATAGTTTTTAACCA-TTTTG
1 AATATATATA-TATAGTTTTTAAACATTTTTG
*
1164331 AA-A-ATATGTATAGTTTTTAAA
1 AATATATATATATAGTTTTTAAA
1164352 AAAAATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 12 0.26
29 4 0.09
30 1 0.02
31 7 0.15
32 10 0.21
33 3 0.06
34 10 0.21
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (31 bp):
AATATATATATATAGTTTTTAAACATTTTTG
Found at i:1164360 original size:31 final size:32
Alignment explanation
Indices: 1164277--1164365 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 32
1164267 AAATATAATA
* *
1164277 TATAGTTTTTAAAAACATTTTTGAATATATATAT
1 TATAGTTTTTAAAAACAATTTTGAA-A-ATATAG
*
1164311 TATAGTTTTT---AACCATTTTGAAAATAT-G
1 TATAGTTTTTAAAAACAATTTTGAAAATATAG
*
1164339 TATAGTTTTTAAAAAAAATTTTGAAAA
1 TATAGTTTTTAAAAACAATTTTGAAAA
1164366 ACATATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.21
29 4 0.09
30 1 0.02
31 22 0.47
34 10 0.21
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (32 bp):
TATAGTTTTTAAAAACAATTTTGAAAATATAG
Found at i:1165639 original size:2 final size:2
Alignment explanation
Indices: 1165632--1165686 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1165622 GGTCCTTATT
1165632 TA TA TA TA TA TA 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 TA TA TA TA TA TA
1165674 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1165687 TTTGCAATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1165972 original size:24 final size:26
Alignment explanation
Indices: 1165919--1165977 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1165909 TATTTAGTAC
**
1165919 CATTTTTTTTATATTTTTTATCTTTT
1 CATTTTTTTTATATTTTTTATCTTAA
1165945 CATTTTTTATT-TATTTTTT-TC-TAA
1 CATTTTTT-TTATATTTTTTATCTTAA
1165969 CATTTTTTT
1 CATTTTTTT
1165978 GCCTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 1 0.03
24 9 0.30
25 2 0.07
26 16 0.53
27 2 0.07
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
CATTTTTTTTATATTTTTTATCTTAA
Found at i:1167235 original size:36 final size:33
Alignment explanation
Indices: 1167171--1167245 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
1167161 AGTGGTAAGA
* * *
1167171 ATTA-TTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTATTTTTTATATTAATATTTTTGTAAATA-TT
1167204 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATTATTTTTTATATTAATAT-TTT-TGTAAATATT
1167239 ATT-TTTT
1 ATTATTTT
1167246 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 4 0.11
34 17 0.47
35 8 0.22
36 7 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
ATTATTTTTTATATTAATATTTTTGTAAATATT
Found at i:1167244 original size:32 final size:33
Alignment explanation
Indices: 1167203--1167278 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 33
1167193 TTTAAATAGT
* *
1167203 TATTATTTTTTATATTAATATAT-TTATGTAAA
1 TATTATTTTTTATATTAAAATATATTATATAAA
*
1167235 TATTA-TTTTT-TATTAAAATATATTATATAAT
1 TATTATTTTTTATATTAAAATATATTATATAAA
1167266 TATTATTTATTTA
1 TATTATTT-TTTA
1167279 GAATTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 10 0.27
31 17 0.46
32 7 0.19
33 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTATTTTTTATATTAAAATATATTATATAAA
Found at i:1169015 original size:21 final size:21
Alignment explanation
Indices: 1168985--1169032 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1168975 GCAGGGGTAC
* *
1168985 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1169006 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1169027 ATGCCA
1 ATGCCA
1169033 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1169062 original size:21 final size:21
Alignment explanation
Indices: 1169036--1169129 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1169026 TATGCCATCT
* *
1169036 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
1169057 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1169078 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1169099 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1169120 CCGCAGGGTT
1 CCGCAGGGTT
1169130 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1169697 original size:33 final size:33
Alignment explanation
Indices: 1169648--1169740 Score: 120
Period size: 31 Copynumber: 2.9 Consensus size: 33
1169638 AAATGTTTTT
1169648 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATA-AAATTATATTATTCGAAATTTAAAATA
* * *
1169682 AAAATAAAATAATATTATTC--AATTTAAATTT
1 AAAATAAAATTATATTATTCGAAATTTAAAATA
*
1169713 AAAAT-AAATTATAGTATTCGAAATTTAA
1 AAAATAAAATTATATTATTCGAAATTTAA
1169741 CATTAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
30 12 0.23
31 14 0.27
32 7 0.13
33 13 0.25
34 6 0.12
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (33 bp):
AAAATAAAATTATATTATTCGAAATTTAAAATA
Found at i:1170578 original size:246 final size:247
Alignment explanation
Indices: 1170128--1170721 Score: 1043
Period size: 246 Copynumber: 2.4 Consensus size: 247
1170118 TTTAAGTTAT
*
1170128 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1170193 GTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCCCG
66 G-CCCCCGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCCCG
1170258 AGGGACATGAATGACATAATAGGGCAATGATAATTCTCTGACGAAATAATGGAAGGCGCCCCCCG
130 AGGGACATGAATGACATAATAGGGCAATGATAATTCTCTGACGAAATAATGGAAGGCGCCCCCCG
* *
1170323 GGAAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
195 GGAAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1170376 TCCCCGAGGGACATGAATGACATAATA-GGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
1170440 GCCCCCGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTGTCCCCGA
66 GCCCCCGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCCCGA
1170505 GGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCG-CCCCC
131 GGGACATGAATGACATAATAGGGCAATGAT-A-ATTCTCTGACGAAATAATGGAAGGCGCCCCCC
*
1170569 GGG-AACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
194 GGGAAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1170622 TCCCCGA-GGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAA-G-
1170686 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
64 GCGCCCCC-GGAACGCGCCTTCACGTGAATAGTGAA
1170722 CCGATTATAG
Statistics
Matches: 333, Mismatches: 7, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
245 19 0.06
246 179 0.54
247 48 0.14
248 60 0.18
249 27 0.08
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (247 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCCCCCGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGACCCCGA
GGGACATGAATGACATAATAGGGCAATGATAATTCTCTGACGAAATAATGGAAGGCGCCCCCCGG
GAAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1170633 original size:123 final size:124
Alignment explanation
Indices: 1170128--1170721 Score: 1054
Period size: 124 Copynumber: 4.8 Consensus size: 124
1170118 TTTAAGTTAT
*
1170128 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1170193 GTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1170252 ACCCCGAGGGACATGAATGACATAATAGGGCAATGAT-A-ATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
1170315 GCCCCCCGGGAAACGCGCCTTCACGTGAATAGTGAAATAGTATGTACTGATATATCTAGTG
66 G-CCCCCGGG-AACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1170376 TCCCCGAGGGACATGAATGACATAATA-GGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1170440 GCCCCC-GGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1170498 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1170563 GCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
66 GCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1170622 TCCCCGA-GGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAA-G-
1170686 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
64 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
1170722 CCGATTATAG
Statistics
Matches: 453, Mismatches: 9, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
122 102 0.23
123 116 0.26
124 173 0.38
125 62 0.14
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (124 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1170808 original size:15 final size:15
Alignment explanation
Indices: 1170790--1170828 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1170780 CACAATCTTT
1170790 CAAATTCTCAATTCC
1 CAAATTCTCAATTCC
* * *
1170805 CAAACTCTAAATTCT
1 CAAATTCTCAATTCC
1170820 CAAATTCTC
1 CAAATTCTC
1170829 TGAAAATGAG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (15 bp):
CAAATTCTCAATTCC
Found at i:1173886 original size:21 final size:23
Alignment explanation
Indices: 1173835--1173889 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 23
1173825 TAGTTATAAT
1173835 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
1173856 TTTTACATAATATAATCG-AA-A
1 TTTTACATAATATAATCGAAACA
1173877 TTTTACATAATAT
1 TTTTACATAATAT
1173890 TTATTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 22 0.69
22 2 0.06
23 8 0.25
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Done.