Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_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: 2159989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1057365 original size:18 final size:18
Alignment explanation
Indices: 1057321--1057368 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1057311 ACAAGTTGGA
*
1057321 AAATATATAAATATTTTAT
1 AAATATAT-AATATTATAT
*
1057340 -AATTTATAATATTATAT
1 AAATATATAATATTATAT
1057357 AAATATATAATA
1 AAATATATAATA
1057369 AGGATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATATAATATTATAT
Found at i:1057504 original size:18 final size:19
Alignment explanation
Indices: 1057481--1057520 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1057471 TTCTCAGTAA
*
1057481 TTTTATT-CTCTGATAATC
1 TTTTATTCCACTGATAATC
1057499 TTTTATTCCCACTGATAATC
1 TTTTATT-CCACTGATAATC
1057519 TT
1 TT
1057521 ACATTCCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTTATTCCACTGATAATC
Found at i:1057526 original size:20 final size:20
Alignment explanation
Indices: 1057490--1057527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1057480 ATTTTATTCT
**
1057490 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
1057510 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
1057528 GTAAATCAAA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:1068577 original size:50 final size:50
Alignment explanation
Indices: 1068518--1068618 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1068508 AGGACTCGAG
1068518 GTGATTCGTGTGCGTTGGGAGAAGGATGCCAGTGGGAAGTTCCAATTCAA
1 GTGATTCGTGTGCGTTGGGAGAAGGATGCCAGTGGGAAGTTCCAATTCAA
1068568 GTGATTCGTGTGCGTTGGGAGAAGGATGCCAGTGGGAAGTTCCAATTCAA
1 GTGATTCGTGTGCGTTGGGAGAAGGATGCCAGTGGGAAGTTCCAATTCAA
1068618 G
1 G
1068619 GAAGTTGAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.26
Consensus pattern (50 bp):
GTGATTCGTGTGCGTTGGGAGAAGGATGCCAGTGGGAAGTTCCAATTCAA
Found at i:1069270 original size:45 final size:45
Alignment explanation
Indices: 1069220--1069311 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1069210 ATGACATAAT
1069220 GGGCACAGTGAGAATTGAAGCATGAAATCCTTTGCAACCACCAGG
1 GGGCACAGTGAGAATTGAAGCATGAAATCCTTTGCAACCACCAGG
1069265 GGGCACAGTGAGAATTGAAGCATGAAATCCTTTGCAACCACCAGG
1 GGGCACAGTGAGAATTGAAGCATGAAATCCTTTGCAACCACCAGG
1069310 GG
1 GG
1069312 ATGCTTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (45 bp):
GGGCACAGTGAGAATTGAAGCATGAAATCCTTTGCAACCACCAGG
Found at i:1072438 original size:29 final size:28
Alignment explanation
Indices: 1072400--1072530 Score: 109
Period size: 29 Copynumber: 4.5 Consensus size: 28
1072390 TTTTTTAAAA
*
1072400 TAATTACCAAAATAACACCTTTTCGAAT
1 TAATTCCCAAAATAACACCTTTTCGAAT
* * *
1072428 TAAATTCCCAAAATAGCACTTTTTTGAAT
1 T-AATTCCCAAAATAACACCTTTTCGAAT
* * * *
1072457 TAAATTCCCGAAATAGCACATTTTTTGAAT
1 T-AATTCCCAAAATAACAC-CTTTTCGAAT
* * *
1072487 TAATTCCCAAAAAAGAGCATCCATTTCAAAT
1 TAATTCCCAAAATA-A-CA-CCTTTTCGAAT
1072518 TAATTCCCAAAAT
1 TAATTCCCAAAAT
1072531 GTCACCCGAT
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.01
29 52 0.61
30 11 0.13
31 20 0.24
32 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (28 bp):
TAATTCCCAAAATAACACCTTTTCGAAT
Found at i:1072483 original size:30 final size:29
Alignment explanation
Indices: 1072401--1072498 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
1072391 TTTTTAAAAT
* * * *
1072401 AATTACCAAAATAACACCTTTTCGAATTA
1 AATTCCCAAAATAGCACTTTTTTGAATTA
1072430 AATTCCCAAAATAGCACTTTTTTGAATTA
1 AATTCCCAAAATAGCACTTTTTTGAATTA
*
1072459 AATTCCCGAAATAGCACATTTTTTGAATT-
1 AATTCCCAAAATAGCAC-TTTTTTGAATTA
1072488 AATTCCCAAAA
1 AATTCCCAAAA
1072499 AAGAGCATCC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
29 51 0.82
30 11 0.18
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATAGCACTTTTTTGAATTA
Found at i:1072587 original size:23 final size:23
Alignment explanation
Indices: 1072540--1072589 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1072530 TGTCACCCGA
***
1072540 TCAACGGGTCGGGTCAGGTCAGG
1 TCAACGGGTCGGGTCAAAACAGG
*
1072563 TCAACGGGTCGGGTCAAAACCGG
1 TCAACGGGTCGGGTCAAAACAGG
1072586 TCAA
1 TCAA
1072590 ACCGGTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (23 bp):
TCAACGGGTCGGGTCAAAACAGG
Found at i:1078736 original size:43 final size:41
Alignment explanation
Indices: 1078673--1078878 Score: 202
Period size: 42 Copynumber: 4.8 Consensus size: 41
1078663 CTATACACCA
*
1078673 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACAAAGCAAAGGGA-CCT-GGAAAACT
* * * *
1078717 GTAAGGTTTATCCTTGCACACAGTAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACAAAGCAAAGGGACCTGGAAAACT
*
1078759 GTAAGGCTTACGCTTGCACACAA-CAAAGGGACCTGGTAAACT
1 GTAAGGCTTAC-CTTGCACA-AAGCAAAGGGACCTGGAAAACT
* *
1078801 GTAAGGCTTACCTTCGCACACAA-CAAAGGGACATGGGAAACT
1 GTAAGGCTTACCTT-GCACA-AAGCAAAGGGACCTGGAAAACT
* *
1078843 GTAAGGCTTACCTTCGCATACAGCAAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACAAAGC-AAAGGGACCTG
1078879 ACAATACTTC
Statistics
Matches: 141, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
41 5 0.04
42 97 0.69
43 25 0.18
44 14 0.10
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACAAAGCAAAGGGACCTGGAAAACT
Found at i:1078764 original size:42 final size:42
Alignment explanation
Indices: 1078712--1078878 Score: 230
Period size: 42 Copynumber: 4.0 Consensus size: 42
1078702 GAGCCTAGGA
* **
1078712 AAACTGTAAGGTTTATCCTT-GCACACAGTAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAACAAAGGGACCTGGG
*
1078754 AAACTGTAAGGCTTACGCTT-GCACACAACAAAGGGACCTGGT
1 AAACTGTAAGGCTTAC-CTTCGCACACAACAAAGGGACCTGGG
*
1078796 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACATGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
* *
1078838 AAACTGTAAGGCTTACCTTCGCATACAGCAAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTCGCACACAAC-AAAGGGACCTG
1078879 ACAATACTTC
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 4 0.04
42 99 0.88
43 10 0.09
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
Found at i:1079912 original size:30 final size:29
Alignment explanation
Indices: 1079811--1079994 Score: 194
Period size: 29 Copynumber: 6.3 Consensus size: 29
1079801 CATTTTACAG
* * *
1079811 AAATAGCATCTTTTTAGAA-TAATTACCA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
*
1079839 AAATAGCACC-TTTTAGAATTAAATTCCCA
1 AAATAGCACCTTTTTCGAATT-AATTCCCA
* * *
1079868 AAATAG-AACTTTTTCGAATTAAATTTCTA
1 AAATAGCACCTTTTTCGAATT-AATTCCCA
1079897 AAATAGCACCTTTTTCGAATTAAATTCCCA
1 AAATAGCACCTTTTTCGAATT-AATTCCCA
*
1079927 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
* ** * *
1079956 AAATAACACCCATTTCAAATTAATTCCTA
1 AAATAGCACCTTTTTCGAATTAATTCCCA
*
1079985 AAATATCACC
1 AAATAGCACC
1079995 CGGTCAACGG
Statistics
Matches: 137, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
27 8 0.06
28 12 0.09
29 77 0.56
30 40 0.29
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATAGCACCTTTTTCGAATTAATTCCCA
Found at i:1079927 original size:59 final size:58
Alignment explanation
Indices: 1079811--1079989 Score: 193
Period size: 59 Copynumber: 3.1 Consensus size: 58
1079801 CATTTTACAG
* * * * *
1079811 AAATAGCATCTTTTTAGAA-TAATTACCAAAATAGCACCTTTTAGAATTAAATTCCCA
1 AAATAGCAACCTTTTCGAATTAATTCCCAAAATAGCACCTTTTCGAATTAAATTCCCA
* * *
1079868 AAATAG-AACTTTTTCGAATTAAATTTCTAAAATAGCACCTTTTTCGAATTAAATTCCCA
1 AAATAGCAACCTTTTCGAATT-AATTCCCAAAATAGCACC-TTTTCGAATTAAATTCCCA
* * * * *
1079927 AAATAGCACCCTTTTCGAATTAATTCCCAAAATAACACCCATTTCAAATT-AATTCCTA
1 AAATAGCAACCTTTTCGAATTAATTCCCAAAATAGCA-CCTTTTCGAATTAAATTCCCA
1079985 AAATA
1 AAATA
1079990 TCACCCGGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
56 10 0.10
57 7 0.07
58 28 0.27
59 45 0.43
60 14 0.13
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (58 bp):
AAATAGCAACCTTTTCGAATTAATTCCCAAAATAGCACCTTTTCGAATTAAATTCCCA
Found at i:1079986 original size:88 final size:86
Alignment explanation
Indices: 1079811--1079994 Score: 221
Period size: 88 Copynumber: 2.1 Consensus size: 86
1079801 CATTTTACAG
*
1079811 AAATAGCATCTTTTTAGAATAATTACCAAAATAGCACCTTTTAGAATTAAATTCCCAAAATAGAA
1 AAATAGCACCTTTTTAGAATAATTACCAAAATAGCACCTTTTAGAATTAAATTCCCAAAATAGAA
** * *
1079876 CTTTTTCGAATTAAATTTCTA
66 CCATTTCAAATTAAATTCCTA
* * *
1079897 AAATAGCACCTTTTTCGAATTAAATTCCCAAAATAGCACCCTTTTCGAATT-AATTCCCAAAATA
1 AAATAGCACCTTTTTAGAA-T-AATTACCAAAATAGCA-CCTTTTAGAATTAAATTCCCAAAATA
1079961 -ACACCCATTTCAAATT-AATTCCTA
63 GA-A-CCATTTCAAATTAAATTCCTA
*
1079985 AAATATCACC
1 AAATAGCACC
1079995 CGGTCAACGG
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
86 17 0.20
87 2 0.02
88 45 0.54
89 20 0.24
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (86 bp):
AAATAGCACCTTTTTAGAATAATTACCAAAATAGCACCTTTTAGAATTAAATTCCCAAAATAGAA
CCATTTCAAATTAAATTCCTA
Found at i:1083744 original size:45 final size:45
Alignment explanation
Indices: 1083680--1083767 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
1083670 GACGATGATT
* *
1083680 ATCAGTATCAGGTTCAGCAGGACTGTTACACGCATCTGTTGCTTC
1 ATCAGTATCAGGTTCAGCAGGACTGCTACACACATCTGTTGCTTC
** * *
1083725 ATCAGTATTGGGTTCAGCAGGGCTGCTGCACACATCTGTTGCT
1 ATCAGTATCAGGTTCAGCAGGACTGCTACACACATCTGTTGCT
1083768 GGCTCAATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (45 bp):
ATCAGTATCAGGTTCAGCAGGACTGCTACACACATCTGTTGCTTC
Found at i:1091909 original size:16 final size:16
Alignment explanation
Indices: 1091888--1091918 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1091878 ATAAATAAAT
1091888 GAATATAAACGAACAC
1 GAATATAAACGAACAC
1091904 GAATATAAACGAACA
1 GAATATAAACGAACA
1091919 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (16 bp):
GAATATAAACGAACAC
Found at i:1092013 original size:16 final size:16
Alignment explanation
Indices: 1091988--1092052 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1091978 TAATAAATAA
*
1091988 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
1092004 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1092020 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1092036 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1092052 A
1 A
1092053 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1092017 original size:10 final size:10
Alignment explanation
Indices: 1091984--1092058 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1091974 CATTTAATAA
*
1091984 ATAAACGAAT
1 ATAAACGAAC
1091994 ATAAACGAAC
1 ATAAACGAAC
1092004 ----ACGAAC
1 ATAAACGAAC
1092010 ATAAACGAAC
1 ATAAACGAAC
** *
1092020 ACGAAC-ATAA
1 ATAAACGA-AC
1092030 ATGAACACGAAC
1 AT-AA-ACGAAC
1092042 ATAAACGAAC
1 ATAAACGAAC
1092052 ATAAACG
1 ATAAACG
1092059 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1093151 original size:24 final size:24
Alignment explanation
Indices: 1093124--1093178 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1093114 TATTGGGTTA
* *
1093124 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
1093148 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
1093172 AACATAA
1 AACATAA
1093179 CCTTACGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:1093161 original size:14 final size:14
Alignment explanation
Indices: 1093144--1093199 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1093134 AATGAACATA
1093144 AACGAACATAACCG
1 AACGAACATAACCG
1093158 AACGAACAT-A---
1 AACGAACATAACCG
*
1093168 AACGAACATAACCT
1 AACGAACATAACCG
* *
1093182 TACGAACAAAACCG
1 AACGAACATAACCG
1093196 AACG
1 AACG
1093200 TTCACAAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1093179 original size:24 final size:24
Alignment explanation
Indices: 1093137--1093198 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1093127 ATAAATGAAT
1093137 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
**
1093161 GAACATAAACGAACATAACCTTAC
1 GAACATAAACGAACATAACCGAAC
1093185 GAACA-AAACCGAAC
1 GAACATAAA-CGAAC
1093199 GTTCACAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1094095 original size:7 final size:7
Alignment explanation
Indices: 1094080--1094116 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1094070 GACCCGACCC
1094080 GACCGTT
1 GACCGTT
*
1094087 GATCGTT
1 GACCGTT
1094094 GACCG-T
1 GACCGTT
1094100 GACCGTT
1 GACCGTT
1094107 GACCGTT
1 GACCGTT
1094114 GAC
1 GAC
1094117 TTCCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:1096388 original size:873 final size:873
Alignment explanation
Indices: 1094697--1096427 Score: 3257
Period size: 873 Copynumber: 2.0 Consensus size: 873
1094687 TATGGTACAT
*
1094697 TGAAATCTATGGTTTATTATTGTTGGTACACCGATTTATTGTTGATGATTTATGGACTTTGATGA
1 TGAAATCTATGGTTTATTATTGTTGGTACACCGATTTATTGTTGATGATTTATGGACTTTAATGA
1094762 CTGGTATATGGATATTGATTTTGGGATGATTGAACTACAATTGTATAGCTCTGATCAAGCTAATA
66 CTGGTATATGGATATTGATTTTGGGATGATTGAACTACAATTGTATAGCTCTGATCAAGCTAATA
1094827 AACGGGCCTAATGTGACTCTTGAGGGCCCCAAGATGTTTCATTAGGTCGGCTTTCCTTTGCTGTG
131 AACGGGCCTAATGTGACTCTTGAGGGCCCCAAGATGTTTCATTAGGTCGGCTTTCCTTTGCTGTG
* *
1094892 TGCTTAGGGTAAGCTATATTGACTTATTGACTTGGGCTTAAGGATACAGGCTTCATAGCTTATCC
196 TGCTTAAGGTAAGCTATATGGACTTATTGACTTGGGCTTAAGGATACAGGCTTCATAGCTTATCC
* * *
1094957 TTAAGTCGACTTTCTTTTTGTTATGTGCATAAAGTAATATATATGGAAAATAATTTTGGGAACTA
261 TTAAGTCGACTTTCTTTTTGCTATGTGCATAAAGTAAGATATACGGAAAATAATTTTGGGAACTA
1095022 CTGATGGTGTACCAGAAAAAGGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTACGAATTTG
326 CTGATGGTGTACCAGAAAAAGGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTACGAATTTG
* *
1095087 TGAGATTTACTGGACAATGCTTTGTTTAATGTACCTATTGTGATTTTATGGTAATGTTGGGACAC
391 TGAGATTTACTGGACAATGATTTGTTTAATGTACCTATTGTGATTTTATGATAATGTTGGGACAC
*
1095152 ACTGAGCCTAGTTCACCTTTCGAAAATATTTTTCCCCTTTCAGATACTGTTGGTTAGATACCTCG
456 ACTGAGCCTAGCTCACCTTTCGAAAATATTTTTCCCCTTTCAGATACTGTTGGTTAGATACCTCG
*
1095217 GTTCGAGCACTTGGAGGATCAACATATCTCTTGAAGTATATCTGATTGTAATATTTTAAAATTGC
521 GTTCGAGCACTTGGAGGATCAACATATCTCTTGAAGTATATATGATTGTAATATTTTAAAATTGC
*
1095282 AAGTTGACTTTATTCTAGTGACATGGACCTATTTTAAAGTATTGGATTTTATAATGATGATACTT
586 AAGTTGACTTTATTCTAGTGACATGGACATATTTTAAAGTATTGGATTTTATAATGATGATACTT
1095347 TTGCTATTACTATTCAGTTTATCGTGGTTTTGATTTTTTTAAGATATGTTTTAAATTAATTTATT
651 TTGCTATTACTATTCAGTTTATCGTGGTTTTGATTTTTTTAAGATATGTTTTAAATTAATTTATT
*
1095412 ACTGATTGGTTTTATATTTAAGAGTTGAGTTTTAAATAGTATAATTTATTATAATTTCATGTCAT
716 ACTGATTGGTTTTATATTTAAGAGTTGAGTTTTAAATAGTATAATTTATTATAATTTCATGTCAC
1095477 GAATAATGTGGTTTTACATTGATTGGATAACAGTTTTGGAAAATGTCTTTGTGATCCACTAGACT
781 GAATAATGTGGTTTTACATTGATTGGATAACAGTTTTGGAAAATGTCTTTGTGATCCACTAGACT
1095542 TAGTCGAAACGCACATGCTCTGATACCA
846 TAGTCGAAACGCACATGCTCTGATACCA
1095570 TGAAATCTATGGTTTATTATTGTTGGTACACCGATTTATTGTTGATGATTTATGGACTTTAATGA
1 TGAAATCTATGGTTTATTATTGTTGGTACACCGATTTATTGTTGATGATTTATGGACTTTAATGA
1095635 CTGGTATATGGATATTGATTTTGGGATGATTGAACTACAATTGTATAGCTCTGATCAAGCTAATA
66 CTGGTATATGGATATTGATTTTGGGATGATTGAACTACAATTGTATAGCTCTGATCAAGCTAATA
*
1095700 AACGGGCCTAATGTGACTCTTGAGGGCCCCAAGATGTTTCATTAGGTCGGCTTTCCTTTGTTGTG
131 AACGGGCCTAATGTGACTCTTGAGGGCCCCAAGATGTTTCATTAGGTCGGCTTTCCTTTGCTGTG
1095765 TGCTTAAGGTAAGCTATATGGACTTATTGACTTGGGCTTAAGGATACAGGCTTCATAGCTTATCC
196 TGCTTAAGGTAAGCTATATGGACTTATTGACTTGGGCTTAAGGATACAGGCTTCATAGCTTATCC
* *
1095830 TTAAGTCGGCTTTCTTTTTGCTATGTGCATAAAGTAAGCTATACGGAAAATAATTTTGGGAACTA
261 TTAAGTCGACTTTCTTTTTGCTATGTGCATAAAGTAAGATATACGGAAAATAATTTTGGGAACTA
1095895 CTGATGGTGTACCA-AAAAAGGGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTACGAATTT
326 CTGATGGTGTACCAGAAAAA-GGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTACGAATTT
*
1095959 GTGAGATTTACTGGACTATGATTTGTTTAATGTACCTATTGTGATTTTATGATAATGTTGGGACA
390 GTGAGATTTACTGGACAATGATTTGTTTAATGTACCTATTGTGATTTTATGATAATGTTGGGACA
*
1096024 CACTGAGCCTAGCTCACCTTTCGAAAATGTTTTTCCCCTTTCAGATACTGTTGGTTAGATACCTC
455 CACTGAGCCTAGCTCACCTTTCGAAAATATTTTTCCCCTTTCAGATACTGTTGGTTAGATACCTC
1096089 GGTTCGAGCACTTGGAGGATCAACATATCTCTTGAAGTATATATGATTGTAATATTTTAAAATTG
520 GGTTCGAGCACTTGGAGGATCAACATATCTCTTGAAGTATATATGATTGTAATATTTTAAAATTG
* *
1096154 CAAGTTGACTTTATTCTGGTGACATTGACATATTTTAAAGTATTGGATTTTATAATGATGATACT
585 CAAGTTGACTTTATTCTAGTGACATGGACATATTTTAAAGTATTGGATTTTATAATGATGATACT
1096219 TTTGCTATTACTATTCAGTTTATCGTGGTTTTGATTTTTTTAAGATATGTTTTAAATTAATTTAT
650 TTTGCTATTACTATTCAGTTTATCGTGGTTTTGATTTTTTTAAGATATGTTTTAAATTAATTTAT
1096284 TACTGATTGGTTTTATATTTAAGAGTTGAGTTTTAAATAGTATAATTTATTATAATTTCATGTCA
715 TACTGATTGGTTTTATATTTAAGAGTTGAGTTTTAAATAGTATAATTTATTATAATTTCATGTCA
* *
1096349 CGAATAATGTGGTTTTACATTGATTGGATAACGGTTTTGGAAAATGTCTTTGTGATCTACTAGAC
780 CGAATAATGTGGTTTTACATTGATTGGATAACAGTTTTGGAAAATGTCTTTGTGATCCACTAGAC
1096414 TTAGTCGAAACGCA
845 TTAGTCGAAACGCA
1096428 TAGGCCGGGT
Statistics
Matches: 836, Mismatches: 21, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
872 5 0.01
873 831 0.99
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (873 bp):
TGAAATCTATGGTTTATTATTGTTGGTACACCGATTTATTGTTGATGATTTATGGACTTTAATGA
CTGGTATATGGATATTGATTTTGGGATGATTGAACTACAATTGTATAGCTCTGATCAAGCTAATA
AACGGGCCTAATGTGACTCTTGAGGGCCCCAAGATGTTTCATTAGGTCGGCTTTCCTTTGCTGTG
TGCTTAAGGTAAGCTATATGGACTTATTGACTTGGGCTTAAGGATACAGGCTTCATAGCTTATCC
TTAAGTCGACTTTCTTTTTGCTATGTGCATAAAGTAAGATATACGGAAAATAATTTTGGGAACTA
CTGATGGTGTACCAGAAAAAGGTTTAAACTATGATTTTCAAAAGTTAAACTCTTTTACGAATTTG
TGAGATTTACTGGACAATGATTTGTTTAATGTACCTATTGTGATTTTATGATAATGTTGGGACAC
ACTGAGCCTAGCTCACCTTTCGAAAATATTTTTCCCCTTTCAGATACTGTTGGTTAGATACCTCG
GTTCGAGCACTTGGAGGATCAACATATCTCTTGAAGTATATATGATTGTAATATTTTAAAATTGC
AAGTTGACTTTATTCTAGTGACATGGACATATTTTAAAGTATTGGATTTTATAATGATGATACTT
TTGCTATTACTATTCAGTTTATCGTGGTTTTGATTTTTTTAAGATATGTTTTAAATTAATTTATT
ACTGATTGGTTTTATATTTAAGAGTTGAGTTTTAAATAGTATAATTTATTATAATTTCATGTCAC
GAATAATGTGGTTTTACATTGATTGGATAACAGTTTTGGAAAATGTCTTTGTGATCCACTAGACT
TAGTCGAAACGCACATGCTCTGATACCA
Found at i:1102089 original size:19 final size:19
Alignment explanation
Indices: 1102065--1102122 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
1102055 GAGGGCTGGA
*
1102065 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
1102084 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1102103 AACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
1102122 A
1 A
1102123 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1102097 original size:9 final size:9
Alignment explanation
Indices: 1102066--1102124 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
1102056 AGGGCTGGAA
*
1102066 ACCGGTTTG
1 ACCGGTCTG
*
1102075 ATCGGTCTG
1 ACCGGTCTG
*
1102084 AACCGGTTTG
1 -ACCGGTCTG
1102094 ACCGGTCTG
1 ACCGGTCTG
* *
1102103 AACCAGTTTG
1 -ACCGGTCTG
1102113 ACCGGTCTG
1 ACCGGTCTG
1102122 ACC
1 ACC
1102125 CGACCCGACT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 25 0.64
10 14 0.36
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1102155 original size:7 final size:7
Alignment explanation
Indices: 1102143--1102183 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
1102133 CTGACCCGAT
1102143 CGTTGAC
1 CGTTGAC
1102150 CGTTGAC
1 CGTTGAC
*
1102157 TGTTGAC
1 CGTTGAC
1102164 CGTT-AC
1 CGTTGAC
1102170 CGTTGAC
1 CGTTGAC
1102177 CGTTGAC
1 CGTTGAC
1102184 TTCCTTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (7 bp):
CGTTGAC
Found at i:1102173 original size:20 final size:21
Alignment explanation
Indices: 1102143--1102183 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1102133 CTGACCCGAT
*
1102143 CGTTGACCGTTGACTGTTGAC
1 CGTTGACCGTTGACCGTTGAC
1102164 CGTT-ACCGTTGACCGTTGAC
1 CGTTGACCGTTGACCGTTGAC
1102184 TTCCTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.32
Consensus pattern (21 bp):
CGTTGACCGTTGACCGTTGAC
Found at i:1105376 original size:12 final size:12
Alignment explanation
Indices: 1105359--1105383 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1105349 TTCACTAAAA
1105359 AAATAATATTTT
1 AAATAATATTTT
1105371 AAATAATATTTT
1 AAATAATATTTT
1105383 A
1 A
1105384 TTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:1110173 original size:19 final size:19
Alignment explanation
Indices: 1110149--1110186 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1110139 TCCAGGACAT
1110149 TTTAACTAGTAAATAAGGG
1 TTTAACTAGTAAATAAGGG
1110168 TTTAACTAGTAAATAAGGG
1 TTTAACTAGTAAATAAGGG
1110187 GGGAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TTTAACTAGTAAATAAGGG
Found at i:1118865 original size:19 final size:19
Alignment explanation
Indices: 1118841--1118905 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 19
1118831 TAAAGAAAAC
* * *
1118841 AAATAAGATAAAGAGAATA
1 AAATAAAATAAAAAAAATA
1118860 AAATAAAATAAAAAAAATA
1 AAATAAAATAAAAAAAATA
* *
1118879 AAA-AAAATAAATAAGATA
1 AAATAAAATAAAAAAAATA
1118897 AAA-AAAATA
1 AAATAAAATA
1118906 GTAAAGTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 22 0.54
19 19 0.46
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.15
Consensus pattern (19 bp):
AAATAAAATAAAAAAAATA
Found at i:1118876 original size:9 final size:9
Alignment explanation
Indices: 1118856--1118905 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
1118846 AGATAAAGAG
1118856 AATAAAATAA
1 AATAAAA-AA
1118866 AATAAAAAA
1 AATAAAAAA
1118875 AATAAAAAA
1 AATAAAAAA
*
1118884 AATAAATAA
1 AATAAAAAA
*
1118893 GATAAAAAA
1 AATAAAAAA
1118902 AATA
1 AATA
1118906 GTAAAGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:1119237 original size:24 final size:23
Alignment explanation
Indices: 1119189--1119238 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1119179 CACAAGATTT
* **
1119189 TAAAAAAATAATATAATAATGAA
1 TAAAAAAATAAAATAATAAAAAA
1119212 TAAAAAAATGAAAATAATAAAAAA
1 TAAAAAAAT-AAAATAATAAAAAA
1119236 TAA
1 TAA
1119239 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
TAAAAAAATAAAATAATAAAAAA
Found at i:1119243 original size:2 final size:2
Alignment explanation
Indices: 1119238--1119268 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1119228 ATAAAAAATA
1119238 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 A
1119269 CATAAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1119367 original size:2 final size:2
Alignment explanation
Indices: 1119328--1119352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1119318 ATAATTAAGA
1119328 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 A
1119353 AATAATAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1119577 original size:17 final size:18
Alignment explanation
Indices: 1119544--1119579 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1119534 ATATATACGT
*
1119544 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1119562 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1119579 A
1 A
1119580 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1120005 original size:35 final size:35
Alignment explanation
Indices: 1119959--1120030 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1119949 TAAAAAAACC
*
1119959 CTATTTTAGACTAGTATTTGAATCCTAATCCAACT
1 CTATTTTAGACTAATATTTGAATCCTAATCCAACT
*
1119994 CTATTTTAGACTAATATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAATATTTGAATCCTAATCCAACT
1120029 CT
1 CT
1120031 TCTTTTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAATATTTGAATCCTAATCCAACT
Found at i:1120706 original size:106 final size:106
Alignment explanation
Indices: 1120516--1120738 Score: 261
Period size: 106 Copynumber: 2.1 Consensus size: 106
1120506 TATTGTTCCC
* * * * *
1120516 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTGTTTGTTGACAGC
1 AGTCCAATATCCTCCGACGTGAAGTTGAAATTGACCCTGAAACTGGAAAATTGTTTGTTGACAAC
* *
1120581 CAACCGCCCATTCGCTGTGAAGTTGAGCTTGTGATATCTTG
66 CAACCGCCCATTCGCTGTGAAGTTAAACTTGTGATATCTTG
* * * * *
1120622 AGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGACGTGAAGTTGAAATTGACCCTGAAACTGGAAAATTGTTTGTTGACAAC
* * * * *
1120687 CAGCCATCCC-TTCGTTGTGAAGTTAAACTTGTG-TCGTCTCG
66 CAACC-GCCCATTCGCTGTGAAGTTAAACTTGTGAT-ATCTTG
1120728 AGTCCAATATC
1 AGTCCAATATC
1120739 AATTATTTGT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
105 1 0.01
106 93 0.96
107 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (106 bp):
AGTCCAATATCCTCCGACGTGAAGTTGAAATTGACCCTGAAACTGGAAAATTGTTTGTTGACAAC
CAACCGCCCATTCGCTGTGAAGTTAAACTTGTGATATCTTG
Found at i:1120758 original size:69 final size:67
Alignment explanation
Indices: 1120670--1120805 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 67
1120660 GAAATTGGGA
* *
1120670 AATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGTTAAACTTGTGTCGTCTCGAGTCCAA
1 AATTATTTGTTGACAACCAGCCATCCCTTCATTGTGAAGTTAAACTTGTG--GTCTCGAGTCCAA
1120735 TATC
64 TATC
* *
1120739 AATTATTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGGTCTCGAGTCCAATA
1 AATTATTTGTTGACAACCAGCCATCCCTTCATTGTGAAGTTAAACTTGTGGTCTCGAGTCCAATA
1120804 TC
66 TC
1120806 CTTCGATGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 17 0.27
69 46 0.73
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (67 bp):
AATTATTTGTTGACAACCAGCCATCCCTTCATTGTGAAGTTAAACTTGTGGTCTCGAGTCCAATA
TC
Found at i:1120820 original size:173 final size:174
Alignment explanation
Indices: 1120564--1120911 Score: 529
Period size: 173 Copynumber: 2.0 Consensus size: 174
1120554 GGAACTGGAA
* * * * * *
1120564 AATTGTTTGTTGACAGCCAACCGCCCATTCGCTGTGAAGTTGAGCTTGTGATATCTTGAGTCTAA
1 AATTATTTGTTGACAACCAACCGCCCATTCACTGTGAAGTTGAACTTGTGA-ATCTCGAGTCCAA
* * *
1120629 TATCCTTCGATGTGAAGTTGAAATTGACCCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCAT
65 TATCCTTCGATGTGAAGTTGAAATTGACCATAAAATTGGGAAATTATTTGTTGACAACCAGCCAT
1120694 CCCTTCGTTGTGAAGTTAAACTTGTGTCGTCTCGAGTCCAATATC
130 CCCTTCGTTGTGAAGTTAAACTTGTGTCGTCTCGAGTCCAATATC
* * *
1120739 AATTATTTGTTGACAACCAGCCGTCCC-TTCATTGTGAAGTTGAACTTGTG-GTCTCGAGTCCAA
1 AATTATTTGTTGACAACCAACCG-CCCATTCACTGTGAAGTTGAACTTGTGAATCTCGAGTCCAA
* *
1120802 TATCCTTCGATGTGAAGTTGAAATTGACCATAAAATTGGGAAATTATTTGTTGACAACCAGTCGT
65 TATCCTTCGATGTGAAGTTGAAATTGACCATAAAATTGGGAAATTATTTGTTGACAACCAGCCAT
*
1120867 CCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAATATC
130 CCCTTCGTTGTGAAGTTAAACTTGTGTCGTCTCGAGTCCAATATC
1120912 CTTCACTATT
Statistics
Matches: 157, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 114 0.73
175 40 0.25
176 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (174 bp):
AATTATTTGTTGACAACCAACCGCCCATTCACTGTGAAGTTGAACTTGTGAATCTCGAGTCCAAT
ATCCTTCGATGTGAAGTTGAAATTGACCATAAAATTGGGAAATTATTTGTTGACAACCAGCCATC
CCTTCGTTGTGAAGTTAAACTTGTGTCGTCTCGAGTCCAATATC
Found at i:1121123 original size:106 final size:106
Alignment explanation
Indices: 1120739--1121320 Score: 782
Period size: 106 Copynumber: 5.6 Consensus size: 106
1120729 GTCCAATATC
* * *
1120739 AATTATTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTG--GTCTCGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
* *
1120802 TATCCTTCGATGTGAAGTTGAAATTGAC-CATAAAATTGGGA
66 TATCCTTCGCTGTGAAGTTGAAATTGACTC-TGAAATTGGGA
* * * *
1120843 AATTATTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
*
1120908 TATCCTTCAC--T--A-TTG-----G-CTCTGAAATTGGGA
66 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGA
* **
1120938 GATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
*
1121003 TATCCTTTGCTGTGAAGTTGAAATTGACTCTGAAATTGGGA
66 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGA
*
1121044 AATTGTTTGTTGACAACCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
* * * *
1121109 CATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGA
66 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGA
1121150 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
*
1121215 TATCCTTCGCTGTGAAGTTGAAATT-AGCTCTGAATGAAATT-GAA
66 TATCCTTCGCTGTGAAGTTGAAATTGA-CTC----TGAAATTGGGA
* * *
1121259 AAGTGGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 AA-TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGT
1121321 GGCGCGATAT
Statistics
Matches: 428, Mismatches: 30, Indels: 34
0.87 0.06 0.07
Matches are distributed among these distances:
95 79 0.18
96 2 0.00
97 1 0.00
99 1 0.00
100 3 0.01
101 3 0.01
102 1 0.00
104 49 0.11
105 1 0.00
106 221 0.52
109 4 0.01
110 63 0.15
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (106 bp):
AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCCCGAGTCCAA
TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGA
Found at i:1122232 original size:36 final size:36
Alignment explanation
Indices: 1122179--1122253 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
1122169 GAAACAATTT
*
1122179 CAAAGGTTTTTTTAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTTTTCAAGGGAAACTGTCTCAAGAGAGA
1122215 CAAA-GTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCAAGGGAAACTGTCTCAAGAGAGA
1122251 CAA
1 CAA
1122254 TAGTGAGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (36 bp):
CAAAGGTTTTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1122767 original size:18 final size:18
Alignment explanation
Indices: 1122740--1122775 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1122730 TGTTGAATCC
*
1122740 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1122758 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1122776 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1123854 original size:18 final size:18
Alignment explanation
Indices: 1123823--1123884 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
1123813 TCCTTTTTCC
*
1123823 TTTGTGCTTATTTTCTTT
1 TTTGTGCTTGTTTTCTTT
*
1123841 TTTGTTCTTGTTTT-TTT
1 TTTGTGCTTGTTTTCTTT
*
1123858 TTT-TGCTTCTTTTCTTT
1 TTTGTGCTTGTTTTCTTT
*
1123875 TTTGTTCTTG
1 TTTGTGCTTG
1123885 ATTGAATCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 8 0.22
17 12 0.33
18 16 0.44
ACGTcount: A:0.02, C:0.11, G:0.11, T:0.76
Consensus pattern (18 bp):
TTTGTGCTTGTTTTCTTT
Found at i:1123859 original size:16 final size:17
Alignment explanation
Indices: 1123834--1123884 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
1123824 TTGTGCTTAT
1123834 TTTCTTTTTTGTTCTTG
1 TTTCTTTTTTGTTCTTG
*
1123851 TTT-TTTTTT-TTGCTTCT
1 TTTCTTTTTTGTT-CTT-G
1123868 TTTCTTTTTTGTTCTTG
1 TTTCTTTTTTGTTCTTG
1123885 ATTGAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 6 0.21
18 9 0.32
19 2 0.07
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTGTTCTTG
Found at i:1127849 original size:31 final size:31
Alignment explanation
Indices: 1127811--1127966 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
1127801 AGGGTTGAGG
1127811 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1127842 GTTTACCTATGTTCTTCAGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1127873 GTTTATCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1127904 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1127935 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1127966 G
1 G
1127967 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1132283 original size:31 final size:31
Alignment explanation
Indices: 1132245--1132400 Score: 249
Period size: 31 Copynumber: 5.0 Consensus size: 31
1132235 AGGGTCGAGG
*
1132245 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1132276 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1132307 GTTTATCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1132338 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1132369 GTTTACCTAGGTTCTTCGGAATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1132400 G
1 G
1132401 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1135139 original size:4 final size:4
Alignment explanation
Indices: 1135120--1135167 Score: 60
Period size: 4 Copynumber: 11.2 Consensus size: 4
1135110 TAAAAGGGAA
*
1135120 AAAT AAAAT AAAAT AAAT AAAT AAAT AAAT AAGAT AAAG AAAT AAAT A
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT A
1135168 GTAAAGTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
4 27 0.68
5 13 0.32
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1135151 original size:21 final size:21
Alignment explanation
Indices: 1135103--1135167 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1135093 AGATAAAGAG
*
1135103 AATAAAATAAAAGGGAA-AAATAA
1 AATAAAAT-AAA-GAAATAAAT-A
*
1135126 AATAAAATAAATAAATAAATA
1 AATAAAATAAAGAAATAAATA
*
1135147 AATAAGATAAAGAAATAAATA
1 AATAAAATAAAGAAATAAATA
1135168 GTAAAGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 22 0.59
22 7 0.19
23 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AATAAAATAAAGAAATAAATA
Found at i:1135178 original size:15 final size:17
Alignment explanation
Indices: 1135125--1135179 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1135115 GGGAAAAATA
*
1135125 AAATAAAATAA-ATAAAT
1 AAAT-AAATAAGATAAAG
1135142 AAATAAATAAGATAAAG
1 AAATAAATAAGATAAAG
1135159 AAATAAAT-AG-TAAAG
1 AAATAAATAAGATAAAG
*
1135174 TAATAA
1 AAATAA
1135180 TTATATATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 10 0.29
16 8 0.23
17 17 0.49
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (17 bp):
AAATAAATAAGATAAAG
Found at i:1135215 original size:2 final size:2
Alignment explanation
Indices: 1135208--1135236 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1135198 GAAAAAGGAA
1135208 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 A
1135237 CATACATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1135298 original size:38 final size:40
Alignment explanation
Indices: 1135229--1135308 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
1135219 TATATATATA
*
1135229 TATATATACATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATACATACAACAAAGTATTAATAAAATAGAA-AAGC
* *
1135269 TATATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATACATACAACAAAGTATTAATAAAATAGAAAAGC
1135307 TA
1 TA
1135309 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (40 bp):
TATATATACATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:1135760 original size:52 final size:54
Alignment explanation
Indices: 1135665--1135780 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
1135655 GATAATTACA
** * *
1135665 ATATATAGTAATAATAGACTTATAAGTAAAATATTAAAGAAAT-ATAT-ATATAT
1 ATATATA-TAATAATAGAAATATAAGTAAAAAATCAAAGAAATAATATAATATAT
*
1135718 ATATATATAATAATA-AAATAT-AGTAAAAAATCAAATGAAAATAATTTAATATAT
1 ATATATATAATAATAGAAATATAAGTAAAAAATCAAA-G-AAATAATATAATATAT
1135772 ATATATATA
1 ATATATATA
1135781 TATGTATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
50 12 0.22
51 5 0.09
52 12 0.22
53 10 0.19
54 15 0.28
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (54 bp):
ATATATATAATAATAGAAATATAAGTAAAAAATCAAAGAAATAATATAATATAT
Found at i:1135819 original size:17 final size:18
Alignment explanation
Indices: 1135786--1135821 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1135776 ATATATATGT
*
1135786 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
1135804 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
1135821 A
1 A
1135822 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:1143325 original size:21 final size:21
Alignment explanation
Indices: 1143284--1143322 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1143274 AAATAGTTTT
*
1143284 TTTATATTTTTAATAATTTAA
1 TTTATATCTTTAATAATTTAA
1143305 TTTATATCTTTAA-AATTT
1 TTTATATCTTTAATAATTT
1143323 TAACATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATCTTTAATAATTTAA
Found at i:1144976 original size:2 final size:2
Alignment explanation
Indices: 1144969--1145003 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1144959 TCTGAATACT
1144969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1145004 TGGATTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1151491 original size:46 final size:46
Alignment explanation
Indices: 1151440--1151531 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
1151430 ATATGCTACC
1151440 TAATCAGAAATCAGGTTCACATGACAAAAGCTAGCATCTCCCCTAA
1 TAATCAGAAATCAGGTTCACATGACAAAAGCTAGCATCTCCCCTAA
* * *
1151486 TAATCAGAAATCATGTTCACGTGACAAAAGCTGGCATCTCCCCTAA
1 TAATCAGAAATCAGGTTCACATGACAAAAGCTAGCATCTCCCCTAA
1151532 AAGTAGCCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (46 bp):
TAATCAGAAATCAGGTTCACATGACAAAAGCTAGCATCTCCCCTAA
Found at i:1154420 original size:2 final size:2
Alignment explanation
Indices: 1154413--1154459 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1154403 TATTTACCTA
1154413 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1154455 AT AT A
1 AT AT A
1154460 ATTATGATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1156691 original size:23 final size:22
Alignment explanation
Indices: 1156642--1156692 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1156632 TTTTATGAAT
*
1156642 ATTATATTTTAATTAAATTACA
1 ATTATATTTTAACTAAATTACA
* *
1156664 TTTATATTTTTAACTAAATTATA
1 ATTATA-TTTTAACTAAATTACA
1156687 ATTATA
1 ATTATA
1156693 CATTTAGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTATATTTTAACTAAATTACA
Found at i:1156698 original size:23 final size:23
Alignment explanation
Indices: 1156649--1156698 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1156639 AATATTATAT
* * **
1156649 TTTAATTAAATTACATTTATATT
1 TTTAACTAAATTACAATTATACA
*
1156672 TTTAACTAAATTATAATTATACA
1 TTTAACTAAATTACAATTATACA
1156695 TTTA
1 TTTA
1156699 GTACTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAACTAAATTACAATTATACA
Found at i:1158976 original size:2 final size:2
Alignment explanation
Indices: 1158969--1159020 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1158959 AATCTAAACT
1158969 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
1159011 TA TA TA TA TA
1 TA TA TA TA TA
1159021 AATAGCAATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1166544 original size:18 final size:18
Alignment explanation
Indices: 1166518--1166561 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1166508 TCACGGAATG
1166518 TAAGATTACCGGCGAGAA
1 TAAGATTACCGGCGAGAA
* *
1166536 TAGGATTACCGGCGGGAA
1 TAAGATTACCGGCGAGAA
1166554 TAAGATTA
1 TAAGATTA
1166562 TTGGAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (18 bp):
TAAGATTACCGGCGAGAA
Found at i:1175106 original size:9 final size:10
Alignment explanation
Indices: 1175084--1175109 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1175074 GATTTGTATC
1175084 AAAATCCTTA
1 AAAATCCTTA
1175094 AAAATCCTTA
1 AAAATCCTTA
1175104 AAAATC
1 AAAATC
1175110 AAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATCCTTA
Found at i:1185237 original size:41 final size:41
Alignment explanation
Indices: 1185188--1185270 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
1185178 TTTTACAATA
1185188 AGCTTATCAATAGGCTACAAGATGACAGCATTGCAATACAG
1 AGCTTATCAATAGGCTACAAGATGACAGCATTGCAATACAG
1185229 AGCTTATCAATAGGCTACAAGATGACAGCATTGCAATACAG
1 AGCTTATCAATAGGCTACAAGATGACAGCATTGCAATACAG
1185270 A
1 A
1185271 CCTGACGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (41 bp):
AGCTTATCAATAGGCTACAAGATGACAGCATTGCAATACAG
Found at i:1188251 original size:21 final size:21
Alignment explanation
Indices: 1188225--1188267 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188215 TAATTTCATC
1188225 ATTTGGGTTAACTACACGTTT
1 ATTTGGGTTAACTACACGTTT
1188246 ATTTGGGTTAACTACACGTTT
1 ATTTGGGTTAACTACACGTTT
1188267 A
1 A
1188268 GTCCCCCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (21 bp):
ATTTGGGTTAACTACACGTTT
Found at i:1195076 original size:36 final size:35
Alignment explanation
Indices: 1194954--1195086 Score: 196
Period size: 35 Copynumber: 3.8 Consensus size: 35
1194944 GTTTCCTTCG
1194954 AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGA
1194989 AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGA
* * * *
1195024 AAAACAAATTTTGTCTCACTTAAGACAATTTATCTG-
1 AAAACAAATTTTGTCTCGCTTGAGAC-AGTTCT-TGA
*
1195060 AAAACAAATTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
1195087 TTTTTCCTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
35 60 0.67
36 27 0.30
37 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGA
Found at i:1195082 original size:71 final size:70
Alignment explanation
Indices: 1194954--1195086 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 70
1194944 GTTTCCTTCG
* * * *
1194954 AAAACAAATTTTGTCTCGCTTGAGACAGTTCTTGAAAAACAAATTTTGTCTCGCTTGAGACAGTT
1 AAAACAAATTTTGTCTCACTTAAGACAGTTATTGAAAAACAAATTTCGTCTCGCTTGAGACAGTT
1195019 CTTGA
66 CTTGA
*
1195024 AAAACAAATTTTGTCTCACTTAAGACAATTTATCTG-AAAACAAATTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCACTTAAGAC-AGTTAT-TGAAAAACAAATTTCGTCTCGCTTGAGACA
1195087 TTTTTCCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
70 24 0.43
71 30 0.54
72 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (70 bp):
AAAACAAATTTTGTCTCACTTAAGACAGTTATTGAAAAACAAATTTCGTCTCGCTTGAGACAGTT
CTTGA
Found at i:1195234 original size:108 final size:108
Alignment explanation
Indices: 1195060--1195305 Score: 410
Period size: 108 Copynumber: 2.3 Consensus size: 108
1195050 AATTTATCTG
*
1195060 AAAACAAATTTCGTCTCGCTTGAGACA---TTTTTCCTTTGAGATACAAATTTTGAATTTGCTTC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTTCCTTTGAGAAACAAATTTTGAATTTGCTTC
*
1195122 ACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTTTTTTA
66 ACTTGAAACAAAATTAATCTCACTTGAGATTGTTG-TTTATTTA
* *
1195166 AAAACAAATTTTGTCTCGCTTGGGACATTTTTTTTCCTTTGA-AAACAAATTTTGAATTTGCTTC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTTCCTTTGAGAAACAAATTTTGAATTTGCTTC
*
1195230 ACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
66 ACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTA
1195273 AAAACAAATTTCGTCTCGCTTGAGACATTTTTT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTT
1195306 CTATGAGATA
Statistics
Matches: 130, Mismatches: 7, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
106 25 0.19
107 37 0.28
108 56 0.43
109 12 0.09
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (108 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTTCCTTTGAGAAACAAATTTTGAATTTGCTTC
ACTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTA
Found at i:1196005 original size:64 final size:62
Alignment explanation
Indices: 1195937--1196081 Score: 166
Period size: 64 Copynumber: 2.3 Consensus size: 62
1195927 TCGTTGAGCT
* *
1195937 TGTTTCTCTGGAAACAATGTTT-TATCCCTTAAAACAATTTCTTTTGAAGAAAAATCTTTGAGTC
1 TGTTTCTTTGGAAACAAT-TTTCTATCCCTCAAAACAATTTC-TTTG-AGAAAAATCTTTGAGTC
* * * * * *
1196001 TGTTTCTTTGGAAACAAAATTTTCTGTCTCTCGAGACAGTTTCTTTGAGAAAAATCTTTGAGTT
1 TGTTTCTTTGGAAAC--AATTTTCTATCCCTCAAAACAATTTCTTTGAGAAAAATCTTTGAGTC
1196065 TGTTTCTTTGGAAACAA
1 TGTTTCTTTGGAAACAA
1196082 AATTTACCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
64 45 0.64
65 7 0.10
66 16 0.23
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (62 bp):
TGTTTCTTTGGAAACAATTTTCTATCCCTCAAAACAATTTCTTTGAGAAAAATCTTTGAGTC
Found at i:1196386 original size:28 final size:28
Alignment explanation
Indices: 1196315--1196396 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
1196305 TAAAAATATC
* * *
1196315 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
1196343 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
1196371 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
1196397 CATAACTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:1196486 original size:46 final size:42
Alignment explanation
Indices: 1196414--1196572 Score: 180
Period size: 46 Copynumber: 3.7 Consensus size: 42
1196404 CCATAGATAA
* *
1196414 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTAAAGATGG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATC-CCT--AGAT-G
*
1196460 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGA--
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATG
* * * *
1196500 CCAGACCTCCCCATCACGTAGGAGCCGTGTCA-CCCTTAGATAG
1 CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCC-TAGAT-G
1196543 CCAGTCGTCCTCATCACGTAGGAACCGTGT
1 CCAGTCGTCCTCATCACGTAGGAACCGTGT
1196573 TATCGCCCTA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
39 3 0.03
40 31 0.32
43 28 0.29
45 3 0.03
46 32 0.33
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATG
Found at i:1196642 original size:134 final size:132
Alignment explanation
Indices: 1196407--1196786 Score: 456
Period size: 134 Copynumber: 2.9 Consensus size: 132
1196397 CATAACTCCA
* *
1196407 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT---C-ACCTAAAGATGGCCAG-TCG
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCCCCTACCTAAAGATGACCAGAAC-
* * * * * *
1196467 TCCTCATCACGTAGGAACCGTGTCAT-CCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTC
65 TCTTCATCACGTATGAGCAGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGGAGCCGCGTC
1196531 ACCCT
129 A-CCT
* * *
1196536 TAGATAGCCAGTCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC-CCCTACCTAAAGATGACCAGAAC
1196601 TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCA
65 TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCA
*
1196666 TCT
130 CCT
*
1196669 TAGATAACCAGCCGTCCTCATCACGTAGGAATC--GTTATCACTCCT-CCT-AAGATGACCAGAA
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC-C-CCTACCTAAAGATGACCAGAA
* * * * ** *
1196730 CTCTTCATCATGTATGAGTAGTGTCATCCCTTGATCAGATTTCCTCATCATGTAGGA
64 CTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGA
1196787 ACATTGTCAC
Statistics
Matches: 220, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
129 38 0.17
130 62 0.28
131 10 0.05
132 3 0.01
133 33 0.15
134 69 0.31
135 5 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (132 bp):
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCCCCTACCTAAAGATGACCAGAACT
CTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCAC
CT
Found at i:1196757 original size:130 final size:131
Alignment explanation
Indices: 1196407--1196786 Score: 450
Period size: 130 Copynumber: 2.9 Consensus size: 131
1196397 CATAACTCCA
* * *
1196407 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCT--AAAGATGGCCAG-TCGT
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCG-GTTATCACCCTCCTAAGATGACCAGAAC-T
* * * * * *
1196468 CCTCATCACGTAGGAACCGTGTCAT-CCCTCGACCAGACCTCCCCATCACGTAGGAGCCGTGTCA
64 CTTCATCACGTATGAGCAGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGGAGCCGCGTCA
1196532 CCCT
128 CCCT
* * * *
1196536 TAGATAGCCAGTCGTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGTCCAGAAC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCG-GTTATCACCCT-CCT-AAGATGACCAGAAC
1196601 TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCA
63 TCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCA
*
1196666 -TCT
128 CCCT
*
1196669 TAGATAACCAGCCGTCCTCATCACGTAGGAATC-GTTATCACTCCTCCTAAGATGACCAGAACTC
1 TAGATAACCAGCCGTCCTCATCACGTAGGAACCGGTTATCAC-CCTCCTAAGATGACCAGAACTC
* * * * ** *
1196733 TTCATCATGTATGAGTAGTGTCATCCCTTGATCAGATTTCCTCATCATGTAGGA
65 TTCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGA
1196787 ACATTGTCAC
Statistics
Matches: 218, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
129 39 0.18
130 65 0.30
131 10 0.05
132 3 0.01
133 32 0.15
134 64 0.29
135 5 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (131 bp):
TAGATAACCAGCCGTCCTCATCACGTAGGAACCGGTTATCACCCTCCTAAGATGACCAGAACTCT
TCATCACGTATGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGCGTCACCC
T
Found at i:1199893 original size:31 final size:31
Alignment explanation
Indices: 1199858--1199934 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1199848 AAATTTCTAG
*
1199858 TTCATGTTCGTTCGTTAAGGAATGTAACTTA
1 TTCATGTTCGTTCATTAAGGAATGTAACTTA
* * *
1199889 TTCATGTTCATTTATTAAGGAATGTAACTTG
1 TTCATGTTCGTTCATTAAGGAATGTAACTTA
* *
1199920 TTCGTGTTTGTTCAT
1 TTCATGTTCGTTCAT
1199935 ATTTGTACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (31 bp):
TTCATGTTCGTTCATTAAGGAATGTAACTTA
Found at i:1205236 original size:17 final size:17
Alignment explanation
Indices: 1205216--1205254 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1205206 TGAATTAAAT
1205216 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1205233 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1205250 -AATTA
1 TAATTA
1205255 ATTGTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1206033 original size:14 final size:14
Alignment explanation
Indices: 1206014--1206052 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1206004 TAATGGGGAG
1206014 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1206028 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1206042 GAATCTCTGCA
1 TAATCCCTGCA
1206053 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1206762 original size:15 final size:16
Alignment explanation
Indices: 1206733--1206763 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1206723 TAACCTCAGC
1206733 TTTAAACATAAATTAA
1 TTTAAACATAAATTAA
1206749 TTTAAACA-AAATTAA
1 TTTAAACATAAATTAA
1206764 AAGATGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAACATAAATTAA
Found at i:1207560 original size:3 final size:3
Alignment explanation
Indices: 1207552--1207576 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1207542 AATTTATATC
1207552 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1207577 TGAATATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1209333 original size:25 final size:22
Alignment explanation
Indices: 1209288--1209337 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 22
1209278 TAGGACTAAA
*
1209288 TTATTAAAATATTTTATATTTT
1 TTATTAAAATATTTTAAATTTT
1209310 TTATTAAAATAAATTTTGAAATTTT
1 TTATTAAAAT--ATTTT-AAATTTT
1209335 TTA
1 TTA
1209338 CTTTTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
24 5 0.21
25 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTAAAATATTTTAAATTTT
Found at i:1210482 original size:26 final size:27
Alignment explanation
Indices: 1210444--1210501 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
1210434 TTCTTTTCAC
* * *
1210444 TTCTTTTATAATTTTTATAAATTTATT
1 TTCTATTATAATTTTAAAAAATTTATT
1210471 TTCTATTA-AATTTTAAAAAATTTATT
1 TTCTATTATAATTTTAAAAAATTTATT
*
1210497 ATCTA
1 TTCTA
1210502 ACATAGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
TTCTATTATAATTTTAAAAAATTTATT
Found at i:1215956 original size:24 final size:24
Alignment explanation
Indices: 1215927--1215975 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1215917 AAGTTAATAT
*
1215927 TTTTCCTTTAAAATG-TTGAAATTA
1 TTTTCCTTCAAAATGATTG-AATTA
1215951 TTTTCCTTCAAAATGATTGAATTA
1 TTTTCCTTCAAAATGATTGAATTA
1215975 T
1 T
1215976 ATATCAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTTCCTTCAAAATGATTGAATTA
Found at i:1217011 original size:13 final size:13
Alignment explanation
Indices: 1216993--1217019 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1216983 TTACAGACAC
1216993 GCATATGAAGACT
1 GCATATGAAGACT
1217006 GCATATGAAGACT
1 GCATATGAAGACT
1217019 G
1 G
1217020 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1217384 original size:77 final size:78
Alignment explanation
Indices: 1217232--1217386 Score: 217
Period size: 77 Copynumber: 2.0 Consensus size: 78
1217222 TATAAAAAAT
1217232 AACATTTTAGGTAGCGCTCAATATTAACATTTCTGCTATAAAAAATAATATTTTAGATAGCGTTT
1 AACATTTTAGGTAGCGCTCAATATTAACATTTCTGC-ATAAAAAATAATATTTTAGATAGCGTTT
***
1217297 TACTGTAAATATTA
65 TACCAAAAATATTA
* *
1217311 AACATTTTAGGTATCG-TCTAATATTAACATTTCTG-ATAAAAAATAATATTTTAGGT-GACGTT
1 AACATTTTAGGTAGCGCTC-AATATTAACATTTCTGCATAAAAAATAATATTTTAGATAG-CGTT
1217373 TTACCAAAAATATT
64 TTACCAAAAATATT
1217387 TAAAAAAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
76 1 0.01
77 35 0.51
78 2 0.03
79 31 0.45
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (78 bp):
AACATTTTAGGTAGCGCTCAATATTAACATTTCTGCATAAAAAATAATATTTTAGATAGCGTTTT
ACCAAAAATATTA
Found at i:1219236 original size:3 final size:3
Alignment explanation
Indices: 1219228--1219259 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1219218 AAAAGAAGCA
*
1219228 ATT ATT ATT ATT CTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1219260 GGGATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1223059 original size:18 final size:20
Alignment explanation
Indices: 1223020--1223060 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1223010 TAACTTAAAT
1223020 ATGTAGTATATGATGATTATA
1 ATGTAGTATATGAT-ATTATA
1223041 ATGTAGTATATG-T-TTATA
1 ATGTAGTATATGATATTATA
1223059 AT
1 AT
1223061 TTCTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (20 bp):
ATGTAGTATATGATATTATA
Found at i:1226448 original size:60 final size:60
Alignment explanation
Indices: 1226355--1226478 Score: 248
Period size: 60 Copynumber: 2.1 Consensus size: 60
1226345 CGTAGTTTGA
1226355 AGTGTAATAATTTGCACCGAGGAAATCAATGGACCCTTTTAACATCTTGGACTCTGCTTT
1 AGTGTAATAATTTGCACCGAGGAAATCAATGGACCCTTTTAACATCTTGGACTCTGCTTT
1226415 AGTGTAATAATTTGCACCGAGGAAATCAATGGACCCTTTTAACATCTTGGACTCTGCTTT
1 AGTGTAATAATTTGCACCGAGGAAATCAATGGACCCTTTTAACATCTTGGACTCTGCTTT
1226475 AGTG
1 AGTG
1226479 AATTTGGGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (60 bp):
AGTGTAATAATTTGCACCGAGGAAATCAATGGACCCTTTTAACATCTTGGACTCTGCTTT
Found at i:1233817 original size:2 final size:2
Alignment explanation
Indices: 1233804--1233834 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1233794 TGAAATCGTT
1233804 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
1233835 CACACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1236098 original size:2 final size:2
Alignment explanation
Indices: 1236091--1236134 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1236081 ATTTCATCTA
1236091 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1236133 AT
1 AT
1236135 TGCATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1236868 original size:18 final size:17
Alignment explanation
Indices: 1236845--1236898 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
1236835 AATTAATATA
1236845 TAAATATATTTTATCAAT
1 TAAATATATTTTAT-AAT
*
1236863 TAAATATATTTAATAAAT
1 TAAATATATTTTAT-AAT
*
1236881 CAAATAT-TTTTATAAT
1 TAAATATATTTTATAAT
1236897 TA
1 TA
1236899 CACACACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 22 0.71
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATATTTTATAAT
Found at i:1240605 original size:72 final size:72
Alignment explanation
Indices: 1240488--1240631 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
1240478 TGGTCAAAAC
1240488 CTATTGTTAGACGTAAAACAAAGATTGTTTGCACTATTGGTCCTTCAACAAACACACGAGAAATG
1 CTATTGTTAGACGTAAAACAAAGATTGTTTGCACTATTGGTCCTTCAACAAACACACGAGAAATG
1240553 ATTCGGA
66 ATTCGGA
1240560 CTATTGTTAGACGTAAAACAAAGATTGTTTGCACTATTGGTCCTTCAACAAACACACGAGAAATG
1 CTATTGTTAGACGTAAAACAAAGATTGTTTGCACTATTGGTCCTTCAACAAACACACGAGAAATG
1240625 ATTCGGA
66 ATTCGGA
1240632 AATTGGCTGA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (72 bp):
CTATTGTTAGACGTAAAACAAAGATTGTTTGCACTATTGGTCCTTCAACAAACACACGAGAAATG
ATTCGGA
Found at i:1242195 original size:20 final size:20
Alignment explanation
Indices: 1242170--1242210 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1242160 CCCAAAATGT
1242170 CAAACTCAACATCTTTACTA
1 CAAACTCAACATCTTTACTA
1242190 CAAACTCAACATCTTTACTA
1 CAAACTCAACATCTTTACTA
1242210 C
1 C
1242211 GGGGAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAACTCAACATCTTTACTA
Found at i:1243866 original size:10 final size:10
Alignment explanation
Indices: 1243851--1243895 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
1243841 AACAAATAAT
1243851 AAATAACATA
1 AAATAACATA
*
1243861 AAATAAAATAAA
1 AAATAACAT--A
1243873 AAATAACATA
1 AAATAACATA
*
1243883 ACATAACATA
1 AAATAACATA
1243893 AAA
1 AAA
1243896 CAAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 20 0.69
12 9 0.31
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (10 bp):
AAATAACATA
Found at i:1243876 original size:22 final size:22
Alignment explanation
Indices: 1243844--1243895 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1243834 AATACAAAAC
*
1243844 AAATAATAAATAACATAAAATA
1 AAATAAAAAATAACATAAAATA
*
1243866 AAATAAAAAATAACATAACATA
1 AAATAAAAAATAACATAAAATA
*
1243888 ACATAAAA
1 AAATAAAA
1243896 CAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATAAAAAATAACATAAAATA
Found at i:1243888 original size:27 final size:26
Alignment explanation
Indices: 1243839--1243905 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
1243829 TTAATAATAC
*
1243839 AAAACAAATAATAAATAACATAAAAT
1 AAAACAAAAAATAAATAACATAAAAT
* *
1243865 AAAATAAAAAATAACATAACATAACAT
1 AAAACAAAAAATAA-ATAACATAAAAT
1243892 AAAAC-AAAAATAAA
1 AAAACAAAAAATAAA
1243906 AATAAGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 1 0.03
26 20 0.56
27 15 0.42
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (26 bp):
AAAACAAAAAATAAATAACATAAAAT
Found at i:1243910 original size:27 final size:27
Alignment explanation
Indices: 1243844--1243910 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
1243834 AATACAAAAC
*
1243844 AAATAATAAATAACATAAAATAAAATAA
1 AAATAA-AAATAACATAAAATAAAACAA
* *
1243872 AAA-ATAACATAACATAACATAAAACAA
1 AAATA-AAAATAACATAAAATAAAACAA
1243899 AAATAAAAATAA
1 AAATAAAAATAA
1243911 GAAACAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (27 bp):
AAATAAAAATAACATAAAATAAAACAA
Found at i:1243936 original size:15 final size:16
Alignment explanation
Indices: 1243918--1243958 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
1243908 TAAGAAACAG
*
1243918 AAAATATAAAATA-TA
1 AAAATATAAAAAATTA
1243933 AAAATATAAAAAATTA
1 AAAATATAAAAAATTA
1243949 AAAATA-AAAA
1 AAAATATAAAA
1243959 CCAAATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATATAAAAAATTA
Found at i:1243938 original size:8 final size:8
Alignment explanation
Indices: 1243918--1243958 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
1243908 TAAGAAACAG
1243918 AAAATAT-
1 AAAATATA
1243925 AAAATATA
1 AAAATATA
1243933 AAAATATA
1 AAAATATA
1243941 AAAA-ATTA
1 AAAATA-TA
1243949 AAAATA-A
1 AAAATATA
1243956 AAA
1 AAA
1243959 CCAAATAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 12 0.39
8 18 0.58
9 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATATA
Found at i:1244909 original size:32 final size:31
Alignment explanation
Indices: 1244832--1244926 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 31
1244822 CCTATGCATA
1244832 TATACTTTATAC-TTATATATATATT-AT-T
1 TATACTTTATACTTTATATATATATTAATAT
1244860 GTATAC-TTATACTTTATATATATATTAATAT
1 -TATACTTTATACTTTATATATATATTAATAT
1244891 TATACTTTAATACTTTATATATATA-TATATAT
1 TATACTTT-ATACTTTATATATATATTA-ATAT
1244923 TATA
1 TATA
1244927 ATTGTTTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
28 6 0.10
29 18 0.30
30 7 0.12
31 5 0.08
32 24 0.40
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (31 bp):
TATACTTTATACTTTATATATATATTAATAT
Found at i:1249807 original size:183 final size:185
Alignment explanation
Indices: 1249574--1249961 Score: 642
Period size: 185 Copynumber: 2.1 Consensus size: 185
1249564 ATTAAATTTT
*
1249574 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
1249639 -TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAATTT
66 TTTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
* *
1249702 TTTATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTT-AATTAAA
131 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
1249757 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
1249821 ATTTTAAGATCCAATAATTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAAT
65 ATTTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAAT
*
1249886 TTTTATTTTATAATTATATGTTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
1249942 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1249962 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 61 0.32
184 64 0.33
185 65 0.34
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:1250110 original size:15 final size:15
Alignment explanation
Indices: 1250090--1250118 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1250080 AAAAAAAGTT
1250090 TGATTAATTCGGTTA
1 TGATTAATTCGGTTA
1250105 TGATTAATTCGGTT
1 TGATTAATTCGGTT
1250119 CGATCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
TGATTAATTCGGTTA
Found at i:1253327 original size:19 final size:19
Alignment explanation
Indices: 1253303--1253370 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
1253293 ATATGAGAAC
1253303 TCTTACAATCAGAGAAAAA
1 TCTTACAATCAGAGAAAAA
* *
1253322 TCTTACCAACCCA-ACAATGAGAA
1 TCTTA-CAA-TCAGAGAA--A-AA
1253345 CTCTTACAATCAGAGAAAAA
1 -TCTTACAATCAGAGAAAAA
1253365 TCTTAC
1 TCTTAC
1253371 CAACCCAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 11 0.29
20 8 0.21
21 3 0.08
22 3 0.08
23 8 0.21
24 5 0.13
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (19 bp):
TCTTACAATCAGAGAAAAA
Found at i:1253345 original size:43 final size:43
Alignment explanation
Indices: 1253295--1253393 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
1253285 AGCCATTTAT
1253295 ATGAGAACTCTTACAATCAGAGAAAAATCTTACCAACCCAACA
1 ATGAGAACTCTTACAATCAGAGAAAAATCTTACCAACCCAACA
1253338 ATGAGAACTCTTACAATCAGAGAAAAATCTTACCAACCCAACA
1 ATGAGAACTCTTACAATCAGAGAAAAATCTTACCAACCCAACA
1253381 ATGAGAACTCTTA
1 ATGAGAACTCTTA
1253394 TAAAGAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (43 bp):
ATGAGAACTCTTACAATCAGAGAAAAATCTTACCAACCCAACA
Found at i:1253350 original size:24 final size:24
Alignment explanation
Indices: 1253322--1253393 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
1253312 CAGAGAAAAA
1253322 TCTTACCAACCCAACAATGAGAAC
1 TCTTACCAACCCAACAATGAGAAC
* *
1253346 TCTTA-CAA-TCAGAGAA--A-AA-
1 TCTTACCAACCCA-ACAATGAGAAC
1253365 TCTTACCAACCCAACAATGAGAAC
1 TCTTACCAACCCAACAATGAGAAC
1253389 TCTTA
1 TCTTA
1253394 TAAAGAGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 3 0.08
22 3 0.08
23 8 0.22
24 10 0.27
ACGTcount: A:0.43, C:0.28, G:0.08, T:0.21
Consensus pattern (24 bp):
TCTTACCAACCCAACAATGAGAAC
Found at i:1253687 original size:24 final size:24
Alignment explanation
Indices: 1253653--1253714 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1253643 TATAAAAAAT
*
1253653 TAAACGAGCTTGTTCATGAACTTA
1 TAAACGAGCTTGTTCATGAACCTA
* *
1253677 TGAACGAGCTTGCTCATGAACCTA
1 TAAACGAGCTTGTTCATGAACCTA
*
1253701 TAAACGACCTTGTT
1 TAAACGAGCTTGTT
1253715 TGTGATCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (24 bp):
TAAACGAGCTTGTTCATGAACCTA
Found at i:1264060 original size:20 final size:20
Alignment explanation
Indices: 1264035--1264086 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1264025 AAATAACAAA
1264035 CAAATTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
1264055 CAAATTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
1264075 CAAATTCGCAAC
1 CAAATTCGCAAC
1264087 GCGATTTTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:1264280 original size:2 final size:2
Alignment explanation
Indices: 1264273--1264301 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1264263 AGATGAAAAC
1264273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1264302 TTTAGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1264407 original size:20 final size:20
Alignment explanation
Indices: 1264382--1264429 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1264372 TTGTTAAGGG
*
1264382 CGCGAATTCGG-AATTAGCGT
1 CGCGAATT-GGAAAATAGCGT
*
1264402 CGCGAATTGGAAAATCGCGT
1 CGCGAATTGGAAAATAGCGT
1264422 CGCGAATT
1 CGCGAATT
1264430 TAGAGTTCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (20 bp):
CGCGAATTGGAAAATAGCGT
Found at i:1264439 original size:20 final size:20
Alignment explanation
Indices: 1264416--1264531 Score: 54
Period size: 20 Copynumber: 5.7 Consensus size: 20
1264406 AATTGGAAAA
1264416 TCGCGTCGCGAATTTAGAGT
1 TCGCGTCGCGAATTTAGAGT
* * * **
1264436 TCGCGTTGCAAATTTGGGGAAA
1 TCGCGTCGCGAATTT--AGAGT
** * *
1264458 TCGCGTTACAAATTTAGAGAA
1 TCGCGTCGCGAATTTAGAG-T
* * *
1264479 CCTCGTTGCGAA-TTAGAGT
1 TCGCGTCGCGAATTTAGAGT
* * *
1264498 TCGCGTCACGAATTCAGAAT
1 TCGCGTCGCGAATTTAGAGT
*
1264518 TAGCGTCGCGAATT
1 TCGCGTCGCGAATT
1264532 CGACGCAAAT
Statistics
Matches: 71, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 8 0.11
20 38 0.54
21 9 0.13
22 16 0.23
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
TCGCGTCGCGAATTTAGAGT
Found at i:1264532 original size:20 final size:20
Alignment explanation
Indices: 1264486--1264532 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1264476 GAACCTCGTT
* *
1264486 GCGAATT-AGAGTTCGCGTC
1 GCGAATTCAGAATTAGCGTC
*
1264505 ACGAATTCAGAATTAGCGTC
1 GCGAATTCAGAATTAGCGTC
1264525 GCGAATTC
1 GCGAATTC
1264533 GACGCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
GCGAATTCAGAATTAGCGTC
Found at i:1264625 original size:41 final size:41
Alignment explanation
Indices: 1264557--1264646 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
1264547 GAATCGAGTT
* * ** *
1264557 GCGAATTTGGGTAATTGCGTCGTGAATTCGGAGTTAGCGTC
1 GCGAATTTGAGTAATCGCGTCACGAATTCGAAGTTAGCGTC
* * * *
1264598 GCGAATTTGAGTAATCGCGTTACGAATTTGAAGTTCGCGTT
1 GCGAATTTGAGTAATCGCGTCACGAATTCGAAGTTAGCGTC
1264639 GCGAATTT
1 GCGAATTT
1264647 ATTGGTTATT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.33
Consensus pattern (41 bp):
GCGAATTTGAGTAATCGCGTCACGAATTCGAAGTTAGCGTC
Found at i:1264637 original size:20 final size:20
Alignment explanation
Indices: 1264599--1264646 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1264589 GTTAGCGTCG
1264599 CGAATTTGAGTAATCGCGTTA
1 CGAATTTGAGT-ATCGCGTTA
*
1264620 CGAATTTGAAGT-TCGCGTTG
1 CGAATTTG-AGTATCGCGTTA
1264640 CGAATTT
1 CGAATTT
1264647 ATTGGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 14 0.56
21 8 0.32
22 3 0.12
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (20 bp):
CGAATTTGAGTATCGCGTTA
Found at i:1265211 original size:30 final size:30
Alignment explanation
Indices: 1265170--1265226 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1265160 TTAAAAAATT
* * *
1265170 ATTATTTTTACAATTAATATCTAATTAAAA
1 ATTAATTTTACAATTAACAACTAATTAAAA
*
1265200 ATTAATTTTACAGTTAACAACTAATTA
1 ATTAATTTTACAATTAACAACTAATTA
1265227 CGTATATCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTAATTTTACAATTAACAACTAATTAAAA
Found at i:1265374 original size:39 final size:41
Alignment explanation
Indices: 1265324--1265414 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
1265314 TTTAAATTGT
1265324 TAAAATATTAATTATAAA-AT-TAATTTTGAATTAGT-TTAC
1 TAAAATATTAATTATAAACATATAATTTTGAATTA-TATTAC
* * *
1265363 TAAAATATTAATTGTAAACATATAATTTTTAATTATATTAT
1 TAAAATATTAATTATAAACATATAATTTTGAATTATATTAC
1265404 TAAAATATTAA
1 TAAAATATTAA
1265415 CTAATTAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 17 0.37
40 3 0.07
41 26 0.57
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (41 bp):
TAAAATATTAATTATAAACATATAATTTTGAATTATATTAC
Found at i:1265408 original size:41 final size:40
Alignment explanation
Indices: 1265267--1265414 Score: 147
Period size: 39 Copynumber: 3.6 Consensus size: 40
1265257 AAAAATTTAC
* * **
1265267 TTTAATTAGATTATTAAAATATAAATTGTAAAAAAATATTTTT
1 TTTAATTATATTATTAAAATATTAATTGT---AAAATATAATT
* * * *
1265310 TTTATTTAAATTGTTAAAATATTAATTATAAAAT-TAATT
1 TTTAATTATATTATTAAAATATTAATTGTAAAATATAATT
* *
1265349 TTGAATTAGT-TTACTAAAATATTAATTGTAAACATATAATT
1 TTTAATTA-TATTATTAAAATATTAATTGTAAA-ATATAATT
1265390 TTTAATTATATTATTAAAATATTAA
1 TTTAATTATATTATTAAAATATTAA
1265415 CTAATTAAAG
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
39 28 0.33
40 8 0.09
41 26 0.30
43 24 0.28
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (40 bp):
TTTAATTATATTATTAAAATATTAATTGTAAAATATAATT
Found at i:1271814 original size:2 final size:2
Alignment explanation
Indices: 1271807--1271852 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1271797 TGATCGTCTC
1271807 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1271849 AT AT
1 AT AT
1271853 CCTAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1273823 original size:17 final size:16
Alignment explanation
Indices: 1273797--1273834 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1273787 AAATTACAAT
1273797 AAAAAATATAA-AAGAG
1 AAAAAATATAACAA-AG
1273813 AAAATAATATAACAAAG
1 AAAA-AATATAACAAAG
1273830 AAAAA
1 AAAAA
1273835 GAAAATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 13 0.65
18 2 0.10
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAAAATATAACAAAG
Found at i:1273848 original size:19 final size:19
Alignment explanation
Indices: 1273806--1273852 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1273796 TAAAAAATAT
* *
1273806 AAAAGAGAAAATAATATAAC
1 AAAAGA-AAAAGAAAATAAC
1273826 -AAAGAAAAAGAAAATAAC
1 AAAAGAAAAAGAAAATAAC
1273844 AAAAGAAAA
1 AAAAGAAAA
1273853 TAACAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.77, C:0.04, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAAGAAAAAGAAAATAAC
Found at i:1273849 original size:13 final size:13
Alignment explanation
Indices: 1273831--1273878 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1273821 ATAACAAAGA
1273831 AAAAGAAAATAAC
1 AAAAGAAAATAAC
1273844 AAAAGAAAATAAC
1 AAAAGAAAATAAC
*
1273857 AAAAGAAAATAAA
1 AAAAGAAAATAAC
*
1273870 AAAACAAAA
1 AAAAGAAAA
1273879 AAATATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAGAAAATAAC
Found at i:1273856 original size:31 final size:30
Alignment explanation
Indices: 1273813--1273902 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
1273803 TATAAAAGAG
*
1273813 AAAATAATATAACAAAGAAAAAGAAAATAAC
1 AAAAAAATATAACAAAGAAAAA-AAAATAAC
1273844 AAAAGAAA-ATAACAAAAGAAAATAAAAA-AAC
1 AAAA-AAATATAAC-AAAGAAAA-AAAAATAAC
* *
1273875 AAAAAAATATAA-AAATAACAAAAAATAA
1 AAAAAAATATAACAAAGAAAAAAAAATAA
1273903 TACGTAGTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
28 5 0.10
29 8 0.16
30 3 0.06
31 20 0.39
32 14 0.27
33 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (30 bp):
AAAAAAATATAACAAAGAAAAAAAAATAAC
Found at i:1273900 original size:18 final size:18
Alignment explanation
Indices: 1273849--1273901 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
1273839 ATAACAAAAG
*
1273849 AAAATAACAAAAGAAAATA
1 AAAATAACAAAA-AATATA
1273868 AAAA-AACAAAAAAATATA
1 AAAATAAC-AAAAAATATA
1273886 AAAATAACAAAAAATA
1 AAAATAACAAAAAATA
1273902 ATACGTAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (18 bp):
AAAATAACAAAAAATATA
Found at i:1273977 original size:14 final size:14
Alignment explanation
Indices: 1273958--1273985 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1273948 TTTTCTACTC
1273958 TAACGTTGAAAATA
1 TAACGTTGAAAATA
1273972 TAACGTTGAAAATA
1 TAACGTTGAAAATA
1273986 GAGATGGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
TAACGTTGAAAATA
Found at i:1281360 original size:21 final size:21
Alignment explanation
Indices: 1281336--1281375 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1281326 AAGACTGAAC
*
1281336 CTTTCGATTAAAGGACTTTTT
1 CTTTCGATGAAAGGACTTTTT
* *
1281357 CTTTTGATGAAATGACTTT
1 CTTTCGATGAAAGGACTTT
1281376 ACTTTTTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (21 bp):
CTTTCGATGAAAGGACTTTTT
Done.