Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold22
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: 1926927
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.27
Warning! 314813 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:1513484 original size:13 final size:13
Alignment explanation
Indices: 1513466--1513490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1513456 AAAGGGGTTG
1513466 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
1513479 TTTTTTTTTTCT
1 TTTTTTTTTTCT
1513491 GCATCTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:1513487 original size:16 final size:16
Alignment explanation
Indices: 1513466--1513517 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1513456 AAAGGGGTTG
1513466 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTCTTTTT
*
1513482 TTTTTTTCTGCATCTTTTT
1 TTTTTTT-T--TTCTTTTT
* *
1513501 TGTTTTGTTTCTTTTT
1 TTTTTTTTTTCTTTTT
1513517 T
1 T
1513518 GGAAAAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 15 0.52
17 1 0.03
18 1 0.03
19 12 0.41
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTT
Found at i:1513778 original size:13 final size:13
Alignment explanation
Indices: 1513762--1513786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1513752 GCACTTTTTC
1513762 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
1513775 TTTTTTTTTTGT
1 TTTTTTTTTTGT
1513787 GTTTACTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:1513782 original size:15 final size:16
Alignment explanation
Indices: 1513757--1513796 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1513747 CCTTTGCACT
*
1513757 TTTTCTTTTTTTTTTG
1 TTTTCTTTTTTTTGTG
1513773 TTTT-TTTTTTTTGTG
1 TTTTCTTTTTTTTGTG
*
1513788 TTTACTTTT
1 TTTTCTTTT
1513797 GACTGTTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTTGTG
Found at i:1520771 original size:52 final size:52
Alignment explanation
Indices: 1520686--1520810 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1520676 ATATGAAAAG
* *
1520686 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1520738 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1520790 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1520811 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1520823 original size:52 final size:51
Alignment explanation
Indices: 1520686--1520830 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
1520676 ATATGAAAAG
*
1520686 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1520738 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1520790 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1520831 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1520837 original size:13 final size:13
Alignment explanation
Indices: 1520819--1520843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1520809 CAAAGATCAG
1520819 TGTATCGATACAA
1 TGTATCGATACAA
1520832 TGTATCGATACA
1 TGTATCGATACA
1520844 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1520926 original size:13 final size:13
Alignment explanation
Indices: 1520908--1520932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1520898 ACAAAAAATA
1520908 TGTATCGATACAT
1 TGTATCGATACAT
1520921 TGTATCGATACA
1 TGTATCGATACA
1520933 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1520928 original size:32 final size:33
Alignment explanation
Indices: 1520887--1520952 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1520877 AGTAGCTTAA
1520887 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
1520919 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
1520952 A
1 A
1520953 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:1522039 original size:27 final size:27
Alignment explanation
Indices: 1522001--1522053 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1521991 GTTTAAAAAC
1522001 AGGGTTGGAGTATCCCCAAAGAATAAT
1 AGGGTTGGAGTATCCCCAAAGAATAAT
* *
1522028 AGGGTTGGAGTATCCTCAATGAATAA
1 AGGGTTGGAGTATCCCCAAAGAATAA
1522054 ATTTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (27 bp):
AGGGTTGGAGTATCCCCAAAGAATAAT
Found at i:1522424 original size:13 final size:13
Alignment explanation
Indices: 1522406--1522430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1522396 ATGTTGCACA
1522406 GTATCGATACATC
1 GTATCGATACATC
1522419 GTATCGATACAT
1 GTATCGATACAT
1522431 GACTAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:1522444 original size:20 final size:21
Alignment explanation
Indices: 1522419--1522469 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1522409 TCGATACATC
**
1522419 GTATCGATACAT-GACTAAAT
1 GTATCGATACATGGAAAAAAT
1522439 GTATCGATAC-TGGAAAAAAT
1 GTATCGATACATGGAAAAAAT
1522459 GTATCGATACA
1 GTATCGATACA
1522470 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
GTATCGATACATGGAAAAAAT
Found at i:1524133 original size:9 final size:9
Alignment explanation
Indices: 1524116--1524160 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
1524106 TCAACCATCA
*
1524116 AAGACGATG
1 AAGATGATG
1524125 AAGATGATG
1 AAGATGATG
1524134 AAGATGATG
1 AAGATGATG
1524143 AAGATGATG
1 AAGATGATG
*
1524152 ATGATGATG
1 AAGATGATG
1524161 GTGACTCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.22
Consensus pattern (9 bp):
AAGATGATG
Found at i:1524142 original size:3 final size:3
Alignment explanation
Indices: 1524121--1524160 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1524111 CATCAAAGAC
* * *
1524121 GAT GAA GAT GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1524161 GTGACTCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1528721 original size:13 final size:13
Alignment explanation
Indices: 1528703--1528738 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1528693 GCATTCTCTA
*
1528703 TATCGATACATTG
1 TATCGATACACTG
1528716 TATCGATACACTG
1 TATCGATACACTG
1528729 TATCGATACA
1 TATCGATACA
1528739 AGGGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACACTG
Found at i:1528913 original size:22 final size:21
Alignment explanation
Indices: 1528870--1528910 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1528860 CAAAATTCTT
1528870 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
1528892 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
1528911 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:1529217 original size:21 final size:20
Alignment explanation
Indices: 1529174--1529224 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
1529164 CCCTTGGCAT
* *
1529174 CACCCACCAGGTCGCGATCGG
1 CACCC-CCAGGTCGCAACCGG
1529195 CACCCCCAGGTCGCAACCAGG
1 CACCCCCAGGTCGCAACC-GG
1529216 CAGCCCCCA
1 CA-CCCCCA
1529225 CACTAGCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 9 0.35
22 6 0.23
ACGTcount: A:0.22, C:0.49, G:0.24, T:0.06
Consensus pattern (20 bp):
CACCCCCAGGTCGCAACCGG
Found at i:1531235 original size:20 final size:20
Alignment explanation
Indices: 1531210--1531260 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1531200 TCGATACATC
**
1531210 GTATCGATACATGACTAAAT
1 GTATCGATACATGAAAAAAT
*
1531230 GTATCGATACTTGAAAAAAT
1 GTATCGATACATGAAAAAAT
1531250 GTATCGATACA
1 GTATCGATACA
1531261 AGTCATTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGAAAAAAT
Found at i:1531317 original size:19 final size:20
Alignment explanation
Indices: 1531293--1531343 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1531283 TAGCTAAACT
**
1531293 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
1531312 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
1531332 TGTATCGATACA
1 TGTATCGATACA
1531344 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:1534350 original size:35 final size:33
Alignment explanation
Indices: 1534277--1534358 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 33
1534267 CTATCTTTTG
1534277 AAGGCTAAGATAG-ATATTCCCTATCTTTTCAC
1 AAGGCTAAGATAGAATATTCCCTATCTTTTCAC
*
1534309 AA-GCTAAGATAGAACCTCTTCCCTATCTTTTTCA-
1 AAGGCTAAGATAGAA--TATTCCCTATC-TTTTCAC
1534343 AAGGCTAAGATAGAAT
1 AAGGCTAAGATAGAAT
1534359 CTTTCAATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
31 10 0.23
32 3 0.07
33 1 0.02
34 12 0.27
35 18 0.41
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
AAGGCTAAGATAGAATATTCCCTATCTTTTCAC
Found at i:1534849 original size:21 final size:21
Alignment explanation
Indices: 1534805--1534859 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
1534795 TTGAGCCATT
* * *
1534805 TGTATCAATACAA-TTCATCA
1 TGTATCGATACAATTTAAACA
1534825 TGTATCGATACAATTTAAACA
1 TGTATCGATACAATTTAAACA
*
1534846 TGTATTGATACAAT
1 TGTATCGATACAAT
1534860 GTATCGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAATTTAAACA
Found at i:1536139 original size:12 final size:12
Alignment explanation
Indices: 1536122--1536153 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1536112 TTCTATAGCT
1536122 TGCTCATCCTCA
1 TGCTCATCCTCA
1536134 TGCTCATCCTCA
1 TGCTCATCCTCA
1536146 TGCTCATC
1 TGCTCATC
1536154 TTCTTCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.41, G:0.09, T:0.34
Consensus pattern (12 bp):
TGCTCATCCTCA
Found at i:1540208 original size:20 final size:20
Alignment explanation
Indices: 1540183--1540231 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1540173 TGATACAATA
*
1540183 TATCGATACTTAGCAATTTG
1 TATCGATACTTAGAAATTTG
1540203 TATCGATACTTAGAAATTTG
1 TATCGATACTTAGAAATTTG
*
1540223 TATTGATAC
1 TATCGATAC
1540232 ATCTGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (20 bp):
TATCGATACTTAGAAATTTG
Found at i:1543223 original size:15 final size:16
Alignment explanation
Indices: 1543197--1543227 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1543187 CTCTCAGAGT
1543197 CTTGATAGAAGCTAAA
1 CTTGATAGAAGCTAAA
1543213 CTTGA-AGAAGCTAAA
1 CTTGATAGAAGCTAAA
1543228 TGGATCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (16 bp):
CTTGATAGAAGCTAAA
Found at i:1544878 original size:14 final size:13
Alignment explanation
Indices: 1544861--1544924 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1544851 AAAAATTGTT
1544861 GTCAAGAAATTATC
1 GTCAAGAAATT-TC
* *
1544875 GTCAAGAACTTTT
1 GTCAAGAAATTTC
1544888 GTCAAG-AATGTTC
1 GTCAAGAAAT-TTC
* *
1544901 GT-TAGAAACTTC
1 GTCAAGAAATTTC
*
1544913 ATCAAGAAATTT
1 GTCAAGAAATTT
1544925 TCATCAATAC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
12 8 0.21
13 20 0.53
14 10 0.26
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
GTCAAGAAATTTC
Found at i:1544893 original size:13 final size:14
Alignment explanation
Indices: 1544843--1544895 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1544833 GTAATTTACC
*
1544843 ATTGTCAAAAAAATT
1 ATTGTC-AAGAAATT
*
1544858 GTTGTCAAGAAATT
1 ATTGTCAAGAAATT
* *
1544872 ATCGTCAAGAACTT
1 ATTGTCAAGAAATT
1544886 -TTGTCAAGAA
1 ATTGTCAAGAA
1544896 TGTTCGTTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 9 0.28
14 18 0.56
15 5 0.16
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (14 bp):
ATTGTCAAGAAATT
Found at i:1545089 original size:32 final size:33
Alignment explanation
Indices: 1544942--1545172 Score: 220
Period size: 33 Copynumber: 7.1 Consensus size: 33
1544932 TACGAATCCC
* **
1544942 TTCTCAAAGCCTACACAAGTTGGTAACAACCTT
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* * * *
1544975 TTTTCAAAGCCCACAAAAGTCAGTGGCAACCTT
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* * *
1545008 TTTTCCAAGCCTACACAAGTCGGTGGCAATCTT
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* *
1545041 TTCCCAAAGCCTACACAAGTCAGTGGCAACC-T
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* *
1545073 TTCTCAAAGCCCACACAAGTCGGTGGCAACC-C
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* * * *
1545105 TTAT-AAAGCCTATACAAGTTGGTGCCAACC--
1 TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
* * * *
1545135 CTCTCAAAAGCCTACACAAATCGGTGGCATCTTT
1 TTCTC-AAAGCCTACACAAGTCGGTGGCAACCTT
1545169 TTCT
1 TTCT
1545173 AAGCCCAATG
Statistics
Matches: 159, Mismatches: 35, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
30 2 0.01
31 22 0.14
32 52 0.33
33 80 0.50
34 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (33 bp):
TTCTCAAAGCCTACACAAGTCGGTGGCAACCTT
Found at i:1545593 original size:61 final size:61
Alignment explanation
Indices: 1545434--1545654 Score: 199
Period size: 61 Copynumber: 3.6 Consensus size: 61
1545424 ACATTGGTAC
* * * * * *
1545434 TTTTGTCATCTTTAAGCCCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTTATCAT
1 TTTTCTCATCTTCAAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTTATCAT
* * * * * * *
1545495 TATTCTCATCTTCAGGGCCGATATCGTTGGCCGTGAATTAGCATATCGACACTTTTATCAT
1 TTTTCTCATCTTCAAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTTATCAT
* * * * * * *
1545556 TTTTCTCATCTTCAAGTCTAATGTCGTTGGTCTTGAATCAGCACATTGGCACTCTTCTCAT
1 TTTTCTCATCTTCAAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTTATCAT
* * * * * * *
1545617 ATTTATCATCTTGAAGTCCAGTGTTGTAGGCCTTGAAT
1 TTTTCTCATCTTCAAGTCCAATATCGTTGGCCTTGAAT
1545655 CTGCACGCTG
Statistics
Matches: 126, Mismatches: 34, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
61 126 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (61 bp):
TTTTCTCATCTTCAAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGCACTTTTATCAT
Found at i:1546502 original size:16 final size:16
Alignment explanation
Indices: 1546481--1546511 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1546471 TGCCCAATTT
1546481 AAATGAGTTCTTCACC
1 AAATGAGTTCTTCACC
*
1546497 AAATGAGTTTTTCAC
1 AAATGAGTTCTTCAC
1546512 ATCATAAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (16 bp):
AAATGAGTTCTTCACC
Found at i:1548845 original size:96 final size:97
Alignment explanation
Indices: 1548598--1548845 Score: 295
Period size: 96 Copynumber: 2.6 Consensus size: 97
1548588 AAAATTTTAT
* * * *
1548598 TCATCGGGGATACTCTAACCCCATTCTTCCGAGGGAATACTCCAACCCCGCTTTTAAACTTGTCA
1 TCATCAGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGTCA
**
1548663 AGATTCAAACCTTATTTTTACCTAAATTATTG
66 AGATTCAAACCTTATTTTTACCTAAATTATCA
* * * * * *
1548695 TCATCAAGGATACTTTAACCCCATTCCTCCAAAGGGATACTTCAACCCTGTTTTTGAAACTTGTC
1 TCATCAGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTT-AAACTTGTC
* *
1548760 -A-ATTTAAA-CTGTATTTTTGCCTAAATTATCA
65 AAGATTCAAACCT-TATTTTTACCTAAATTATCA
* * * *
1548791 TCATCAGGGACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCCCATTTTT
1 TCATCAGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTT
1548846 CAATAGAAAA
Statistics
Matches: 125, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
95 2 0.02
96 68 0.54
97 46 0.37
98 9 0.07
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (97 bp):
TCATCAGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCCCGTTTTTAAACTTGTCA
AGATTCAAACCTTATTTTTACCTAAATTATCA
Found at i:1552064 original size:23 final size:24
Alignment explanation
Indices: 1552027--1552071 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
1552017 CATGCGGTGC
1552027 TAATTTTCTTATATGCATAATCGT
1 TAATTTTCTTATATGCATAATCGT
1552051 TAATTTT-TTATATGCATAATC
1 TAATTTTCTTATATGCATAATC
1552072 AACTCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (24 bp):
TAATTTTCTTATATGCATAATCGT
Found at i:1554128 original size:4 final size:4
Alignment explanation
Indices: 1554119--1554152 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1554109 GTGCAAGGTT
*
1554119 TTTC TTTC TTTC TTTC TTTC TTTC ATTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1554153 GATGCACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:1554245 original size:22 final size:21
Alignment explanation
Indices: 1554220--1554263 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1554210 TTTCAAAAAA
*
1554220 TATATATATTTTTAAAAATGAC
1 TATATATA-ATTTAAAAATGAC
*
1554242 TATATGTAATTTAAAAATGAC
1 TATATATAATTTAAAAATGAC
1554263 T
1 T
1554264 GATTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (21 bp):
TATATATAATTTAAAAATGAC
Found at i:1554957 original size:28 final size:28
Alignment explanation
Indices: 1554925--1554987 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
1554915 AATTTTAATC
*
1554925 CTATTTATTATATAAAAGAAATTGATTT
1 CTATTTATTATATAAAAGAAACTGATTT
1554953 CTATTTATTATATAAAAGAAACTGATTT
1 CTATTTATTATATAAAAGAAACTGATTT
*
1554981 CTTTTTA
1 CTATTTA
1554988 GGGTTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (28 bp):
CTATTTATTATATAAAAGAAACTGATTT
Found at i:1555638 original size:20 final size:20
Alignment explanation
Indices: 1555608--1555653 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1555598 TATATTTATT
1555608 ATTTATTTAATATTAAAAATA
1 ATTT-TTTAATATTAAAAATA
* *
1555629 ATTTTTTAATATTTAAAATT
1 ATTTTTTAATATTAAAAATA
1555649 ATTTT
1 ATTTT
1555654 AATTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTTTAATATTAAAAATA
Found at i:1555655 original size:18 final size:19
Alignment explanation
Indices: 1555613--1555661 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1555603 TTATTATTTA
*
1555613 TTTAATATTAAAAATAATTT
1 TTTAATATTAAAAAT-ATAT
*
1555633 TTTAATATTTAAAAT-TAT
1 TTTAATATTAAAAATATAT
1555651 TTTAAT-TTAAA
1 TTTAATATTAAA
1555662 TTTATCAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 8 0.31
20 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATATTAAAAATATAT
Found at i:1557198 original size:30 final size:31
Alignment explanation
Indices: 1557164--1557224 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1557154 CCTAATAATC
* *
1557164 TAAATGATACTATTTTTTA-AAAATAAAATA
1 TAAATAATACTATTTTTAATAAAATAAAATA
**
1557194 TAAATAATTTTATTTTTAATAAAATAAAATA
1 TAAATAATACTATTTTTAATAAAATAAAATA
1557225 ATTTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
TAAATAATACTATTTTTAATAAAATAAAATA
Found at i:1557217 original size:26 final size:27
Alignment explanation
Indices: 1557185--1557250 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
1557175 ATTTTTTAAA
*
1557185 AATAAAATATAAATAATTTTATTT-TT
1 AATAAAATATAAATAATTTAATTTATT
1557211 AATAAAATA-AAATAATTTAATTTATT
1 AATAAAATATAAATAATTTAATTTATT
*
1557237 AATAATATATAAAT
1 AATAAAATATAAAT
1557251 TTATAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 13 0.36
26 19 0.53
27 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATAAAATATAAATAATTTAATTTATT
Found at i:1557542 original size:18 final size:17
Alignment explanation
Indices: 1557516--1557559 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1557506 TTTAGAAATA
* *
1557516 ATATATATATATATGTTT
1 ATATTTATATA-ATATTT
1557534 ATATTTATATAATATTT
1 ATATTTATATAATATTT
1557551 ATTATTTAT
1 A-TATTTAT
1557560 TTTCAACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTTATATAATATTT
Found at i:1557644 original size:17 final size:18
Alignment explanation
Indices: 1557611--1557644 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1557601 CATAGGGTCC
*
1557611 ATTTGGCTTTGTTTTCCA
1 ATTTGGCTTTGTATTCCA
1557629 ATTTGGCTTTG-ATTCC
1 ATTTGGCTTTGTATTCC
1557645 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.53
Consensus pattern (18 bp):
ATTTGGCTTTGTATTCCA
Found at i:1559847 original size:14 final size:16
Alignment explanation
Indices: 1559829--1559864 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1559819 ATTTTACGAA
1559829 AAAAATT-TTATATAG
1 AAAAATTATTATATAG
*
1559844 AAAAATTATTATATAT
1 AAAAATTATTATATAG
1559860 AAAAA
1 AAAAA
1559865 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAAATTATTATATAG
Found at i:1559920 original size:22 final size:21
Alignment explanation
Indices: 1559895--1559945 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
1559885 AATTAAACTT
1559895 TTTAAAACTAAT-TTA-ATGAGA
1 TTTAAAA-TAATATTAGATGA-A
1559916 GTTTAATAATAATATTAGATGAA
1 -TTTAA-AATAATATTAGATGAA
1559939 TTTAAAA
1 TTTAAAA
1559946 GATTTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.08
22 14 0.54
23 6 0.23
24 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTAAAATAATATTAGATGAA
Found at i:1560326 original size:166 final size:166
Alignment explanation
Indices: 1559888--1560339 Score: 469
Period size: 164 Copynumber: 2.7 Consensus size: 166
1559878 TGAAATAAAT
* * * * * *
1559888 TAAACTTTTTAAAACTAATTTAATGA-GAGTTTAATAATAATATTAGATGAA-TTTAAAAGATTT
1 TAAATTTTTTAAAACTAATTTAAT-ATAAATTAAATAATAATATTTGATGAATTTTAAAA-ATTA
* * *
1559951 AAAAC-GAGAAAAATCTCC-CTGAAAATATTTATAGAATAAAAAATT-AATTTTTTCAAAAATAA
64 AAAACTGAGAAAAATC-CCTCTGAAAACATTTATAGAATAGAAAATTCAATTATTTCAAAAATAA
** ** *
1560013 AGAAATTTCAAAGAAAAATTCAAAACTTATGAAGATAGA
128 AGAAATTTCAAAGAAAAATAAAAAACCCATGAAAATAGA
* ** * * *
1560052 TTAATTTTTCGAAACTGATTTAATATGAAA-TAACTGATAATATTTGATG-ATTTTAAAAATTAA
1 TAAATTTTTTAAAACTAATTTAATAT-AAATTAAATAATAATATTTGATGAATTTTAAAAATTAA
* * * * * * * *
1560115 AAACTAAGAAAAATCCTTCCGAAAACATTTACAAAAT-GAAAAATTCTA-TATTTCGAAAATAGA
65 AAACTGAGAAAAATCCCTCTGAAAACATTTATAGAATAG-AAAATTCAATTATTTCAAAAATAAA
1560178 GAGAATTTC-AAGAAAAAATAAAAAACCCATGAAAAT-GAA
129 GA-AATTTCAAAG-AAAAATAAAAAACCCATGAAAATAG-A
1560217 TAAATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TAAATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
* **
1560282 AACTGAGAAAAATCCCTCTGAAAACATTTATAGAGTAGAAAATTC-CGTATTTCAAAAA
66 AACTGAGAAAAATCCCTCTGAAAACATTTATAGAATAGAAAATTCAATTATTTCAAAAA
1560340 AGTAAGAATT
Statistics
Matches: 232, Mismatches: 42, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
163 11 0.05
164 92 0.40
165 66 0.28
166 62 0.27
167 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (166 bp):
TAAATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAA
AACTGAGAAAAATCCCTCTGAAAACATTTATAGAATAGAAAATTCAATTATTTCAAAAATAAAGA
AATTTCAAAGAAAAATAAAAAACCCATGAAAATAGA
Found at i:1560393 original size:166 final size:164
Alignment explanation
Indices: 1560054--1560426 Score: 416
Period size: 166 Copynumber: 2.3 Consensus size: 164
1560044 AAGATAGATT
** * *
1560054 AATTTTTCGAAACTGATTTAATATGAAATAACTGATAATATTTGATGATTTTAAAAATTAAAAAC
1 AATTTTTTAAAACTGATTTAATAT-AAATAAATAATAATATTTGATGATTTTAAAAATTAAAAAC
* * *
1560119 TAAGAAAAATCCTTCCGAAAACATTTACAAAATGAAAAATTCTATATTTCGAAAATAGAGAGAAT
65 TAAGAAAAATCCCTCCGAAAACATTTACAAAATGAAAAATTCCATATTTCGAAAAAAGAGAGAAT
* * *
1560184 TTCAAGAAAAAATAAAAAACCCATGAAAATGAATA
130 TCCAAGAAAAAATAAAAAACCCATGAAAATAAAAA
*
1560219 AATTTTTTAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
1 AATTTTTTAAAACTGATTTAATATAAA-TAAATAATAATATTTGATG-ATTTTAAAAATTAAAAA
* * * * * *
1560284 CTGAGAAAAATCCCTCTGAAAACATTTATAGAGT-AGAAAATTCCGTATTTC-AAAAAAGTA-AG
64 CTAAGAAAAATCCCTCCGAAAACATTTACAAAATGA-AAAATTCCATATTTCGAAAAAAG-AGAG
** *
1560346 AATTCCAA-AAGAAAATCAGTAAA-GCAT-AAAATAAAAA
127 AATTCCAAGAA-AAAAT-AAAAAACCCATGAAAATAAAAA
* **
1560383 GAATTTTTTTAAAATTGATTTAATGGAAATAAATAATAATATTT
1 -AA-TTTTTTAAAACTGATTTAATATAAATAAATAATAATATTT
1560427 AAAGAGTTTT
Statistics
Matches: 176, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
164 13 0.07
165 79 0.45
166 84 0.48
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.31
Consensus pattern (164 bp):
AATTTTTTAAAACTGATTTAATATAAATAAATAATAATATTTGATGATTTTAAAAATTAAAAACT
AAGAAAAATCCCTCCGAAAACATTTACAAAATGAAAAATTCCATATTTCGAAAAAAGAGAGAATT
CCAAGAAAAAATAAAAAACCCATGAAAATAAAAA
Found at i:1563543 original size:21 final size:21
Alignment explanation
Indices: 1563519--1563561 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1563509 GACCATGAGA
1563519 TGCTTTATGCCATATTTATGT
1 TGCTTTATGCCATATTTATGT
*
1563540 TGCTTTATGCTATATTTATGT
1 TGCTTTATGCCATATTTATGT
1563561 T
1 T
1563562 CATCTTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (21 bp):
TGCTTTATGCCATATTTATGT
Found at i:1564549 original size:10 final size:10
Alignment explanation
Indices: 1564530--1564560 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1564520 GTATCGATAC
*
1564530 ATGAACAGTG
1 ATGAATAGTG
1564540 ATGAATAGTG
1 ATGAATAGTG
1564550 ATGAATAGTG
1 ATGAATAGTG
1564560 A
1 A
1564561 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:1564606 original size:13 final size:13
Alignment explanation
Indices: 1564588--1564625 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1564578 TGCCAATGCT
1564588 ATGTATCGATACA
1 ATGTATCGATACA
1564601 ATGTATCGATACA
1 ATGTATCGATACA
*
1564614 ATGTATCAATAC
1 ATGTATCGATAC
1564626 TTAGCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1566968 original size:13 final size:13
Alignment explanation
Indices: 1566950--1566974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1566940 CATAAAGTGT
1566950 TGTATCGATACAA
1 TGTATCGATACAA
1566963 TGTATCGATACA
1 TGTATCGATACA
1566975 TATTTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1566986 original size:19 final size:18
Alignment explanation
Indices: 1566962--1566997 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1566952 TATCGATACA
1566962 ATGTATCGATACATATTTT
1 ATGTATCGATACA-ATTTT
1566981 ATGTATCGATACAATTT
1 ATGTATCGATACAATTT
1566998 AAGCTACTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
ATGTATCGATACAATTTT
Found at i:1567032 original size:11 final size:11
Alignment explanation
Indices: 1567016--1567051 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
1567006 GCCAAAAAAA
1567016 AATGTATCGAT
1 AATGTATCGAT
1567027 AATGTATCGAT
1 AATGTATCGAT
1567038 ACATTGTATCGAT
1 A-A-TGTATCGAT
1567051 A
1 A
1567052 CACTGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 1 0.04
13 10 0.43
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (11 bp):
AATGTATCGAT
Found at i:1567047 original size:13 final size:12
Alignment explanation
Indices: 1567017--1567053 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
1567007 CCAAAAAAAA
1567017 ATGTATCGATA-
1 ATGTATCGATAC
1567028 ATGTATCGATAC
1 ATGTATCGATAC
1567040 ATTGTATCGATAC
1 A-TGTATCGATAC
1567053 A
1 A
1567054 CTGATCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 1 0.04
13 12 0.50
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1567120 original size:52 final size:52
Alignment explanation
Indices: 1567062--1567186 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1567052 CACTGATCTT
* *
1567062 TGTATCGATACATGCAGGCGAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1567114 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1567166 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
1567187 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1573878 original size:13 final size:13
Alignment explanation
Indices: 1573860--1573884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1573850 TGCCAATGCT
1573860 ATGTATCGATACA
1 ATGTATCGATACA
1573873 ATGTATCGATAC
1 ATGTATCGATAC
1573885 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1576087 original size:21 final size:21
Alignment explanation
Indices: 1576061--1576106 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1576051 ATGCAAGATG
*
1576061 AACATAAATATAGCATAAAGC
1 AACATAAATATAGCATAAAAC
1576082 AACATAAATATAGCATAAAAC
1 AACATAAATATAGCATAAAAC
1576103 AACA
1 AACA
1576107 GTTAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.17
Consensus pattern (21 bp):
AACATAAATATAGCATAAAAC
Found at i:1576632 original size:11 final size:10
Alignment explanation
Indices: 1576607--1576633 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1576597 TATACACTTT
1576607 GAAAAATAAA
1 GAAAAATAAA
1576617 GAAAAATAAA
1 GAAAAATAAA
1576627 GAAAAAT
1 GAAAAAT
1576634 CTATATTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
GAAAAATAAA
Found at i:1577353 original size:21 final size:19
Alignment explanation
Indices: 1577327--1577366 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1577317 TAATTATCAA
*
1577327 AATAAATAAATAAATAAAAAT
1 AATAAA-AAAGAAA-AAAAAT
1577348 AATAAAAAAGAAAAAAAAT
1 AATAAAAAAGAAAAAAAAT
1577367 CCTAGAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (19 bp):
AATAAAAAAGAAAAAAAAT
Found at i:1577355 original size:27 final size:27
Alignment explanation
Indices: 1577299--1577355 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
1577289 AATTTAAATC
* * * *
1577299 AAATCAAATAAAAAGTAATAATTATCA
1 AAATCAAATAAAAAATAAAAATAATAA
1577326 AAAT-AAATAAATAAATAAAAATAATAA
1 AAATCAAATAAA-AAATAAAAATAATAA
1577353 AAA
1 AAA
1577356 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (27 bp):
AAATCAAATAAAAAATAAAAATAATAA
Found at i:1581543 original size:20 final size:20
Alignment explanation
Indices: 1581518--1581593 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1581508 CAAAACTCAG
* *
1581518 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATTAAA
***
1581538 AATGTATCGATACAATTCCT
1 AATGTATCGATACAATTAAA
* *
1581558 TATGTATCGATACATTTAAA
1 AATGTATCGATACAATTAAA
1581578 AATGTATCGATACAAT
1 AATGTATCGATACAAT
1581594 ATCCTTCCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACAATTAAA
Found at i:1581581 original size:40 final size:41
Alignment explanation
Indices: 1581519--1581599 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 41
1581509 AAAACTCAGA
*
1581519 ATGTATCGATACAATGAGAAATGTATCGATACAAT-TCCTT
1 ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
* *
1581559 ATGTATCGATACATTTAAAAATGTATCGATACAATATCCTT
1 ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
1581600 CCAGAATCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 32 0.86
41 5 0.14
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (41 bp):
ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
Found at i:1581690 original size:21 final size:21
Alignment explanation
Indices: 1581637--1581691 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1581627 TATATTTTAG
1581637 AATGTATCGATACATTCACTT
1 AATGTATCGATACATTCACTT
*
1581658 -ATGTATCAATACATTGC-CTT
1 AATGTATCGATACATT-CACTT
*
1581678 AATGTATTGATACA
1 AATGTATCGATACA
1581692 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTCACTT
Found at i:1584140 original size:13 final size:13
Alignment explanation
Indices: 1584122--1584147 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1584112 CAATTTTTTG
1584122 TGTATCGATACAT
1 TGTATCGATACAT
1584135 TGTATCGATACAT
1 TGTATCGATACAT
1584148 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1588289 original size:20 final size:21
Alignment explanation
Indices: 1588264--1588320 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
1588254 AAAAACCCAG
1588264 AATGTATCGATACAATGA-GA
1 AATGTATCGATACAATGAGGA
1588284 AATGTATCGATACAATGAGGA
1 AATGTATCGATACAATGAGGA
1588305 AGCATGTATCGATACA
1 A--ATGTATCGATACA
1588321 TTTACTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 18 0.53
21 3 0.09
23 13 0.38
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (21 bp):
AATGTATCGATACAATGAGGA
Found at i:1589139 original size:20 final size:19
Alignment explanation
Indices: 1589075--1589141 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
1589065 TTTTACCCAG
* *
1589075 ATGTATCAATATAGTTTTTA
1 ATGTATCGATACA-TTTTTA
* *
1589095 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTTA
*
1589115 GTGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTT-A
1589135 ATGTATC
1 ATGTATC
1589142 AATGCATTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.92
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTTA
Found at i:1589907 original size:15 final size:15
Alignment explanation
Indices: 1589887--1589922 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1589877 TGATACATTC
*
1589887 ATTTTCTGTTTTGTT
1 ATTTTCTGTTCTGTT
1589902 ATTTTCTGTTCTGTT
1 ATTTTCTGTTCTGTT
1589917 ATTTTC
1 ATTTTC
1589923 ATCCTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.69
Consensus pattern (15 bp):
ATTTTCTGTTCTGTT
Found at i:1591179 original size:27 final size:26
Alignment explanation
Indices: 1591141--1591191 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
1591131 TTTGATTATC
1591141 GGGGATACTCCAACCCCGCTCTTTTGA
1 GGGGATACTCCAACCCCGCT-TTTTGA
1591168 GGGGATACTCCAACCCCGCTTTTT
1 GGGGATACTCCAACCCCGCTTTTT
1591192 CTTCAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGCTTTTTGA
Found at i:1597605 original size:21 final size:21
Alignment explanation
Indices: 1597581--1597623 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1597571 GACCATGAGA
1597581 TGCTTTATGCCATATTTATGT
1 TGCTTTATGCCATATTTATGT
*
1597602 TGCTTTATGCTATATTTATGT
1 TGCTTTATGCCATATTTATGT
1597623 T
1 T
1597624 CATCTTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (21 bp):
TGCTTTATGCCATATTTATGT
Found at i:1598611 original size:10 final size:10
Alignment explanation
Indices: 1598592--1598622 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1598582 GTATCGATAC
*
1598592 ATGAACAGTG
1 ATGAATAGTG
1598602 ATGAATAGTG
1 ATGAATAGTG
1598612 ATGAATAGTG
1 ATGAATAGTG
1598622 A
1 A
1598623 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:1598668 original size:13 final size:13
Alignment explanation
Indices: 1598650--1598687 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1598640 TGCCAATGCT
1598650 ATGTATCGATACA
1 ATGTATCGATACA
1598663 ATGTATCGATACA
1 ATGTATCGATACA
*
1598676 ATGTATCAATAC
1 ATGTATCGATAC
1598688 TTAGCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1601031 original size:13 final size:13
Alignment explanation
Indices: 1601013--1601037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1601003 CATAAAGTGT
1601013 TGTATCGATACAA
1 TGTATCGATACAA
1601026 TGTATCGATACA
1 TGTATCGATACA
1601038 TATTTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1601049 original size:19 final size:18
Alignment explanation
Indices: 1601025--1601060 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1601015 TATCGATACA
1601025 ATGTATCGATACATATTTT
1 ATGTATCGATACA-ATTTT
1601044 ATGTATCGATACAATTT
1 ATGTATCGATACAATTT
1601061 AAGCTACTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
ATGTATCGATACAATTTT
Found at i:1601095 original size:11 final size:11
Alignment explanation
Indices: 1601079--1601114 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
1601069 GCCAAAAAAA
1601079 AATGTATCGAT
1 AATGTATCGAT
1601090 AATGTATCGAT
1 AATGTATCGAT
1601101 ACATTGTATCGAT
1 A-A-TGTATCGAT
1601114 A
1 A
1601115 CACTGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 1 0.04
13 10 0.43
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (11 bp):
AATGTATCGAT
Found at i:1601110 original size:13 final size:12
Alignment explanation
Indices: 1601080--1601116 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
1601070 CCAAAAAAAA
1601080 ATGTATCGATA-
1 ATGTATCGATAC
1601091 ATGTATCGATAC
1 ATGTATCGATAC
1601103 ATTGTATCGATAC
1 A-TGTATCGATAC
1601116 A
1 A
1601117 CTGATCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 1 0.04
13 12 0.50
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1601183 original size:52 final size:52
Alignment explanation
Indices: 1601125--1601249 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1601115 CACTGATCTT
* *
1601125 TGTATCGATACATGCAGGCGAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1601177 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1601229 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
1601250 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1607940 original size:13 final size:13
Alignment explanation
Indices: 1607922--1607946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1607912 TGCCAATGCT
1607922 ATGTATCGATACA
1 ATGTATCGATACA
1607935 ATGTATCGATAC
1 ATGTATCGATAC
1607947 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1610149 original size:21 final size:21
Alignment explanation
Indices: 1610123--1610168 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1610113 ATGCAAGATG
*
1610123 AACATAAATATAGCATAAAGC
1 AACATAAATATAGCATAAAAC
1610144 AACATAAATATAGCATAAAAC
1 AACATAAATATAGCATAAAAC
1610165 AACA
1 AACA
1610169 GTTAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.07, T:0.17
Consensus pattern (21 bp):
AACATAAATATAGCATAAAAC
Found at i:1610694 original size:11 final size:10
Alignment explanation
Indices: 1610669--1610695 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1610659 TATACACTTT
1610669 GAAAAATAAA
1 GAAAAATAAA
1610679 GAAAAATAAA
1 GAAAAATAAA
1610689 GAAAAAT
1 GAAAAAT
1610696 CTATATTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
GAAAAATAAA
Found at i:1611415 original size:21 final size:19
Alignment explanation
Indices: 1611389--1611428 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1611379 TAATTATCAA
*
1611389 AATAAATAAATAAATAAAAAT
1 AATAAA-AAAGAAA-AAAAAT
1611410 AATAAAAAAGAAAAAAAAT
1 AATAAAAAAGAAAAAAAAT
1611429 CCTAGAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (19 bp):
AATAAAAAAGAAAAAAAAT
Found at i:1611417 original size:27 final size:27
Alignment explanation
Indices: 1611361--1611417 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
1611351 AATTTAAATC
* * * *
1611361 AAATCAAATAAAAAGTAATAATTATCA
1 AAATCAAATAAAAAATAAAAATAATAA
1611388 AAAT-AAATAAATAAATAAAAATAATAA
1 AAATCAAATAAA-AAATAAAAATAATAA
1611415 AAA
1 AAA
1611418 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (27 bp):
AAATCAAATAAAAAATAAAAATAATAA
Found at i:1615604 original size:20 final size:20
Alignment explanation
Indices: 1615579--1615654 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1615569 CAAAACTCAG
* *
1615579 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATTAAA
***
1615599 AATGTATCGATACAATTCCT
1 AATGTATCGATACAATTAAA
* *
1615619 TATGTATCGATACATTTAAA
1 AATGTATCGATACAATTAAA
1615639 AATGTATCGATACAAT
1 AATGTATCGATACAAT
1615655 ATCCTTCCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACAATTAAA
Found at i:1615642 original size:40 final size:41
Alignment explanation
Indices: 1615580--1615660 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 41
1615570 AAAACTCAGA
*
1615580 ATGTATCGATACAATGAGAAATGTATCGATACAAT-TCCTT
1 ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
* *
1615620 ATGTATCGATACATTTAAAAATGTATCGATACAATATCCTT
1 ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
1615661 CCAGAATCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 32 0.86
41 5 0.14
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (41 bp):
ATGTATCGATACAATGAAAAATGTATCGATACAATATCCTT
Found at i:1615751 original size:21 final size:21
Alignment explanation
Indices: 1615698--1615752 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1615688 TATATTTTAG
1615698 AATGTATCGATACATTCACTT
1 AATGTATCGATACATTCACTT
*
1615719 -ATGTATCAATACATTGC-CTT
1 AATGTATCGATACATT-CACTT
*
1615739 AATGTATTGATACA
1 AATGTATCGATACA
1615753 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTCACTT
Found at i:1618201 original size:13 final size:13
Alignment explanation
Indices: 1618183--1618208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1618173 CAATTTTTTG
1618183 TGTATCGATACAT
1 TGTATCGATACAT
1618196 TGTATCGATACAT
1 TGTATCGATACAT
1618209 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1622349 original size:20 final size:21
Alignment explanation
Indices: 1622324--1622380 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
1622314 AAAAACCCAG
1622324 AATGTATCGATACAATGA-GA
1 AATGTATCGATACAATGAGGA
1622344 AATGTATCGATACAATGAGGA
1 AATGTATCGATACAATGAGGA
1622365 AGCATGTATCGATACA
1 A--ATGTATCGATACA
1622381 TTTACTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 18 0.53
21 3 0.09
23 13 0.38
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (21 bp):
AATGTATCGATACAATGAGGA
Found at i:1623199 original size:20 final size:19
Alignment explanation
Indices: 1623135--1623201 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
1623125 TTTTACCCAG
* *
1623135 ATGTATCAATATAGTTTTTA
1 ATGTATCGATACA-TTTTTA
* *
1623155 ATGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTTA
*
1623175 GTGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTT-A
1623195 ATGTATC
1 ATGTATC
1623202 AATGCATTCT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.92
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTTA
Found at i:1623967 original size:15 final size:15
Alignment explanation
Indices: 1623947--1623982 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1623937 TGATACATTC
*
1623947 ATTTTCTGTTTTGTT
1 ATTTTCTGTTCTGTT
1623962 ATTTTCTGTTCTGTT
1 ATTTTCTGTTCTGTT
1623977 ATTTTC
1 ATTTTC
1623983 ATCCTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.69
Consensus pattern (15 bp):
ATTTTCTGTTCTGTT
Found at i:1625239 original size:27 final size:26
Alignment explanation
Indices: 1625201--1625251 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
1625191 TTTGATTATC
1625201 GGGGATACTCCAACCCCGCTCTTTTGA
1 GGGGATACTCCAACCCCGCT-TTTTGA
1625228 GGGGATACTCCAACCCCGCTTTTT
1 GGGGATACTCCAACCCCGCTTTTT
1625252 CTTCAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGCTTTTTGA
Found at i:1630608 original size:98 final size:99
Alignment explanation
Indices: 1630498--1630693 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 99
1630488 GCTAAGGCCT
*
1630498 TCCTCAATCAATATCAACACATCTTAGATTGGGCCCCGAATCGCCTTACTCTTATGAATATAGAG
1 TCCTCAATCAATACCAACACATCTTAGATTGGGCCCCGAATCGCCTTACTCTTATGAATATAGAG
*
1630563 AAGAAACCCA-CAAGAGTTTTAGGCAATATTCCA
66 AACAAACCCACCAAGAGTTTTAGGCAATATTCCA
1630596 TCCTCAATCAATACCAACACATCTTAGATTGGGCCCCGAATCGCCTTACTCTTATGAATATAGAG
1 TCCTCAATCAATACCAACACATCTTAGATTGGGCCCCGAATCGCCTTACTCTTATGAATATAGAG
1630661 AACAAACCCACCAAGAGTTTTAGGCAATATTCC
66 AACAAACCCACCAAGAGTTTTAGGCAATATTCC
1630694 CAACGATGGA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 73 0.77
99 22 0.23
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (99 bp):
TCCTCAATCAATACCAACACATCTTAGATTGGGCCCCGAATCGCCTTACTCTTATGAATATAGAG
AACAAACCCACCAAGAGTTTTAGGCAATATTCCA
Found at i:1636997 original size:16 final size:15
Alignment explanation
Indices: 1636986--1637021 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
1636976 ATAAAAGAAC
1636986 AAAAAAAAAAAACAA
1 AAAAAAAAAAAACAA
1637001 AAGAAAAAAAAAACAA
1 AA-AAAAAAAAAACAA
1637017 AAAAA
1 AAAAA
1637022 GAGGGGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.92, C:0.06, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAACAA
Found at i:1637010 original size:19 final size:19
Alignment explanation
Indices: 1636978--1637023 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
1636968 CATCATTCAT
*
1636978 AAAAGAACAAAAAAAAAAAA
1 AAAAGAA-AAAAAAAACAAA
1636998 CAAAAGAAAAAAAAAACAAA
1 -AAAAGAAAAAAAAAACAAA
1637018 AAAAGA
1 AAAAGA
1637024 GGGGTCTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAAACAAA
Found at i:1638296 original size:13 final size:13
Alignment explanation
Indices: 1638278--1638303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1638268 ATATTGCACA
1638278 GTATCGATACATT
1 GTATCGATACATT
1638291 GTATCGATACATT
1 GTATCGATACATT
1638304 ACCAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1638315 original size:20 final size:19
Alignment explanation
Indices: 1638290--1638342 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
1638280 ATCGATACAT
1638290 TGTATCGATACATTACCA-AA
1 TGTATCGATACATTA--AGAA
1638310 TGTATCGATACTTATTAAGAA
1 TGTATCGATAC--ATTAAGAA
1638331 TGTATCGATACA
1 TGTATCGATACA
1638343 GGTGATTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 13 0.43
22 4 0.13
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATTAAGAA
Found at i:1638420 original size:13 final size:13
Alignment explanation
Indices: 1638402--1638427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1638392 TACACACAAG
1638402 ATGTATCGATACA
1 ATGTATCGATACA
1638415 ATGTATCGATACA
1 ATGTATCGATACA
1638428 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1638444 original size:33 final size:32
Alignment explanation
Indices: 1638384--1638447 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1638374 CTTAACTATT
*
1638384 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1638416 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1638448 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1644536 original size:20 final size:20
Alignment explanation
Indices: 1644511--1644576 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1644501 AAAACTCAAA
1644511 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
1644531 TGTATCGATACAG-------
1 TGTATCGATACAGCATTCTC
1644544 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
1644564 TGTATCGATACAG
1 TGTATCGATACAG
1644577 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAGCATTCTC
Found at i:1644549 original size:13 final size:13
Alignment explanation
Indices: 1644531--1644588 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1644521 CAGCATTCTC
1644531 TGTATCGATACAG
1 TGTATCGATACAG
1644544 TGTATCGATACAG
1 TGTATCGATACAG
**
1644557 CAT-TC--T-C--
1 TGTATCGATACAG
1644564 TGTATCGATACAG
1 TGTATCGATACAG
1644577 TGTATCGATACA
1 TGTATCGATACA
1644589 AAGGGTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
7 1 0.03
8 2 0.06
9 1 0.03
10 2 0.06
11 1 0.03
12 2 0.06
13 26 0.74
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1644553 original size:33 final size:33
Alignment explanation
Indices: 1644511--1644588 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
1644501 AAAACTCAAA
1644511 TGTATCGATACAGCATTCTCTGTATCGATACAG
1 TGTATCGATACAGCATTCTCTGTATCGATACAG
1644544 TGTATCGATACAGCATTCTCTGTATCGATACAG
1 TGTATCGATACAGCATTCTCTGTATCGATACAG
1644577 TGTATCGATACA
1 TGTATCGATACA
1644589 AAGGGTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (33 bp):
TGTATCGATACAGCATTCTCTGTATCGATACAG
Found at i:1646481 original size:20 final size:22
Alignment explanation
Indices: 1646447--1646489 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
1646437 AGATATTGTT
1646447 AAATTGTTTTATTAAGGGGGAG
1 AAATTGTTTTATTAAGGGGGAG
1646469 AAATT-TTTT-TTAAGGGGGAG
1 AAATTGTTTTATTAAGGGGGAG
1646489 A
1 A
1646490 CAAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 4 0.19
22 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (22 bp):
AAATTGTTTTATTAAGGGGGAG
Found at i:1647194 original size:20 final size:20
Alignment explanation
Indices: 1647151--1647202 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1647141 CTTAACTGTT
*
1647151 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
1647170 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1647190 TGTATCGATACAT
1 TGTATCGATACAT
1647203 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1648098 original size:13 final size:13
Alignment explanation
Indices: 1648080--1648105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1648070 TACACCAAGT
1648080 ATGTATCGATACA
1 ATGTATCGATACA
1648093 ATGTATCGATACA
1 ATGTATCGATACA
1648106 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1648103 original size:32 final size:33
Alignment explanation
Indices: 1648062--1648125 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1648052 TAGCCAAACT
* **
1648062 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1648094 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1648126 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1648626 original size:34 final size:35
Alignment explanation
Indices: 1648563--1648629 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1648553 CTAAGTGATT
1648563 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1648599 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1648630 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1651811 original size:13 final size:13
Alignment explanation
Indices: 1651793--1651817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1651783 TTTTCCAGAT
1651793 TGTATCGATACAA
1 TGTATCGATACAA
1651806 TGTATCGATACA
1 TGTATCGATACA
1651818 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1653699 original size:13 final size:13
Alignment explanation
Indices: 1653681--1653706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1653671 TACACCAAGT
1653681 ATGTATCGATACA
1 ATGTATCGATACA
1653694 ATGTATCGATACA
1 ATGTATCGATACA
1653707 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1653704 original size:32 final size:33
Alignment explanation
Indices: 1653663--1653726 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1653653 TAGCCAAACT
* **
1653663 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1653695 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1653727 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1654227 original size:34 final size:35
Alignment explanation
Indices: 1654164--1654230 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1654154 CTAAGTGATT
1654164 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1654200 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1654231 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1655146 original size:28 final size:28
Alignment explanation
Indices: 1655066--1655278 Score: 234
Period size: 28 Copynumber: 7.5 Consensus size: 28
1655056 TACAACCCTT
*
1655066 TTTCAAAAGCCCACAAGTTAGTGGCACTCA
1 TTTC-AAAGCCCACAAGTTAGTGGCA-TCC
* *
1655096 TCTCAAAAGCCCACATGTTAGTGGCATCC
1 TTTC-AAAGCCCACAAGTTAGTGGCATCC
* * *
1655125 TTTCAAATCCCACAAGTCAGTGGTATCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
*
1655153 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTTAGTGGCATCC
*
1655180 TTTTCAAAGCCCACAAGTTAGTGGCA-CT
1 -TTTCAAAGCCCACAAGTTAGTGGCATCC
*
1655208 TTCTCAAAGCCCACAAGTCAGTGGCA-CC
1 TT-TCAAAGCCCACAAGTTAGTGGCATCC
* * *
1655236 ATTTCAAAGCCTATAAGTTAGTGGCATCT
1 -TTTCAAAGCCCACAAGTTAGTGGCATCC
*
1655265 TTTCAAAGCTCACA
1 TTTCAAAGCCCACA
1655279 TATGTCGGTG
Statistics
Matches: 158, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
27 4 0.03
28 122 0.77
29 8 0.05
30 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTTAGTGGCATCC
Found at i:1655175 original size:56 final size:56
Alignment explanation
Indices: 1655066--1655311 Score: 262
Period size: 56 Copynumber: 4.2 Consensus size: 56
1655056 TACAACCCTT
* * * *
1655066 TTTCAAAAGCCCACAAGTTAGTGGCACTCATCTCAAAAGCCCACATGTTAGTGGCATCC-
1 TTTC-AAAGCCCACAAGTTAGTGGCA-TCTTTTC-AAAGCCCACAAGTCAGTGGCA-CCA
* * * * *
1655125 TTTCAAATCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCA
1655181 TTTCAAAGCCCACAAGTTAGTGGCA-CTTTCTCAAAGCCCACAAGTCAGTGGCACCA
1 TTTCAAAGCCCACAAGTTAGTGGCATCTTT-TCAAAGCCCACAAGTCAGTGGCACCA
* * * * *
1655237 TTTCAAAGCCTATAAGTTAGTGGCATCTTTTCAAAGCTCACATATGTCGGTGGCAACCC
1 TTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACA-A-GTCAGTGGC-ACCA
1655296 TTCTCAAAAGCCCACA
1 TT-TC-AAAGCCCACA
1655312 CAAGTTGGTG
Statistics
Matches: 160, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
55 5 0.03
56 100 0.62
57 10 0.06
58 26 0.16
59 9 0.06
60 2 0.01
61 8 0.05
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCA
Found at i:1655215 original size:84 final size:84
Alignment explanation
Indices: 1655066--1655278 Score: 268
Period size: 84 Copynumber: 2.5 Consensus size: 84
1655056 TACAACCCTT
* * *
1655066 TTTCAAAAGCCCACAAGTTAGTGGCACTCATCTCAAAAGCCCACATGTTAGTGGCATCCTTTCAA
1 TTTC-AAAGCCCACAAGTTAGTGGCAC-CTTTTC-AAAGCCCACAAGTTAGTGGCATCCTTTCAA
* *
1655131 ATCCCACAAGTCAGTGGTATCC-
63 AGCCCACAAGTCAGTGGCA-CCA
* *
1655153 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCA-CTTTCTCAAAG
1 TTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATCCTT-TCAAAG
1655217 CCCACAAGTCAGTGGCACCA
65 CCCACAAGTCAGTGGCACCA
* * * *
1655237 TTTCAAAGCCTATAAGTTAGTGGCATCTTTTCAAAGCTCACA
1 TTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACA
1655279 TATGTCGGTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
83 5 0.04
84 78 0.70
85 4 0.04
86 21 0.19
87 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (84 bp):
TTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGC
CCACAAGTCAGTGGCACCA
Found at i:1655330 original size:32 final size:33
Alignment explanation
Indices: 1655285--1655364 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 33
1655275 CACATATGTC
1655285 GGTGGCAACCCTTCTCAAAAGCCCACACAAGTT
1 GGTGGCAACCCTTCTCAAAAGCCCACACAAGTT
* * *
1655318 GGTGGCAA-CCTTCTCTAAAGCCTACAGAAGTT
1 GGTGGCAACCCTTCTCAAAAGCCCACACAAGTT
1655350 GGTGGCAACCCTTCT
1 GGTGGCAACCCTTCT
1655365 AAACCCAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (33 bp):
GGTGGCAACCCTTCTCAAAAGCCCACACAAGTT
Found at i:1656187 original size:51 final size:51
Alignment explanation
Indices: 1656076--1656190 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
1656066 TGAGCAGTAC
1656076 ATGTATCGATACA-TTATGTTTTTTACCCAGATGTATCGATGCATTTTTCA
1 ATGTATCGATACATTTATGTTTTTTACCCAGATGTATCGATGCATTTTTCA
* * *
1656126 ATATAGCGATACATTCTAT-TTTTTTACCTAGATGTATCGA-GACATTTTTCA
1 ATGTATCGATACATT-TATGTTTTTTACCCAGATGTATCGATG-CATTTTTCA
*
1656177 ATGTCTCGATACAT
1 ATGTATCGATACAT
1656191 CTAGTTAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 12 0.21
51 41 0.73
52 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTTATGTTTTTTACCCAGATGTATCGATGCATTTTTCA
Found at i:1664124 original size:32 final size:33
Alignment explanation
Indices: 1664047--1664127 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 33
1664037 CATTTAATAG
*
1664047 TGTATCGATACATTTGGGCAAATTTGCCTGCATAAAA
1 TGTATCGATACATCTGGGCAAATTTGCCTGC----AA
1664084 TGTATCGATACATCTGGGCAAATTTGCCTGC-A
1 TGTATCGATACATCTGGGCAAATTTGCCTGCAA
1664116 TGTATCGATACA
1 TGTATCGATACA
1664128 AAGATCAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 13 0.30
37 30 0.70
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATCTGGGCAAATTTGCCTGCAA
Found at i:1664154 original size:13 final size:13
Alignment explanation
Indices: 1664136--1664160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1664126 CAAAGATCAG
1664136 TGTATCGATACAA
1 TGTATCGATACAA
1664149 TGTATCGATACA
1 TGTATCGATACA
1664161 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1664227 original size:19 final size:18
Alignment explanation
Indices: 1664203--1664299 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1664193 TAGCTTAAAT
1664203 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1664222 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1664235 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1664254 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1664267 TGTATCGA-ACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1664286 TGTATCGATACAAA
1 TGTATCGATACAAA
1664300 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.03
13 19 0.30
14 2 0.03
15 1 0.02
16 3 0.05
18 2 0.03
19 31 0.48
20 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1664240 original size:13 final size:13
Alignment explanation
Indices: 1664222--1664274 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 13
1664212 ACAAAACTTA
1664222 TGTATCGATACAT
1 TGTATCGATACAT
1664235 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1664253 ATGTATCGATACAT
1 -TGTATCGATACAT
1664267 TGTATCGA
1 TGTATCGA
1664275 ACAACACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 17 0.50
14 1 0.03
16 6 0.18
18 1 0.03
19 9 0.26
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1664242 original size:32 final size:32
Alignment explanation
Indices: 1664201--1664297 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
1664191 AGTAGCTTAA
*
1664201 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1664233 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1664265 ATTGTATCGA-ACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1664297 A
1 A
1664298 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 7 0.11
32 56 0.89
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1668010 original size:20 final size:19
Alignment explanation
Indices: 1667985--1668079 Score: 109
Period size: 20 Copynumber: 4.8 Consensus size: 19
1667975 TTTACCCAGA
*
1667985 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
*
1668005 TGTATCGATACATGGCTCAT
1 TGTATCGATACAT-TCTCAT
1668025 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* * *
1668045 TATATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
1668065 TGTATCGATACATTC
1 TGTATCGATACATTC
1668080 AAGCATTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 62 0.97
21 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:1670511 original size:51 final size:51
Alignment explanation
Indices: 1670451--1670568 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
1670441 GTTTTCGAGA
* * * * *
1670451 GGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAGTTGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATAGG
* * *
1670502 GGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAATAGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATAGG
1670553 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1670569 TTATTTCTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATAGG
Found at i:1670621 original size:130 final size:127
Alignment explanation
Indices: 1670396--1670643 Score: 286
Period size: 130 Copynumber: 1.9 Consensus size: 127
1670386 TCTCGGTTTC
* * * * * *
1670396 ATTTCCAAAGCATCAATTTTTCATCGGGGATACTCCAACCCTGTTGTTTTCGAGAGGATACTCCA
1 ATTTCCAAAACACCAATTTTTCATAGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCCA
** * * *
1670461 ACCCCGATTTTATTTCTAAAATACCAATTTTCCATAGTTGGGGATACTCCAACTCTGATTTT
66 ACCCCGACCTTATTTCTAAAATACCAATTTTCCACAATCGGGGATACTCCAACTCTGATTTT
1670523 ATTTCCAAAACACCAATTTTTCACAATAGGGGATACTCCAACCCCGTTA-TTTCTAAG-GGAATA
1 ATTTCCAAAACACCAATTTTT--C-ATAGGGGATACTCCAACCCCGTTATTTTC-AAGAGG-ATA
* * * *
1670586 CTTCAACCCCGACCTTATTTCT-AAATCATCGATTTTTCACAATCGGGGATACTCCAAC
61 CTCCAACCCCGACCTTATTTCTAAAAT-ACCAATTTTCCACAATCGGGGATACTCCAAC
1670644 CCCATTATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
127 19 0.19
129 11 0.11
130 70 0.70
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (127 bp):
ATTTCCAAAACACCAATTTTTCATAGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCCA
ACCCCGACCTTATTTCTAAAATACCAATTTTCCACAATCGGGGATACTCCAACTCTGATTTT
Found at i:1670778 original size:78 final size:79
Alignment explanation
Indices: 1670500--1670806 Score: 318
Period size: 79 Copynumber: 3.9 Consensus size: 79
1670490 TTCCATAGTT
* * *
1670500 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTTCACAAT-AGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCA-GGGATACTCCAA
1670564 CCCCGTTATTTCTAA
65 CCCCGTTATTTCTAA
* * ** * * * *
1670579 GGGAATACTTCAACCCCGACCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
*
1670644 CCCATTATTT-TCAA
66 CCCGTTATTTCT-AA
* * ** *
1670658 GGGGATACTTCAACCCCG-TTTTCATTT-TCAAAATACTGATTTTT-ATAATCAGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTT-ATTTCT-AAAACACCAATTTTTCACAATCAGGGATACTCCA
* *
1670720 ACCCTGTTATTTCTGA
64 ACCCCGTTATTTCTAA
** * * * *
1670736 GGGGATACTCCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATCGGGGATACTCCAGC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
1670801 CCCGTT
66 CCCGTT
1670807 GTTATCTCCA
Statistics
Matches: 186, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
78 61 0.33
79 125 0.67
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAAC
CCCGTTATTTCTAA
Found at i:1679452 original size:20 final size:20
Alignment explanation
Indices: 1679427--1679475 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1679417 ACCAATTGTG
*
1679427 TCGATACAATTCACCATGTA
1 TCGATACAATTCAACATGTA
1679447 TCGATACAATTCAACATGTA
1 TCGATACAATTCAACATGTA
*
1679467 TTGATACAA
1 TCGATACAA
1679476 AGTGAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (20 bp):
TCGATACAATTCAACATGTA
Done.