Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 26
Found at i:1443270 original size:26 final size:26
Alignment explanation
Indices: 1443240--1443291 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1443230 TAATGCACCG
*
1443240 AAAGTGCATTAGTTGGCAACAATGAT
1 AAAGTGCATTAGTTAGCAACAATGAT
*
1443266 AAAGTGCATTAGTTAGCAGCAATGAT
1 AAAGTGCATTAGTTAGCAACAATGAT
1443292 TCATCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAGTGCATTAGTTAGCAACAATGAT
Found at i:1444514 original size:10 final size:10
Alignment explanation
Indices: 1444499--1444535 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
1444489 AATTTTTTAA
1444499 AAAAATATAT
1 AAAAATATAT
1444509 AAAAATATAT
1 AAAAATATAT
1444519 AAAAATCATAAT
1 AAAAAT-AT-AT
1444531 AAAAA
1 AAAAA
1444536 AAATTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.64
11 2 0.08
12 7 0.28
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATATAT
Found at i:1446679 original size:23 final size:22
Alignment explanation
Indices: 1446653--1446703 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
1446643 TTTTGGCGAC
*
1446653 ATATTAATTTATATTATATTTAA
1 ATATTAATTTAGATTAT-TTTAA
**
1446676 ATATTTCTTTAGATTATTTTAA
1 ATATTAATTTAGATTATTTTAA
1446698 ATATTA
1 ATATTA
1446704 TTTTTTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTAATTTAGATTATTTTAA
Found at i:1446838 original size:2 final size:2
Alignment explanation
Indices: 1446831--1446864 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1446821 ATTTAGTGAC
1446831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1446865 GTGGTGGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448546 original size:27 final size:25
Alignment explanation
Indices: 1448503--1448552 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
1448493 TCACACATGT
1448503 TTTTGTTGTGTATACATTATTTTTCA
1 TTTTGTTGTGTATACATT-TTTTTCA
1448529 TTTT-TTGTGTCATCACATTTTTTT
1 TTTTGTTGTGT-AT-ACATTTTTTT
1448553 AATTCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.64
Consensus pattern (25 bp):
TTTTGTTGTGTATACATTTTTTTCA
Found at i:1451977 original size:25 final size:28
Alignment explanation
Indices: 1451943--1452017 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 28
1451933 AAACTCGTCT
1451943 AGTTTTCATTCTCTTATTTTTG-T-T-A
1 AGTTTTCATTCTCTTATTTTTGTTGTAA
1451968 AGTTTTCATTCTCTTATTTTTGTTGTCAA
1 AGTTTTCATTCTCTTATTTTTGTTGT-AA
*
1451997 AGTTTTTATTCTCTTATTTTT
1 AGTTTTCATTCTCTTATTTTT
1452018 ATTTACTTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 22 0.49
26 1 0.02
27 1 0.02
29 21 0.47
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (28 bp):
AGTTTTCATTCTCTTATTTTTGTTGTAA
Found at i:1453675 original size:23 final size:23
Alignment explanation
Indices: 1453639--1453704 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1453629 GTCGAGGGTT
1453639 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* *
1453662 CTATGTCGTACTTCGGTG-CAAAC
1 CTATGTGGTCCTTCGG-GACAAAC
1453685 CTATGTGGTCCTTCGGGACA
1 CTATGTGGTCCTTCGGGACA
1453705 GTTATGTGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:1453726 original size:44 final size:45
Alignment explanation
Indices: 1453639--1453727 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
1453629 GTCGAGGGTT
*
1453639 CTATGTGGTCCTTCGGGACAAACCTATGTCGTACTTCGGTGCAAAC
1 CTATGTGGTCCTTCGGGAC-AACCTATGTCGCACTTCGGTGCAAAC
** *
1453685 CTATGTGGTCCTTCGGGAC-AGTTATGTGGCACTTCGGTGCAAA
1 CTATGTGGTCCTTCGGGACAACCTATGTCGCACTTCGGTGCAAA
1453728 TTACGAGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 20 0.51
46 19 0.49
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (45 bp):
CTATGTGGTCCTTCGGGACAACCTATGTCGCACTTCGGTGCAAAC
Found at i:1454765 original size:53 final size:53
Alignment explanation
Indices: 1454685--1454795 Score: 204
Period size: 53 Copynumber: 2.1 Consensus size: 53
1454675 GACTCGAGAT
*
1454685 TGATGTAGTTGTTTATAGTGATTGTGGTGTTTAAAACTTAGATGAAATGATAG
1 TGATGTAGTCGTTTATAGTGATTGTGGTGTTTAAAACTTAGATGAAATGATAG
*
1454738 TGATGTAGTCGTTTATAGTGATTGTGGTGTTTAAAACTTGGATGAAATGATAG
1 TGATGTAGTCGTTTATAGTGATTGTGGTGTTTAAAACTTAGATGAAATGATAG
1454791 TGATG
1 TGATG
1454796 AATGGTTCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.29, C:0.03, G:0.28, T:0.41
Consensus pattern (53 bp):
TGATGTAGTCGTTTATAGTGATTGTGGTGTTTAAAACTTAGATGAAATGATAG
Found at i:1457084 original size:79 final size:79
Alignment explanation
Indices: 1456919--1457409 Score: 378
Period size: 81 Copynumber: 6.1 Consensus size: 79
1456909 TTGTTTGTAA
* * * *
1456919 GAAAACACCGCTAGAAACACGTACTTTAGTGGCGTTTATGTAAAAAAATGCCACTATAGCCAGAT
1 GAAAACGCCGCTAAAAACAC--ACTTTAGTGGCGTTTATGTAAAAACA--CCGCTATAGCCAGAT
* *
1456984 ATATAGTGACGTTTTTAT
62 ATATAGTGGCGTTTTTGT
* * * * *
1457002 GAAAACGCCGCTAAAAACACACTTTAATAGCGTTTATGTAAAAACACCGTTATATCCAGATATGT
1 GAAAACGCCGCTAAAAACACACTTTAGTGGCGTTTATGTAAAAACACCGCTATAGCCAGATATAT
*
1457067 CGTGGCGTTTTTGT
66 AGTGGCGTTTTTGT
* * * * *
1457081 GAAAATGCCGCTAAAAACACACACTTTTGT-GCATTTATGTAAACAACGCTGCTATAGCCAGATA
1 GAAAACGCCGCT-AAAA-ACACACTTTAGTGGCGTTTATGTAAA-AACACCGCTATAGCCAGATA
* * *
1457145 TATAGTGGTGTGTATGT
63 TATAGTGGCGTTTTTGT
* *** **
1457162 GAAAACGCCGCTAAAAAGGCATACTTTAGTGGCGTTTATGTAAAAATGTCGCTATAGATAGATAT
1 GAAAACGCCGCTAAAAA--CACACTTTAGTGGCGTTTATGTAAAAACACCGCTATAGCCAGATAT
* * *
1457227 ATAGTAGCATTTTTTT
64 ATAGTGGCGTTTTTGT
* * ** ** **
1457243 GAAAACGTCGTTAAAAACGTGTACTTTAGTGGCGTTTATGTAAAAATGCTACTATAGCCAG--AT
1 GAAAACGCCGCTAAAAAC--ACACTTTAGTGGCGTTTATGTAAAAACACCGCTATAGCCAGATAT
*
1457306 ATAGTGGCATTTTTGT
64 ATAGTGGCGTTTTTGT
* * * * * ** *
1457322 GTAAACGTCACTAAAGTACGAGTACTTTAGTGGAATTTATGTTAAAAACACCGCAATAGCCTA-A
1 GAAAACGCCGCTAAA-AAC-A-CACTTTAGTGGCGTTTATG-TAAAAACACCGCTATAGCC-AGA
*
1457386 TATATAGTGGCGTTTATGT
61 TATATAGTGGCGTTTTTGT
*
1457405 TAAAA
1 GAAAA
1457410 ATGTCACTAT
Statistics
Matches: 327, Mismatches: 67, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
79 67 0.20
80 39 0.12
81 171 0.52
82 13 0.04
83 37 0.11
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (79 bp):
GAAAACGCCGCTAAAAACACACTTTAGTGGCGTTTATGTAAAAACACCGCTATAGCCAGATATAT
AGTGGCGTTTTTGT
Found at i:1457215 original size:41 final size:39
Alignment explanation
Indices: 1457147--1457288 Score: 97
Period size: 41 Copynumber: 3.5 Consensus size: 39
1457137 GCCAGATATA
* * * *
1457147 TAGTGGTGTGTATGTGAAAACGCCGCTAAAAAGGCATACTT
1 TAGTGGCGTTTATGTAAAAACGTCGCTAAAAA-G-ATACTT
* * *
1457188 TAGTGGCGTTTATGTAAAAATGTCGCTATAGATAGATA-TA
1 TAGTGGCGTTTATGTAAAAACGTCGCTA-A-AAAGATACTT
* * * * * * *
1457228 TAGTAGCATTTTTTTGAAAACGTCGTTAAAAACGTGTACTT
1 TAGTGGCGTTTATGTAAAAACGTCGCTAAAAA-G-ATACTT
1457269 TAGTGGCGTTTATGTAAAAA
1 TAGTGGCGTTTATGTAAAAA
1457289 TGCTACTATA
Statistics
Matches: 74, Mismatches: 22, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 24 0.32
41 42 0.57
42 2 0.03
43 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (39 bp):
TAGTGGCGTTTATGTAAAAACGTCGCTAAAAAGATACTT
Found at i:1461328 original size:22 final size:21
Alignment explanation
Indices: 1461248--1461327 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1461238 TGATTTATTA
*
1461248 TTATGGATTTCAAGTTGGTTG
1 TTATAGATTTCAAGTTGGTTG
1461269 TTATAGATTTCAAGTTGGTTG
1 TTATAGATTTCAAGTTGGTTG
*
1461290 TTATAGATTTCAAGTTTGTTTG
1 TTATAGATTTCAAG-TTGGTTG
* *
1461312 TTATGGATGTCAAGTT
1 TTATAGATTTCAAGTT
1461328 TATTGGATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 36 0.67
22 18 0.33
ACGTcount: A:0.23, C:0.05, G:0.24, T:0.49
Consensus pattern (21 bp):
TTATAGATTTCAAGTTGGTTG
Found at i:1464699 original size:82 final size:82
Alignment explanation
Indices: 1464613--1464809 Score: 220
Period size: 71 Copynumber: 2.5 Consensus size: 82
1464603 TTATTAGAGT
* *
1464613 TTTTTTATTAATCCTAGAGAATTTAAAGAAATGACACACGTTAAAAGTTAATCTTAAC-AACAAC
1 TTTTTAATTAATCCTAGAGAATTTAAAGAAATGACACACGTCAAAAGTTAATCTTAACTAA-AAC
*
1464677 ACAACAATTGTTCAGAAC
65 ACAACAATTGATCAGAAC
* * **
1464695 TTTTTAATAAATCCT--AG-------AG--ATGACACGCGTCATGAGTTAATCTTAACTAAAACA
1 TTTTTAATTAATCCTAGAGAATTTAAAGAAATGACACACGTCAAAAGTTAATCTTAACTAAAACA
1464749 CAACAATTGATCAGAAC
66 CAACAATTGATCAGAAC
* *
1464766 TTTTTGATTAATCCTAGAGAATTTAAAGAAATGACACGCGTCAA
1 TTTTTAATTAATCCTAGAGAATTTAAAGAAATGACACACGTCAA
1464810 GAATTGATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
71 57 0.61
72 2 0.02
73 4 0.04
80 4 0.04
82 26 0.28
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (82 bp):
TTTTTAATTAATCCTAGAGAATTTAAAGAAATGACACACGTCAAAAGTTAATCTTAACTAAAACA
CAACAATTGATCAGAAC
Found at i:1466192 original size:31 final size:31
Alignment explanation
Indices: 1466157--1466226 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1466147 TAATGAACAT
* * *
1466157 TTTATAACAGTTTGATGAATCTAATGATTAA
1 TTTATAACACTTTGATAAATCTAATAATTAA
* * *
1466188 TTTATGACACTTTGATAAATTTAATAATTAT
1 TTTATAACACTTTGATAAATCTAATAATTAA
1466219 TTTATAAC
1 TTTATAAC
1466227 TTTTAAAAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (31 bp):
TTTATAACACTTTGATAAATCTAATAATTAA
Found at i:1467496 original size:18 final size:18
Alignment explanation
Indices: 1467475--1467521 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1467465 CCAATTAACC
*
1467475 TCAGCGTCCCACTTTGGT
1 TCAGCATCCCACTTTGGT
1467493 TCAGCATCCCACTTTGGT
1 TCAGCATCCCACTTTGGT
1467511 TCAGCATCCCA
1 TCAGCATCCCA
1467522 AATTGGACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.36, G:0.17, T:0.30
Consensus pattern (18 bp):
TCAGCATCCCACTTTGGT
Found at i:1467527 original size:18 final size:18
Alignment explanation
Indices: 1467488--1467527 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1467478 GCGTCCCACT
**
1467488 TTGGTTCAGCATCCCACT
1 TTGGTTCAGCATCCCAAA
1467506 TTGGTTCAGCATCCCAAA
1 TTGGTTCAGCATCCCAAA
1467524 TTGG
1 TTGG
1467528 ACCTGGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (18 bp):
TTGGTTCAGCATCCCAAA
Found at i:1469525 original size:29 final size:29
Alignment explanation
Indices: 1469483--1469542 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1469473 CATTTAGAAC
*
1469483 CTAAGAAATTTACCAAGATGAGATAACTG
1 CTAAGAAATTTACCAAGATGAGATAAATG
*
1469512 CTAAGAAATTTACCAAGATGAGGTAAATG
1 CTAAGAAATTTACCAAGATGAGATAAATG
1469541 CT
1 CT
1469543 TAATGGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (29 bp):
CTAAGAAATTTACCAAGATGAGATAAATG
Found at i:1485956 original size:24 final size:25
Alignment explanation
Indices: 1485929--1486001 Score: 89
Period size: 24 Copynumber: 3.0 Consensus size: 25
1485919 TTAAATGGAG
* *
1485929 ATATTAGATATTAGAACAGAAA-TC
1 ATATAAGATATCAGAACAGAAATTC
1485953 ATATAAGATATCAGAACA-AAATTC
1 ATATAAGATATCAGAACAGAAATTC
* *
1485977 AGATAAGAAATCAGAACAG-AATTC
1 ATATAAGATATCAGAACAGAAATTC
1486001 A
1 A
1486002 AATCGGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.07
24 40 0.93
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.23
Consensus pattern (25 bp):
ATATAAGATATCAGAACAGAAATTC
Found at i:1489957 original size:21 final size:22
Alignment explanation
Indices: 1489918--1489982 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
1489908 TCGTTATAAA
1489918 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1489940 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1489961 TACACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1489983 ATGTCCATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 20 0.49
22 21 0.51
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1490241 original size:30 final size:31
Alignment explanation
Indices: 1490200--1490259 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1490190 TAGACATAGT
*
1490200 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1490230 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1490260 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1490308 original size:28 final size:28
Alignment explanation
Indices: 1490273--1490342 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1490263 TTTTCTGCAT
**
1490273 ATTCATGTCATGTAATACATATAATA-TG
1 ATTCATGTCATGTAATACAT-TAATACAA
*
1490301 ATTCATGTCATGTAATACATTTATACAA
1 ATTCATGTCATGTAATACATTAATACAA
1490329 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1490343 TCATAATGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 4 0.11
28 34 0.89
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATTAATACAA
Found at i:1490728 original size:21 final size:21
Alignment explanation
Indices: 1490702--1490744 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1490692 TATACGATGA
*
1490702 GGGGGTATCGGTTCCCCCCTT
1 GGGGGTATCGATTCCCCCCTT
*
1490723 GGGGGTATCGATTCCCCTCTT
1 GGGGGTATCGATTCCCCCCTT
1490744 G
1 G
1490745 CATTCTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.30, G:0.33, T:0.30
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCCTT
Found at i:1490795 original size:21 final size:21
Alignment explanation
Indices: 1490765--1490807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1490755 ATTCATTTCG
* *
1490765 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1490786 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1490807 T
1 T
1490808 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1490796 original size:67 final size:65
Alignment explanation
Indices: 1490658--1490807 Score: 169
Period size: 67 Copynumber: 2.3 Consensus size: 65
1490648 CGTTTCCCCC
* *
1490658 TGGGTATCGATTCCCCTCAAGCATCTGAATTTCATATACGATGAGGGGGTATCGGTTCCCCCCTT
1 TGGGTATCGATTCCCCTCAAGCATCTGAAATTCATATACGATGAAGGGGTATCGGTT-CCCCCTT
1490723 G
65 G
* ** * *
1490724 GGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTGAAGGGGTATCGGTT-CCCCT
1 TGGGTATCGATTCCCCTCAAGCA-TCT-GAAATTCATATACGATGAAGGGGTATCGGTTCCCCCT
1490787 TG
64 TG
*
1490789 AATGGGTACCGATTCCCCT
1 --TGGGTATCGATTCCCCT
1490808 AACCCAGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
65 7 0.10
66 20 0.28
67 36 0.51
68 8 0.11
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (65 bp):
TGGGTATCGATTCCCCTCAAGCATCTGAAATTCATATACGATGAAGGGGTATCGGTTCCCCCTTG
Found at i:1496782 original size:22 final size:22
Alignment explanation
Indices: 1496765--1496831 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1496755 CTCGTATAAA
1496765 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1496787 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1496809 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1496831 T
1 T
1496832 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1497088 original size:30 final size:31
Alignment explanation
Indices: 1497047--1497106 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1497037 TAGACATAGT
*
1497047 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
1497077 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
1497107 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:1497162 original size:29 final size:29
Alignment explanation
Indices: 1497120--1497191 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1497110 TTTTCTGCAT
**
1497120 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1497149 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1497178 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1497192 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1497300 original size:18 final size:18
Alignment explanation
Indices: 1497277--1497316 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1497267 TATATTCATA
1497277 CTATGCATATGCACTCAC
1 CTATGCATATGCACTCAC
*
1497295 CTATGCTTATGCACTCAC
1 CTATGCATATGCACTCAC
1497313 CTAT
1 CTAT
1497317 ACTTCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.33
Consensus pattern (18 bp):
CTATGCATATGCACTCAC
Found at i:1497606 original size:21 final size:21
Alignment explanation
Indices: 1497580--1497622 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1497570 TATACGATGA
*
1497580 GGGGGTATCGGTTCCCCCCTT
1 GGGGGTATCGATTCCCCCCTT
*
1497601 GGGGGTATCGATTCCCCTCTT
1 GGGGGTATCGATTCCCCCCTT
1497622 G
1 G
1497623 CATTCTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.30, G:0.33, T:0.30
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCCTT
Found at i:1497663 original size:67 final size:68
Alignment explanation
Indices: 1497521--1497663 Score: 207
Period size: 68 Copynumber: 2.1 Consensus size: 68
1497511 TGGGGGAATT
* *
1497521 GGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGT
1 GGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAAGGGGT
1497586 ATC
66 ATC
* ** * * *
1497589 GGTTCCCCCCTTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTGAAGGGGT
1 GGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAAGGGGT
1497653 ATC
66 ATC
1497656 GGTTCCCC
1 GGTTCCCC
1497664 TTGAATGGGT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 22 0.33
68 45 0.67
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.30
Consensus pattern (68 bp):
GGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAAGGGGT
ATC
Found at i:1497673 original size:21 final size:21
Alignment explanation
Indices: 1497643--1497685 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1497633 ATTCATTTCG
* *
1497643 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1497664 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1497685 T
1 T
1497686 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1501855 original size:21 final size:20
Alignment explanation
Indices: 1501825--1501865 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1501815 AAATAAAATT
**
1501825 ATTTAAAATTATTAATGAAA
1 ATTTAAAATTAAAAATGAAA
1501845 ATTTAAAAATTAAAAATGAAA
1 ATTT-AAAATTAAAAATGAAA
1501866 GCAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTTAAAATTAAAAATGAAA
Found at i:1505434 original size:30 final size:28
Alignment explanation
Indices: 1505400--1505473 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1505390 GTTACATACG
* * *
1505400 TAATTGCATCAAGGAAAAAACTTAGGTACT
1 TAATTGCACCAAAGAAAAAA--TAGGTACC
* *
1505430 TAATTGAACCAAAGAAAAAATGGGTACC
1 TAATTGCACCAAAGAAAAAATAGGTACC
1505458 TAATTGCACCAAAGAA
1 TAATTGCACCAAAGAA
1505474 GTTAGGTACC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 21 0.55
30 17 0.45
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (28 bp):
TAATTGCACCAAAGAAAAAATAGGTACC
Found at i:1510917 original size:30 final size:29
Alignment explanation
Indices: 1510881--1510944 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
1510871 CCAAGTACTG
*
1510881 AAGTATTTTTTTTGTCAAAATAGGTACTTA
1 AAGTA-TTTTTTTGTCAAAATAGGTACATA
*
1510911 AAGTA-TTTTTTGTCAAAGTAGGTACATA
1 AAGTATTTTTTTGTCAAAATAGGTACATA
1510939 AAGTAT
1 AAGTAT
1510945 ATCATCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 26 0.84
30 5 0.16
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (29 bp):
AAGTATTTTTTTGTCAAAATAGGTACATA
Found at i:1510919 original size:28 final size:28
Alignment explanation
Indices: 1510888--1510944 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1510878 CTGAAGTATT
*
1510888 TTTTTTGTCAAAATAGGTACTTAAAGTA
1 TTTTTTGTCAAAATAGGTACATAAAGTA
*
1510916 TTTTTTGTCAAAGTAGGTACATAAAGTA
1 TTTTTTGTCAAAATAGGTACATAAAGTA
1510944 T
1 T
1510945 ATCATCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTTTGTCAAAATAGGTACATAAAGTA
Found at i:1521379 original size:2 final size:2
Alignment explanation
Indices: 1521372--1521418 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1521362 GTTGAACTTA
1521372 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
1521414 AT AT A
1 AT AT A
1521419 ATGTATTTAA
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:1521548 original size:28 final size:28
Alignment explanation
Indices: 1521517--1521570 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1521507 AATTTTAATT
*
1521517 ATTAATTAATTTAGTTTCTAGTTATTCG
1 ATTAATTAATTTAGTTTATAGTTATTCG
1521545 ATTAATTAATTTAGTTTATAGTTATT
1 ATTAATTAATTTAGTTTATAGTTATT
1521571 TAATCAACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (28 bp):
ATTAATTAATTTAGTTTATAGTTATTCG
Found at i:1522485 original size:20 final size:21
Alignment explanation
Indices: 1522460--1522508 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1522450 TTTTCCCAAT
*
1522460 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
1522480 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATTAAGAAAA
1522501 TCGCAATG
1 TCGCAATG
1522509 TGATACTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1522525 original size:20 final size:20
Alignment explanation
Indices: 1522500--1522614 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1522490 AATTGAGAAA
*
1522500 ATCGCAATGTGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1522520 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1522540 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1522561 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1522581 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1522601 TTCGCAACGCGATA
1 ATCGCAATGCGATA
1522615 ATATATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1522528 original size:61 final size:62
Alignment explanation
Indices: 1522460--1522628 Score: 148
Period size: 61 Copynumber: 2.8 Consensus size: 62
1522450 TTTTCCCAAT
* * * *
1522460 TCGCAATGCGAATAAGTA-AATCGCAACGCGA-ATTGAGAAAATCGCAATGTGATACTGACTA
1 TCGCAATGCGAATAAGTACAATCGCAACGCGATAAT-ACAAAATCGCAACGAGATACTGACTA
** * * *
1522521 TCGCAATGCG-ATACTTACTATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTT
1 TCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTA
* * ** ** * *
1522582 TCGCAACGCGATTCTG-ACTTTCGCAACGCGATAATATATAATCGCAA
1 TCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAA
1522629 TGCGATTTTC
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
60 5 0.06
61 79 0.91
62 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (62 bp):
TCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTA
Found at i:1522830 original size:22 final size:22
Alignment explanation
Indices: 1522802--1522845 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1522792 CACTCTCTCA
1522802 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1522824 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1522846 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1523162 original size:20 final size:20
Alignment explanation
Indices: 1523108--1523166 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1523098 GCGATTCTCT
**
1523108 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1523128 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1523148 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1523167 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1523357 original size:25 final size:24
Alignment explanation
Indices: 1523303--1523357 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1523293 TGTTTATTAT
* *
1523303 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1523327 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1523353 TGTTT
1 TGTTT
1523358 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1524507 original size:18 final size:18
Alignment explanation
Indices: 1524486--1524530 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1524476 TCCACTTCGG
*
1524486 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1524504 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1524522 GAGCCATCA
1 GAGCCATCA
1524531 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1524741 original size:21 final size:21
Alignment explanation
Indices: 1524696--1524742 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1524686 GTTAGGGGAG
* *
1524696 TTACGTGATGAGGTCAATGCC
1 TTACGTGAGGAGGTCAATACC
* *
1524717 TTACGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACC
1524738 TTACG
1 TTACG
1524743 CAAAGACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACC
Found at i:1525066 original size:19 final size:20
Alignment explanation
Indices: 1525012--1525067 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1525002 TAGTTTACTT
* *
1525012 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1525032 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1525052 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1525068 AAATCGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1525093 original size:33 final size:33
Alignment explanation
Indices: 1525051--1525137 Score: 140
Period size: 32 Copynumber: 2.7 Consensus size: 33
1525041 GGAAATGGCT
*
1525051 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1525084 ATCGCAATGCGAAATG-AAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1525116 ATCGCAACGCGAAATGAAAATC
1 ATCGCAATGCGAAATGAAAATC
1525138 ACAATGCGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 29 0.58
33 21 0.42
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1525119 original size:14 final size:14
Alignment explanation
Indices: 1525067--1525124 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1525057 ATGCGAAATG
* *
1525067 AAAATCGTAACGAC
1 AAAATCGCAACGAT
1525081 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
1525099 GAAATCGCAACGAT
1 AAAATCGCAACGAT
1525113 AAAATCGCAACG
1 AAAATCGCAACG
1525125 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:1525177 original size:14 final size:14
Alignment explanation
Indices: 1525158--1525248 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1525148 TTGTGTTTCG
1525158 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1525172 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1525188 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1525204 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
1525221 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
1525237 CGTTGCGATTTT
1 CGTTGCGATTTT
1525249 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 28 0.45
15 3 0.05
16 10 0.16
17 2 0.03
18 12 0.19
19 7 0.11
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1525228 original size:33 final size:33
Alignment explanation
Indices: 1525153--1525264 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
1525143 GCGATTTGTG
*
1525153 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1525185 TTTCGTATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1525218 TTTCACATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1525251 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1525265 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 25 0.34
33 49 0.66
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1525283 original size:20 final size:19
Alignment explanation
Indices: 1525249--1525304 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1525239 TTGCGATTTT
*
1525249 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1525268 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1525288 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1525305 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1525765 original size:40 final size:40
Alignment explanation
Indices: 1525670--1525756 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
1525660 GACTCACCTG
* *
1525670 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCACTA
* *
1525712 TCCTCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
1525752 TCATC
1 TCATC
1525757 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 20 0.50
41 2 0.05
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
Found at i:1527195 original size:14 final size:14
Alignment explanation
Indices: 1527176--1527211 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1527166 ATTGTTTAAT
1527176 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1527190 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1527204 TGATTTGT
1 TGATTTGT
1527212 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1527372 original size:19 final size:19
Alignment explanation
Indices: 1527348--1527395 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1527338 ATCGCAACGA
1527348 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1527367 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1527386 G-AAATCGCAA
1 GAAAATCGCAA
1527396 CGAGAAATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1527457 original size:20 final size:20
Alignment explanation
Indices: 1527432--1527507 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
1527422 TCGCATTGCG
*
1527432 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
1527452 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
1527473 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
1527492 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
1527508 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:1527465 original size:34 final size:34
Alignment explanation
Indices: 1527420--1527523 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
1527410 GCGATTTTCA
*
1527420 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
1527454 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
1527494 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
1527524 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:1527745 original size:20 final size:20
Alignment explanation
Indices: 1527720--1527769 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1527710 TTGAAGATGA
1527720 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1527740 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
*
1527760 TTGTGATTTT
1 TTGCGATTTT
1527770 GTATTATCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1527840 original size:20 final size:21
Alignment explanation
Indices: 1527796--1527847 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1527786 ATAGTCAGTA
*
1527796 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1527817 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1527837 TCGCATTGCGA
1 TCGCATTGCGA
1527848 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1528646 original size:24 final size:24
Alignment explanation
Indices: 1528619--1528672 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1528609 GTATTCGAAA
*
1528619 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1528643 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1528667 TTTGAT
1 TTTGAT
1528673 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1528864 original size:12 final size:12
Alignment explanation
Indices: 1528847--1528883 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1528837 ATATAATCCT
1528847 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1528859 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
1528871 GAATAAGAAAAA
1 GAAGAAGAAAAA
1528883 G
1 G
1528884 TCCCCGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1531194 original size:19 final size:19
Alignment explanation
Indices: 1531172--1531302 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
1531162 GAAAATTACT
1531172 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1531191 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1531205 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1531224 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1531238 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1531257 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1531271 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1531290 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1531303 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1531214 original size:33 final size:33
Alignment explanation
Indices: 1531172--1531298 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1531162 GAAAATTACT
1531172 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1531205 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1531237 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1531271 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1531299 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1531279 original size:66 final size:66
Alignment explanation
Indices: 1531173--1531305 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1531163 AAAATTACTA
*
1531173 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1531238 T
66 T
*
1531239 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1531304 T
66 T
1531305 T
1 T
1531306 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1531480 original size:14 final size:14
Alignment explanation
Indices: 1531461--1531497 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1531451 CATCAATTAA
1531461 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1531475 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1531489 ACAAATCAA
1 ACAAATCAA
1531498 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1532894 original size:21 final size:21
Alignment explanation
Indices: 1532870--1532985 Score: 63
Period size: 21 Copynumber: 5.5 Consensus size: 21
1532860 GTGGGAGGGA
1532870 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * ** *
1532891 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGATGACAGTGG
* * * * *
1532912 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGTGG
* *
1532933 CCTCTTCAACGATAAGAGTGG
1 CCTCTTCAACGATGACAGTGG
* * **
1532954 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
*
1532975 CCTCTTGAACG
1 CCTCTTCAACG
1532986 GTGGGAGGGG
Statistics
Matches: 66, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.89
22 4 0.06
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:1532909 original size:42 final size:41
Alignment explanation
Indices: 1532850--1533000 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
1532840 GTGAATCGGG
* *
1532850 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1532892 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * ** * *
1532934 CTCTTCAACGATAAGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
1532976 CTCTTGAACGGTGGGAGGGGACTCT
1 CTCTTGAACGGTGGGA-GGGACTCT
1533001 CGAGGAATTT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
41 5 0.06
42 73 0.85
43 8 0.09
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1533384 original size:91 final size:93
Alignment explanation
Indices: 1533205--1533389 Score: 297
Period size: 91 Copynumber: 2.0 Consensus size: 93
1533195 ATTTCAAACT
*
1533205 TTCAACCAAAAGACAAAATAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1533270 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
*
1533298 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-TTTA
1 TTCAACCAAAAGAC-AAA-AAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
*
1533359 GCAGTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
1533389 T
1 T
1533390 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 34 0.39
92 1 0.01
93 17 0.20
94 7 0.08
95 28 0.32
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:1535058 original size:20 final size:19
Alignment explanation
Indices: 1535027--1535115 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
1535017 TCTTTTGGTT
1535027 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1535046 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1535067 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1535086 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1535100 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1535116 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 2 0.04
19 11 0.20
20 29 0.52
21 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1535113 original size:33 final size:34
Alignment explanation
Indices: 1535052--1535115 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
1535042 ACGAGATAAT
**
1535052 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
1535086 GAGAATCGCAACGC-GAAATGAAAATCGCAA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAA
1535116 TGCGATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGA
Found at i:1535739 original size:20 final size:20
Alignment explanation
Indices: 1535687--1535726 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1535677 GCGCTATGTA
1535687 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1535707 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1535727 TATTTCGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1535773 original size:20 final size:20
Alignment explanation
Indices: 1535748--1535801 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1535738 GATTTTGTAT
1535748 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1535768 TATCGCATTGCGATAGTTAG
1 TATCGCATTGCGATAGTAAG
1535788 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1535802 GCCCAATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1536310 original size:40 final size:36
Alignment explanation
Indices: 1536235--1536305 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
1536225 CCTCCACTCT
1536235 ATTTCTTTCTCGTAATCGTTGACTATATATCTATCC
1 ATTTCTTTCTCGTAATCGTTGACTATATATCTATCC
*
1536271 ATTTCTTTCTCGTAATTGTTGACTATATATCTATC
1 ATTTCTTTCTCGTAATCGTTGACTATATATCTATC
1536306 TATCCGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.49
Consensus pattern (36 bp):
ATTTCTTTCTCGTAATCGTTGACTATATATCTATCC
Found at i:1537284 original size:18 final size:19
Alignment explanation
Indices: 1537261--1537311 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1537251 TTACTGTAGA
1537261 AAAACAGACTGTAGA-AAG
1 AAAACAGACTGTAGAGAAG
* *
1537279 AAAACAGACTGTATAGTAG
1 AAAACAGACTGTAGAGAAG
*
1537298 AAAACAAACTGTAG
1 AAAACAGACTGTAG
1537312 GAAACAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.16
Consensus pattern (19 bp):
AAAACAGACTGTAGAGAAG
Found at i:1537299 original size:19 final size:19
Alignment explanation
Indices: 1537256--1537311 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1537246 GATTGTTACT
1537256 GTAGAAAAACAGACTGTAGA
1 GTAG-AAAACAGACTGTAGA
* *
1537276 -AAGAAAACAGACTGTATA
1 GTAGAAAACAGACTGTAGA
*
1537294 GTAGAAAACAAACTGTAG
1 GTAGAAAACAGACTGTAG
1537312 GAAACAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.52, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
GTAGAAAACAGACTGTAGA
Found at i:1545217 original size:49 final size:48
Alignment explanation
Indices: 1545098--1545217 Score: 134
Period size: 49 Copynumber: 2.4 Consensus size: 48
1545088 TCTCGATAAA
** * *
1545098 TTTACTTAATTATCAACACTTAATTACATTGGTATGAGTTAGTTCTTTC
1 TTTACTTAATTATC-ACACTTAATTACACCGGTATAAATTAGTTCTTTC
* *
1545147 GTTA-TTAATTTATCCATACTTAATTACACCGGTATAAATTAGTTCTTTCC
1 TTTACTTAA-TTAT-CACACTTAATTACACCGGTATAAATTAGTTCTTT-C
*
1545197 TTTACTGAATTATCACACTTA
1 TTTACTTAATTATCACACTTA
1545218 TTTATAGCGG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
48 4 0.07
49 42 0.72
50 9 0.16
51 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (48 bp):
TTTACTTAATTATCACACTTAATTACACCGGTATAAATTAGTTCTTTC
Found at i:1545679 original size:2 final size:2
Alignment explanation
Indices: 1545672--1545704 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1545662 CATTATTTTC
1545672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1545705 AATTATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1550794 original size:20 final size:20
Alignment explanation
Indices: 1550769--1550809 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1550759 TTTAAAGAAT
1550769 CACAATGAATCTCCTATAAA
1 CACAATGAATCTCCTATAAA
1550789 CACAATGAATCTCCTATAAA
1 CACAATGAATCTCCTATAAA
1550809 C
1 C
1550810 GTTATGGCAA
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:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (20 bp):
CACAATGAATCTCCTATAAA
Found at i:1552855 original size:63 final size:64
Alignment explanation
Indices: 1552774--1552929 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 64
1552764 TTCAGTGTGT
* * *
1552774 ATCGATGCACAGGAAGTGCATCGATGCACCCT-TTAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCTCTTAAAATGAAAACATCAAATGCAATTAGTGC
* * * * ** * *
1552837 ATCGATGCATAAGG-AGTGCATCGATACACCCTCTTAAGATTAAAACATTAAATGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCACCCTCTTAAAATGAAAACATCAAATGCAATTAGTGC
* *
1552901 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
1552930 ATGTTAAGGG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 28 0.36
64 49 0.64
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (64 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCTCTTAAAATGAAAACATCAAATGCAATTAGTGC
Found at i:1554445 original size:23 final size:23
Alignment explanation
Indices: 1554411--1554454 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1554401 CATTTTATAT
*
1554411 GGCACTTCGGTGTAATTCTACAC
1 GGCACTTCGGTGCAATTCTACAC
*
1554434 GGCACTTTGGTGCAATTCTAC
1 GGCACTTCGGTGCAATTCTAC
1554455 GAGTTGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACAC
Found at i:1557005 original size:16 final size:16
Alignment explanation
Indices: 1556984--1557020 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1556974 AAAAGATATT
*
1556984 ATTTGTGTAGAAGGAG
1 ATTTGTGTAAAAGGAG
1557000 ATTTGTGTAAAAGGAG
1 ATTTGTGTAAAAGGAG
1557016 ATTTG
1 ATTTG
1557021 GATTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (16 bp):
ATTTGTGTAAAAGGAG
Found at i:1560247 original size:17 final size:18
Alignment explanation
Indices: 1560225--1560258 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1560215 TTTAAAATAA
1560225 TGTATAATAT-TTATATG
1 TGTATAATATGTTATATG
*
1560242 TGTATAGTATGTTATAT
1 TGTATAATATGTTATAT
1560259 ATATATAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TGTATAATATGTTATATG
Found at i:1570287 original size:44 final size:44
Alignment explanation
Indices: 1570109--1570686 Score: 232
Period size: 44 Copynumber: 13.3 Consensus size: 44
1570099 GTCTATCTCT
* * *
1570109 TTCTGTGATAGAATCAAGCAAAAAGTTGATGCTGATACAACTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
** * * * ** * *
1570153 TTCTACGATGGATTTGAGTGAAAAA--AAATG-TCGATCTACCTCC
1 TTCTGTGATGGAATCGAG-CAAAAAGTTGATGCT-GATCCAACTCC
* * * * * * *
1570196 TTCTGTGATGGAATCGAACGAGATGTTGGTGCTGAT-CTACATTC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAAC-TCC
* *
1570240 TTCTGTGATAGAATCGAGCTAAAAGTTGATGCTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
* ** *
1570284 TTCTGCGATGGATAT-GAGCGAAATAAAATG-T-C-GATCCATCTCC
1 TTCTGTGATGGA-ATCGAGC-AAA-AAGTTGATGCTGATCCAACTCC
* * * * * * * * * * *
1570327 TTCTCTGATGGAATCGAACGAGATG-TCAGTACCGATCTACCTCA
1 TTCTGTGATGGAATCGAGCAAAAAGTTGA-TGCTGATCCAACTCC
* *
1570371 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
* * * ** * *
1570415 TTCTGCGATGGATTTGAGCGAAAAAAAT-AT-C-AATCCATCTCC
1 TTCTGTGATGGAATCGAGC-AAAAAGTTGATGCTGATCCAACTCC
* * * * * * * * *
1570457 TTCTGTGATGTAATAGAACAAGATGTTGGTACTGATCTACCTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
** * * *
1570501 TTCTGAAATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
* * * * * *
1570545 TTCTGCGATGGATTTGAGCGAAAAA---AATGTTGATCCACCTCC
1 TTCTGTGATGGAATCGAGC-AAAAAGTTGATGCTGATCCAACTCC
* ** * * * * * * * *
1570587 TTCTGTGATGGATTTAAACGAGATGTTGGTGCTGATCTACCTCT
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
* * ** *
1570631 TTCTGCGATTGAATCGAGTTAAAAGTTGACGCTGATCCAACTCC
1 TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
*
1570675 TTCTGCGATGGA
1 TTCTGTGATGGA
1570687 TTTGAGCGAA
Statistics
Matches: 373, Mismatches: 137, Indels: 48
0.67 0.25 0.09
Matches are distributed among these distances:
40 1 0.00
41 7 0.02
42 61 0.16
43 51 0.14
44 222 0.60
45 27 0.07
46 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
TTCTGTGATGGAATCGAGCAAAAAGTTGATGCTGATCCAACTCC
Found at i:1570520 original size:130 final size:130
Alignment explanation
Indices: 1569875--1570728 Score: 985
Period size: 130 Copynumber: 6.5 Consensus size: 130
1569865 TGTTGATGAT
* * * * * * *
1569875 GCTGATCCAACTTCGTATGCGATGGTTTTGAGTGAAATGAAAACATCGATCCATCTCCTTCTGTG
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA--AAAATATCGATCCACCTCCTTCTGTG
* * * * * *
1569940 ATGAAATCGAACAAGATGTCGATGA-TGATCTATCTCTTTCTGTGATAGAATCAAGCAAAAAATT
64 ATGGAATCGAACGAGATGTCGGT-ACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTT
*
1570004 GAT
128 GAC
* * *
1570007 GCTGACCCAACTCCTTCTGCGATGGATTTGAGCGAAATGAAAACATCGATCCACCTCCTTTTGTG
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA--AAAATATCGATCCACCTCCTTCTGTG
* ** * * * * * * *
1570072 ATAGTGTCGAATGGGATATCGATGA-TGGTCTATCTCTTTCTGTGATAGAATCAAGCAAAAAGTT
64 ATGGAATCGAACGAGATGTCGGT-ACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTT
*
1570136 GAT
128 GAC
* * * * *
1570139 GCTGATACAACTCCTTCTACGATGGATTTGAGTGAAAAAAAATGTCGATCTACCTCCTTCTGTGA
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCG-AAAAAAATATCGATCCACCTCCTTCTGTGA
* * * *
1570204 TGGAATCGAACGAGATGTTGGTGCTGATCTACAT-TCTTCTGTGATAGAATCGAGCTAAAAGTTG
65 TGGAATCGAACGAGATGTCGGTACTGATCTACCTCT-TTCTGTGATAGAATCGAGCAAAAAGTTG
*
1570268 AT
129 AC
* * * *
1570270 GCTGATCCAACTCCTTCTGCGATGGATATGAGCGAAATAAAATGTCGATCCATCTCCTTCTCTGA
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAA-AAAATATCGATCCACCTCCTTCTGTGA
* * *
1570335 TGGAATCGAACGAGATGTCAGTACCGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
65 TGGAATCGAACGAGATGTCGGTACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTTGA
1570400 C
130 C
* *
1570401 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATATCAATCCATCTCCTTCTGTGAT
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATATCGATCCACCTCCTTCTGTGAT
* * * * * **
1570466 GTAATAGAACAAGATGTTGGTACTGATCTACCTCCTTCTGAAATAGAATCGAGCAAAAAGTTGAC
66 GGAATCGAACGAGATGTCGGTACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTTGAC
* * *
1570531 GTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATGTTGATCCACCTCCTTCTGTGAT
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATATCGATCCACCTCCTTCTGTGAT
* ** * * * * **
1570596 GGATTTAAACGAGATGTTGGTGCTGATCTACCTCTTTCTGCGATTGAATCGAGTTAAAAGTTGAC
66 GGAATCGAACGAGATGTCGGTACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTTGAC
1570661 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATATCGATCCACCTCCTTCTGT
1 GCTGATCCAACTCCTTCTGCGATGGATTTGAGCG--AA-AAAAATATCGATCCACCTCCTTCTGT
1570726 GAT
63 GAT
1570729 AGATTTGAAC
Statistics
Matches: 626, Mismatches: 88, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
130 231 0.37
131 219 0.35
132 146 0.23
133 30 0.05
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (130 bp):
GCTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAAAAATATCGATCCACCTCCTTCTGTGAT
GGAATCGAACGAGATGTCGGTACTGATCTACCTCTTTCTGTGATAGAATCGAGCAAAAAGTTGAC
Found at i:1571240 original size:39 final size:39
Alignment explanation
Indices: 1571177--1571542 Score: 391
Period size: 39 Copynumber: 9.7 Consensus size: 39
1571167 ATTTTAAGAA
* * *
1571177 AAACTTTCTCAAGTGAGATAAAAT-TTCTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTC-TGTTTCAAGGG
* *
1571216 AAACTGTCTCAAGCGAGACGAAAT-TT-TGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* *
1571253 AAACTGTCTCAAGGGAGACAAAA--TT-TGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* * *
1571289 AAACTATCTCAA---AG-----TTTTTATGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* * * *
1571320 AAACCATCTCAAGGGAGACAAGATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* * *
1571359 AAACTATCTCAAGCGAGATAAAATCTTCTGTTCCGAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* * *
1571398 AAACTATCTCAAGCGAGATAAAGATCTTCCGTTTCAAAGG
1 AAACTATCTCAAGCGAGACAAA-ATCTTCTGTTTCAAGGG
*
1571438 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* *
1571477 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* *
1571516 CAACTATCTCAAGCGAGATAAAATCTT
1 AAACTATCTCAAGCGAGACAAAATCTT
1571543 GTTTTAAGAA
Statistics
Matches: 287, Mismatches: 28, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
30 2 0.01
31 22 0.08
33 2 0.01
34 2 0.01
36 24 0.08
37 32 0.11
39 169 0.59
40 34 0.12
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
Found at i:1571446 original size:79 final size:79
Alignment explanation
Indices: 1571316--1571542 Score: 359
Period size: 79 Copynumber: 2.9 Consensus size: 79
1571306 TTATGTTTCA
* * *
1571316 AGGGAAACCATCTCAAGGGAGA-CAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAA
1 AGGGAAACTATCTCAAGCGAGATAAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAA
1571380 AATCTTCTGTTCCG
66 AATCTTCTGTTCCG
* * * *
1571394 AGGGAAACTATCTCAAGCGAGATAAAGATCTTCCGTTTCAAAGGAAACTATCTCAAGCGAGACAA
1 AGGGAAACTATCTCAAGCGAGATAAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAA
*
1571459 AATCTTCTGTTTCG
66 AATCTTCTGTTCCG
*
1571473 AGGGAAACTATCTCAAGCGAGATAAA-ATCTTCTGTTTCGAGGGCAACTATCTCAAGCGAGATAA
1 AGGGAAACTATCTCAAGCGAGATAAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAA
1571537 AATCTT
66 AATCTT
1571543 GTTTTAAGAA
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
78 59 0.44
79 76 0.56
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (79 bp):
AGGGAAACTATCTCAAGCGAGATAAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAA
AATCTTCTGTTCCG
Found at i:1571521 original size:118 final size:117
Alignment explanation
Indices: 1571310--1571542 Score: 403
Period size: 118 Copynumber: 2.0 Consensus size: 117
1571300 AAGTTTTTAT
* * *
1571310 GTTTCAAGGGAAACCATCTCAAGGGAGACAAGATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
1 GTTTCAAAGGAAACCATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
1571375 GATAAAATCTTCTGTTCCGAGGGAAACTATCTCAAGCGAGATAAAGATCTTCC
66 GATAAAATCTTCTGTTCCGAGGGAAACTATCTCAAGCGAGATAAA-ATCTTCC
*
1571428 GTTTCAAAGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
1 GTTTCAAAGGAAACCATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
* *
1571493 GATAAAATCTTCTGTTTCGAGGGCAACTATCTCAAGCGAGATAAAATCTT
66 GATAAAATCTTCTGTTCCGAGGGAAACTATCTCAAGCGAGATAAAATCTT
1571543 GTTTTAAGAA
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 5 0.05
118 104 0.95
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (117 bp):
GTTTCAAAGGAAACCATCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGA
GATAAAATCTTCTGTTCCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCC
Found at i:1573342 original size:2 final size:2
Alignment explanation
Indices: 1573335--1573360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1573325 ACAACAAGGG
1573335 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
1573361 GTGGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1576567 original size:20 final size:20
Alignment explanation
Indices: 1576530--1576571 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1576520 AACTTCAAGG
1576530 ATTAAAATGGTAAAAATAGAA
1 ATTAAAATGGTAAAAATA-AA
*
1576551 ATTAAAA-GGTTAAAATAAA
1 ATTAAAATGGTAAAAATAAA
1576570 AT
1 AT
1576572 AACATAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (20 bp):
ATTAAAATGGTAAAAATAAA
Found at i:1587168 original size:45 final size:45
Alignment explanation
Indices: 1587119--1587206 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
1587109 AAAATAGCCA
* * *
1587119 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATTAAATGCACT
1 GAGTGCATCGATGCATGGTATGTGCATCGATGAATAAAATGCACT
*
1587164 GAGTGCATTGATGCATGGTATGTGCATCGATGAATAAAATGCA
1 GAGTGCATCGATGCATGGTATGTGCATCGATGAATAAAATGCA
1587207 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGAATAAAATGCACT
Found at i:1596430 original size:3 final size:3
Alignment explanation
Indices: 1596422--1596471 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1596412 GTTGTTTCTT
* *
1596422 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1596470 TT
1 TT
1596472 TCTACAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1601226 original size:32 final size:31
Alignment explanation
Indices: 1601157--1601244 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 31
1601147 GTGACACTTG
* * *
1601157 GGTAGGCTCTGAGGCCCTAAGGTATTTCCTC
1 GGTAGGCTCTAAGGCCCTAAGGTATTCCCTA
*
1601188 GTGTAGGGTCTAAGGCCCTAAGGTATTCCCTTA
1 G-GTAGGCTCTAAGGCCCTAAGGTATTCCC-TA
* *
1601221 GGTAGGCTCTTAGGCCCCAAGGTA
1 GGTAGGCTCTAAGGCCCTAAGGTA
1601245 CACTCTTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.02
32 45 0.94
33 2 0.04
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (31 bp):
GGTAGGCTCTAAGGCCCTAAGGTATTCCCTA
Found at i:1601257 original size:32 final size:31
Alignment explanation
Indices: 1601153--1601265 Score: 100
Period size: 32 Copynumber: 3.5 Consensus size: 31
1601143 TAAGGTGACA
* *
1601153 CTTGGGTAGGCTCTGAGGCCCTAAGGTATTT
1 CTTGGGTAGGCTCTAAGGCCCTAAGGTATCT
* * * *
1601184 CCTCGTGTAGGGTCTAAGGCCCTAAGGTATTCC
1 -CTTGGGTAGGCTCTAAGGCCCTAAGGTA-TCT
* * * *
1601217 CTTAGGTAGGCTCTTAGGCCCCAAGGTACACT
1 CTTGGGTAGGCTCTAAGGCCCTAAGGTA-TCT
*
1601249 CTTGGGTAGGCTTTAAG
1 CTTGGGTAGGCTCTAAG
1601266 ACCTCAAGAT
Statistics
Matches: 62, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
32 61 0.98
33 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (31 bp):
CTTGGGTAGGCTCTAAGGCCCTAAGGTATCT
Found at i:1602986 original size:78 final size:78
Alignment explanation
Indices: 1602836--1602986 Score: 167
Period size: 78 Copynumber: 1.9 Consensus size: 78
1602826 TCAATCAATA
* * * * ****
1602836 GCATAATTATTAACAAACTCGAACAATTTTGCATATAGATGTGTTTATGGATGCAAGGTTTTTAT
1 GCATAATTATTAACAAACTCAAACAATTTTGCATACAGATGTGTTTATGGAAGCAACGTCAGCAT
*
1602901 ACTCAAACCAAGG
66 ACCCAAACCAAGG
* * ** *
1602914 GCATAATTCTTAATAAACTCAAACAATTTTGTGTACAGATGTGTTTCTGGAAGCAACGTCAGCAT
1 GCATAATTATTAACAAACTCAAACAATTTTGCATACAGATGTGTTTATGGAAGCAACGTCAGCAT
*
1602979 GCCCAAAC
66 ACCCAAAC
1602987 TAAAACTTAG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
78 58 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (78 bp):
GCATAATTATTAACAAACTCAAACAATTTTGCATACAGATGTGTTTATGGAAGCAACGTCAGCAT
ACCCAAACCAAGG
Found at i:1606056 original size:17 final size:18
Alignment explanation
Indices: 1606034--1606072 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1606024 TCATTGTTGT
1606034 AAAATAAAAACAGAGA-G
1 AAAATAAAAACAGAGATG
* *
1606051 AAAATAATAACATAGATG
1 AAAATAAAAACAGAGATG
1606069 AAAA
1 AAAA
1606073 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (18 bp):
AAAATAAAAACAGAGATG
Found at i:1608497 original size:29 final size:29
Alignment explanation
Indices: 1608448--1608511 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1608438 TTGAAAAGTG
** * *
1608448 ATCAAAATATAAATTTTAAAAGTTTGATA
1 ATCAAAATATAAACATAAAAAGTTTAATA
*
1608477 GTCAAAATATAAACATAAAAAGTTTAATA
1 ATCAAAATATAAACATAAAAAGTTTAATA
1608506 ATCAAA
1 ATCAAA
1608512 GTGATAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (29 bp):
ATCAAAATATAAACATAAAAAGTTTAATA
Found at i:1611796 original size:24 final size:26
Alignment explanation
Indices: 1611747--1611807 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
1611737 GAAAACAATA
1611747 ATATATTCTTTTTAAAAGAATGTAACTT
1 ATATATT-TTTTTAAAAGAA-GTAACTT
*
1611775 GTATATTTTTTTAAAAG-A-TAACTT
1 ATATATTTTTTTAAAAGAAGTAACTT
1611799 ATATATTTT
1 ATATATTTT
1611808 AATGTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 14 0.45
26 1 0.03
27 10 0.32
28 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (26 bp):
ATATATTTTTTTAAAAGAAGTAACTT
Found at i:1612280 original size:34 final size:36
Alignment explanation
Indices: 1612195--1612274 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
1612185 TAATGTTCCT
1612195 TAATATCTTGAGTATACTATGATAAAAAAATAAGTA
1 TAATATCTTGAGTATACTATGATAAAAAAATAAGTA
1612231 TAATATCTTGAGTATACTATGATAAAAAAATAAGTA
1 TAATATCTTGAGTATACTATGATAAAAAAATAAGTA
*
1612267 TGATATCT
1 TAATATCT
1612275 CGTATAAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (36 bp):
TAATATCTTGAGTATACTATGATAAAAAAATAAGTA
Found at i:1616920 original size:26 final size:26
Alignment explanation
Indices: 1616890--1616939 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1616880 TCTCCAATTG
1616890 TACTTTTAGTTAAAATTAAGGGCTAC
1 TACTTTTAGTTAAAATTAAGGGCTAC
1616916 TACTTTTAGTTAAAATTAAGGGCT
1 TACTTTTAGTTAAAATTAAGGGCT
1616940 TTCAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (26 bp):
TACTTTTAGTTAAAATTAAGGGCTAC
Found at i:1620950 original size:23 final size:23
Alignment explanation
Indices: 1620924--1620971 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1620914 ATAAAGTACA
1620924 ATAACATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1620947 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1620970 AT
1 AT
1620972 TTACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1621232 original size:118 final size:118
Alignment explanation
Indices: 1621024--1621264 Score: 466
Period size: 118 Copynumber: 2.1 Consensus size: 118
1621014 ATTACAAATT
*
1621024 TACCTATTACATTATAATATGTTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTT
1 TACCTATTACATTATAATATGTTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTTTT
1621089 TAAAGTTATGTAATTTATTTTTCAATTTCTTTTAATAGTGTTTCATGTTTTCC
66 TAAAGTTATGTAATTTATTTTTCAATTTCTTTTAATAGTGTTTCATGTTTTCC
1621142 TACCTATTACATTATAATATGTTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTTTT
1 TACCTATTACATTATAATATGTTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTTTT
1621207 TAAAGTTATGTAATTTATTTTTCAATTTCTTTTAATAGTGTTTCATGTTTTCC
66 TAAAGTTATGTAATTTATTTTTCAATTTCTTTTAATAGTGTTTCATGTTTTCC
1621260 -ACCTA
1 TACCTA
1621265 CAATATTAAT
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
117 5 0.04
118 117 0.96
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (118 bp):
TACCTATTACATTATAATATGTTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTTTT
TAAAGTTATGTAATTTATTTTTCAATTTCTTTTAATAGTGTTTCATGTTTTCC
Found at i:1621591 original size:23 final size:23
Alignment explanation
Indices: 1621565--1621637 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1621555 ATATTTTACA
1621565 ATATAACCACTACCTATTACATT
1 ATATAACCACTACCTATTACATT
* *
1621588 ATATAAACGA-TATCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* * *
1621611 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
1621634 ATAT
1 ATAT
1621638 TTTTACCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.05
23 35 0.85
24 4 0.10
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:1622028 original size:23 final size:23
Alignment explanation
Indices: 1622002--1622064 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1621992 ATATAACCAC
1622002 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1622025 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1622048 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1622065 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1622127 original size:427 final size:430
Alignment explanation
Indices: 1621399--1623617 Score: 2771
Period size: 429 Copynumber: 5.0 Consensus size: 430
1621389 ATGCTTATTG
* *
1621399 TTTTTAATTTAATAATAATATATATAGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1621463 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
1621528 TATAGACACTTTTATAAAAAAAGATAGATATTTTACAATATAACCACTACCTATTACATTATATA
131 TATAGACACTTTTAT-AAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATA
*
1621593 AACGATATCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA
195 AACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA
* *
1621658 GTGT-CTATAATTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAAT
260 GTGTAC-ATACTTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAAT
1621722 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
324 TTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
1621787 ATTATTTGATTGTTTTGATATTTTATAAAAT-ATATTTAGAA
389 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1621828 TTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1621891 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1621956 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1622021 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
1622086 TGTACATACTTTTTATAAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
261 TGTACATACTTTTTATAAAAAAGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAATT
1622150 TTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
325 TTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
*
1622214 ATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAA
389 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
* * ** * * ** * * ** *
1622256 TTTAT-ATTTAACAAT-AT-TA-A-CCAAAGGTAATAAAATATGTAATATATGTTATTGTTTTTA
1 TTTTTAATTTAATAATAATATATATCGTAACGTAA-AAAAGAAATCAT-TA-G--A-CGCCTATA
* * *** * * *
1622316 ATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAA-TTACTAAATT
60 A-TTACTAA-ATTA-ATATC-T----T-AAAACTCACTCA--A-AAG---ATAACCT--TAAATT
* * * * * * * ** * * ** ** * * ** *
1622380 AATATCTT-AAAACTCACTCAAAAG-ATA-AC-CTTAAAT-TAATGTTTTCCACAGTAAAAAAAG
108 AATGTTTTCCACAGTGA--AAAAAGTATAGACACTTTTATAAAAAG-GATAGATACT-TTACAA-
*** * *
1622440 TATAGA-CACTTTTTATAAAAAGGATAGATACTTTACAATATAATC-ACTACCTATTACATTATA
168 TATA-ACCACTACCTAT---TA-CAT---TA---T---ATA-AA-CGA-TACCTATTACATTATA
* * * *** * * ** * *
1622503 TAAACGATACCTATTACATTATATAAGCGCTACCTATTACA-TCATATTTTTACCTA-TTATATT
216 TAAGCGCTACCTATTACATCATAT---TTTTACCTATTATATTGA-AAGTGTACATACTT-T-TT
*** ** **
1622566 GA-AAGTGTACATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTT
275 -ATAA----A-A-AAGATCGATACT-------------TCTTTTAAAGTTATGTAATTTATGTTT
1622630 CAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
320 CAATTTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
1622695 AAAAATTATTTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
385 AAAAATTA-TTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1622742 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
* *
1622807 AAATTAATATCTTAAAACTCACTCAAAATATAACTTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
1622872 TATAGACACTTTTACAAAAAGGATAAATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1622937 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
1623002 TGTCCATAC-TTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTACATACTTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
1623066 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
326 TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
1623131 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
391 TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1623171 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1623236 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
*
1623301 TATAGACACTTTTATAAAAAAGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
1623366 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCGATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
* *
1623431 TGTCCATACTTTTTATAAAAAAGATCAATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTACATACTTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TT
*
1623496 TTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
325 TTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
*
1623560 AGTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
389 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
* *
1623602 -TTTAAATTTAACAATA
1 TTTTTAATTTAATAATA
1623618 TTAACCAAAG
Statistics
Matches: 1539, Mismatches: 152, Indels: 197
0.82 0.08 0.10
Matches are distributed among these distances:
425 7 0.00
426 12 0.01
427 289 0.19
428 126 0.08
429 317 0.21
430 168 0.11
431 108 0.07
432 6 0.00
433 3 0.00
434 5 0.00
435 1 0.00
439 1 0.00
440 8 0.01
442 1 0.00
443 7 0.00
444 4 0.00
445 11 0.01
446 13 0.01
447 26 0.02
448 7 0.00
449 4 0.00
450 2 0.00
451 19 0.01
452 2 0.00
454 40 0.03
455 3 0.00
456 3 0.00
457 1 0.00
459 1 0.00
460 3 0.00
461 3 0.00
462 40 0.03
464 4 0.00
465 20 0.01
466 5 0.00
467 1 0.00
468 6 0.00
469 26 0.02
470 14 0.01
471 11 0.01
472 8 0.01
473 1 0.00
474 1 0.00
476 8 0.01
477 1 0.00
481 1 0.00
482 5 0.00
483 3 0.00
484 6 0.00
485 100 0.06
486 45 0.03
487 9 0.01
488 3 0.00
489 4 0.00
490 9 0.01
491 7 0.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (430 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTACATACTTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAAT
TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:1622513 original size:23 final size:23
Alignment explanation
Indices: 1622487--1622549 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1622477 ATATAATCAC
1622487 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1622510 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1622533 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1622550 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1622944 original size:23 final size:23
Alignment explanation
Indices: 1622918--1622980 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1622908 ATATAACCAC
1622918 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1622941 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1622964 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1622981 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1622979 original size:916 final size:914
Alignment explanation
Indices: 1621163--1623187 Score: 3672
Period size: 916 Copynumber: 2.2 Consensus size: 914
1621153 TTATAATATG
*
1621163 TTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATTTT
1 TTGAAAGTGTCCATA-CTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
1621228 TCAATTTCTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
64 TCAATTT-TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
1621293 C-AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
128 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTATATTTAACAATAT
1621357 TAACCAAAGATAATAATAAATATGTAATATATATGCTTATTGTTTTTAATTTAATAATAATATAT
193 TAACCAAAGATAATAATAAATATGTAATATATATGCTTATTGTTTTTAATTTAATAATAATATAT
*
1621422 ATAGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
258 ATAGTAACGTAAAAAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
1621487 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAAAGA
323 AAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATAGACACTTTTATAAAAAAAGA
* *
1621552 TAGATATTTTACAATATAACCACTACCTATTACATTATATAAACGATATCTATTACATTATATAA
388 TAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
1621617 GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATAATTTTTATAAAAATG
453 GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATAATTTTTATAAAAATG
1621682 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTC
518 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTC
1621747 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
583 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
1621812 TAAAATATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGTAAAAAAGAAATCATTAGA
648 TAAAATATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGTAAAAAAGAAATCATTAGA
1621877 CGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
713 CGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
* *
1621942 CACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCT
778 CACAGTGAAAAAAGTATAGACACTTTTACAAAAAGGATAAATACTTTACAATATAACCACTACCT
1622007 ATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
843 ATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1622072 TATTATA
908 TATTATA
*
1622079 TTGAAAGTGTACATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTT-TTTAAAGTTATGTAATTTATGTT
1622144 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
64 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
1622209 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTATATTTAACAATATT
129 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTATATTTAACAATATT
*
1622274 AACCAAAGGTAAT-A-AAATATGT-A-ATATATG-TTATTGTTTTTAATTTAATAATAATATATA
194 AACCAAAGATAATAATAAATATGTAATATATATGCTTATTGTTTTTAATTTAATAATAATATATA
*
1622334 TCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
259 TAGTAACGT-AAAAAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
1622399 AAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATAGACACTTTT-TATAAAAAGG
323 AAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATAGACACTTTTATA-AAAAAAG
*
1622463 ATAGATACTTTACAATATAATCACTACCTATTACATTATATAAACGATACCTATTACATTATATA
387 ATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATA
*
1622528 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTAC-ATACTTTTTATAAAAA
452 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGT-CTATAATTTTTATAAAAA
1622592 TGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTT
516 TGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTT
1622657 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTTGATTGTTTTGATATT
581 TCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTA-TTTGATTGTTTTGATATT
1622722 TTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATC
645 TTATAAAAT-ATATTTAGAATTTTTAATTTAATAAT-A-ATATATCGTAACGTAAAAAAGAAATC
* *
1622787 ATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAATATAACTTTAAATTAAT
707 ATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAAT
1622852 GTTTTCCACAGTGAAAAAAGTATAGACACTTTTACAAAAAGGATAAATACTTTACAATATAACCA
772 GTTTTCCACAGTGAAAAAAGTATAGACACTTTTACAAAAAGGATAAATACTTTACAATATAACCA
1622917 CTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATT
837 CTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATT
1622982 TTTACCTATTATA
902 TTTACCTATTATA
*
1622995 TTGAAAGTGTCCATACTTTTATAAAAAAGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTT-TTTTAAAGTTATGTAATTTATGTTT
1623060 CAATTTTTTTAAGTA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
65 CAATTTTTTTAA-TAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
* * *
1623124 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
129 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAT-ATTTAACAATA
1623188 ATATATATCG
Statistics
Matches: 1075, Mismatches: 21, Indels: 26
0.96 0.02 0.02
Matches are distributed among these distances:
911 40 0.04
912 354 0.33
913 29 0.03
914 34 0.03
915 221 0.21
916 397 0.37
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (914 bp):
TTGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTC
AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTATATTTAACAATATTAA
CCAAAGATAATAATAAATATGTAATATATATGCTTATTGTTTTTAATTTAATAATAATATATATA
GTAACGTAAAAAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
AGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATAGACACTTTTATAAAAAAAGATAG
ATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCG
CTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCTATAATTTTTATAAAAATGATC
GATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAAGTATGTTTCATGTTTTCCAC
CTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAA
AATATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGTAAAAAAGAAATCATTAGACGC
CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCAC
AGTGAAAAAAGTATAGACACTTTTACAAAAAGGATAAATACTTTACAATATAACCACTACCTATT
ACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTAT
TATA
Found at i:1623373 original size:23 final size:23
Alignment explanation
Indices: 1623347--1623409 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1623337 ATATAACCAC
1623347 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1623370 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1623393 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1623410 TTTTACCGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1624995 original size:12 final size:12
Alignment explanation
Indices: 1624979--1625066 Score: 104
Period size: 12 Copynumber: 7.3 Consensus size: 12
1624969 CTTGTTTGGA
* *
1624979 TCATCATCATCA
1 TCATCTTCATCG
1624991 TCATCTTCATCG
1 TCATCTTCATCG
*
1625003 TCAGCTTCATCG
1 TCATCTTCATCG
* *
1625015 TCAGCTTCATTG
1 TCATCTTCATCG
*
1625027 TCATCATCATCG
1 TCATCTTCATCG
1625039 TCATCTTCATCG
1 TCATCTTCATCG
* *
1625051 TCAGCTTCATCT
1 TCATCTTCATCG
1625063 TCAT
1 TCAT
1625067 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1625038 original size:36 final size:36
Alignment explanation
Indices: 1624991--1625060 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1624981 ATCATCATCA
*
1624991 TCATCTTCATCGTCAGCTTCATCGTCAGCTTCATTG
1 TCATCATCATCGTCAGCTTCATCGTCAGCTTCATTG
*
1625027 TCATCATCATCGTCATCTTCATCGTCAGCTTCAT
1 TCATCATCATCGTCAGCTTCATCGTCAGCTTCAT
1625061 CTTCATTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (36 bp):
TCATCATCATCGTCAGCTTCATCGTCAGCTTCATTG
Found at i:1625064 original size:6 final size:6
Alignment explanation
Indices: 1624979--1625066 Score: 70
Period size: 6 Copynumber: 14.7 Consensus size: 6
1624969 CTTGTTTGGA
* * * * * *
1624979 TCATCA TCATCA TCATCT TCATCG TCAGCT TCATCG TCAGCT TCAT-T
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1625026 GTCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 -TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1625067 TGACCGCTTG
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 1 0.02
6 63 0.98
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:1626885 original size:199 final size:199
Alignment explanation
Indices: 1626538--1627493 Score: 1709
Period size: 199 Copynumber: 4.8 Consensus size: 199
1626528 GACACAAACT
*
1626538 AAAAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
*
1626603 TGAAAAATTACATATTACAATATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
* * **
1626668 TGGATCGACACCTTATGGTTGCACACTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTTT
131 TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTAA
1626733 TTTA
196 TTTA
** *
1626737 AATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1626802 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
**
1626867 TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTTT
131 TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTAA
1626932 TTTA
196 TTTA
**
1626936 AATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1627001 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
66 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
1627066 TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACAC-AA
131 TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTAA
**
1627130 ACTA
196 TTTA
1627134 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1627199 TG-AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTATAT
*
1627263 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAA
130 ATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTA
* *
1627328 ACTAA
195 ATTTA
1627333 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1 AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
1627398 TGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATAT
66 TGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTATAT
*
1627463 ATGGTTCGACACTTTATGGTTGCACCCTGTT
130 ATGGATCGACACTTTATGGTTGCACCCTGTT
1627494 GGCCATATTG
Statistics
Matches: 736, Mismatches: 18, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
197 29 0.04
198 162 0.22
199 453 0.62
200 92 0.12
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (199 bp):
AAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGAT
TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATA
TGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACTAA
TTTA
Found at i:1627355 original size:397 final size:397
Alignment explanation
Indices: 1626524--1627493 Score: 1721
Period size: 397 Copynumber: 2.4 Consensus size: 397
1626514 TTTAAATTAG
*
1626524 TATCGACACAAACT-AAAAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
1626588 TTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTTTTGGGTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
* *
1626653 GACACTTTTTATATATGGATCGACACCTTATGGTTGCACACTGTTTTCCATTCATTCTGGACCAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
**** **
1626718 AAATATCGACACTTTTTTAAATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGT
196 AAATATCGACACTAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGT
1626783 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGG
261 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGG
1626848 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
1626913 CCAAAAA
391 CCAAAAA
**** **
1626920 TATCGACACTTTTTTAAATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACAC-AAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1626985 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
1627050 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
*
1627115 AAAATATCGACAC-AAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACTAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAG
1627179 TATACTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTT
260 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTT
1627243 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
324 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTG
1627308 GACCAAAAA
389 GACCAAAAA
1627317 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1627382 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGA
*
1627447 TCGACACTTTTTATATATGGTTCGACACTTTATGGTTGCACCCTGTT
129 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
1627494 GGCCATATTG
Statistics
Matches: 545, Mismatches: 24, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
396 39 0.07
397 258 0.47
398 248 0.46
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (397 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
AAATATCGACACTAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGT
ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA
CCAAAAA
Found at i:1627658 original size:19 final size:19
Alignment explanation
Indices: 1627611--1627660 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1627601 ATTATATTCA
*
1627611 TATACAAAAATATAAATCG
1 TATACAAAATTATAAATCG
*
1627630 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
1627649 TATACAAAATTA
1 TATACAAAATTA
1627661 ACCCTACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:1629580 original size:21 final size:21
Alignment explanation
Indices: 1629555--1629598 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1629545 CCCCTTATGC
1629555 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
1629576 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
1629597 CT
1 CT
1629599 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:1632075 original size:181 final size:181
Alignment explanation
Indices: 1631771--1632243 Score: 675
Period size: 181 Copynumber: 2.6 Consensus size: 181
1631761 CGTACTTACG
* * * *
1631771 AAAGTATCGACACTTTCAATATATCTGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATA-CGGTTT
* * *
1631836 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
1631901 AGG-TGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAT-CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
1631952 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACAGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATAC-GGTTT
* *
1632017 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
1632082 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGATCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * *
1632134 AAAGTA-CTGACACTTTAAATGTATTCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGT
1 AAAGTATC-GACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATA-CGGT
* * *
1632197 TTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
63 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1632244 AATTTAGATC
Statistics
Matches: 263, Mismatches: 23, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
180 1 0.00
181 164 0.62
182 96 0.37
183 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGATCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1633737 original size:2 final size:2
Alignment explanation
Indices: 1633726--1633760 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1633716 TCTTTTCATC
1633726 TA TA -A 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
1633761 CACACGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1636400 original size:298 final size:301
Alignment explanation
Indices: 1635830--1636640 Score: 940
Period size: 303 Copynumber: 2.7 Consensus size: 301
1635820 TGTTACACTT
* * * *
1635830 GTGCCCTTTAGTCATATGTTTTGATTGCATTGGAAT-CACCTAACCTTTTCATATTTAGAATCCT
1 GTGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATGCA--TAACCTTCT-GTATTTAGAATCCT
* * * * * * *
1635894 TGACTTTTATTAGTTTTTAGGAAGCTCTATATGGTTTTGAAGT-GCCGGTGTGTGTGAAGGGTCA
63 TGATTTTTATTAGTTGTTAGGAAGCTCTATGTGGCTTTGAAGTCGTCGGTGTGTGTGAAAGGACA
* ** *
1635958 ATAAATGAATAATATATCCGGAATTGATGTGAAATAACCGAAGAGAACATTAAATTTCAATGTTA
128 ATAAATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTCA
* * **
1636023 CCACGTGGGGGAGAGATCTTTCTGTTGATTGGTCACTTTCTCCTTTCCAGAAAACTTGTGTCCTA
193 CCACAT--GGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTA
* *
1636088 AAAGATCATAACTACTATCTTTA-AACGTTACTTGTATTGCATG-T-A
256 AAAGATCATAACTACTATC-TTAGAACATTACTTGCA-TGCATGATAA
*
1636133 -TGCCCTTTTGTCATATTTTTTGATTGCCTTGGAATGCATAACC-TCTGTATTTAGAATCCTTGA
1 GTGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATGCATAACCTTCTGTATTTAGAATCCTTGA
* * * *
1636196 TTTTTATTAGTTGTTAGGAAGCTCTGTGTGGCTTTGAAGTCGTTGGAGTGTGTGAAAGGACTATA
66 TTTTTATTAGTTGTTAGGAAGCTCTATGTGGCTTTGAAGTCGTCGGTGTGTGTGAAAGGACAATA
* * * * * *
1636261 AATGAATAATATACCCGAAAAAGATGTGAAATAACCGAAGAGAACGTGGAATCTCGATGTCACCA
131 AATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTCACCA
* * * * *
1636326 CATGGGAGAGATCTTTTTGGTGGTTGTTCATTTTCTCTTTTCCAGAAAACCCGTGTCCTAAAAGA
196 CATGGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTAAAAGA
* *
1636391 TCATAACTACTATCTTAGAACATTATTTGCATGTATGATACA
261 TCATAACTACTATCTTAGAACATTACTTGCATGCATGATA-A
* * * *
1636433 TGTGCTCTTTTG-CTGTATGTTTTGATTGCCTTGGAATTGCGTAACCTGTCCGTATTTAGAATCC
1 -GTGCCCTTTTGTC-ATATGTTTTGATTGCCTTGGAA-TGCATAACCT-TCTGTATTTAGAATCC
* * * * * *
1636497 TTGATTTTTATTAGTTGTTTGGAATCTCTACGTGGCTTTGAAGACATCGGTGTGTGTG--AGGAA
62 TTGATTTTTATTAGTTGTTAGGAAGCTCTATGTGGCTTTGAAGTCGTCGGTGTGTGTGAAAGGAC
* * * * *
1636560 AATGAAGGGATAATATATCTGGAAATGATGTGAAATAACCGAAGAGAACTTGGAATTTCAATGTC
127 AATAAATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTC
* *
1636625 ACTACATGTGAGAGAT
192 ACCACATGGGAGAGAT
1636641 ATTACTGCTG
Statistics
Matches: 430, Mismatches: 66, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
297 8 0.02
298 79 0.18
299 51 0.12
300 78 0.18
301 6 0.01
302 61 0.14
303 82 0.19
305 65 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (301 bp):
GTGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATGCATAACCTTCTGTATTTAGAATCCTTGA
TTTTTATTAGTTGTTAGGAAGCTCTATGTGGCTTTGAAGTCGTCGGTGTGTGTGAAAGGACAATA
AATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACATGGAATTTCAATGTCACCA
CATGGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTAAAAGA
TCATAACTACTATCTTAGAACATTACTTGCATGCATGATAA
Found at i:1636640 original size:303 final size:298
Alignment explanation
Indices: 1635831--1636640 Score: 909
Period size: 298 Copynumber: 2.7 Consensus size: 298
1635821 GTTACACTTG
* * ** * * *
1635831 TGCCCTTTAGTCATATGTTTTGATTGCATTGGAATCACCTAACCTTTTCATATTTAGAATCCTTG
1 TGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATTGCATAACC-TTCCGTATTTAGAATCCTTG
* * * * *
1635896 ACTTTTATTAGTT-TTTAGGAAGCTCTATATGGTTTTGAAGTGC-CGGTGTGTGTGAAGGGTCAA
65 ATTTTTATTAGTTGTTT-GGAAGCTCTATGTGGCTTTGAAG-ACTCGGTGTGTGTGAA-GGACAA
* * *
1635959 TAAATGAATAATATATCCGGAATTGATGTGAAATAACCGAAGAGAACATT-AAATTTCAATGTTA
127 TAAATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAAC-TTGGAATTTCAATGTCA
* * **
1636023 CCACGTGGGGGAGAGATCTTTCTGTTGATTGGTCACTTTCTCCTTTCCAGAAAACTTGTGTCCTA
191 CCACAT--GGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTA
* *
1636088 AAAGATCATAACTACTATCTTTAAACGTTACTTGTATTGCATGTA
254 AAAGATCATAACTACTATCTTTAAACATTACTTGCATTGCATGTA
* *
1636133 TGCCCTTTTGTCATATTTTTTGATTGCCTTGGAA-TGCATAACC-TCTGTATTTAGAATCCTTGA
1 TGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATTGCATAACCTTCCGTATTTAGAATCCTTGA
* * * * * *
1636196 TTTTTATTAGTTGTTAGGAAGCTCTGTGTGGCTTTGAAGTCGTTGGAGTGTGTGAAAGGACTATA
66 TTTTTATTAGTTGTTTGGAAGCTCTATGTGGCTTTGAAGAC-TCGGTGTGTGTG-AAGGACAATA
* * * * * *
1636261 AATGAATAATATACCCGAAAAAGATGTGAAATAACCGAAGAGAACGTGGAATCTCGATGTCACCA
129 AATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACTTGGAATTTCAATGTCACCA
* * * * *
1636326 CATGGGAGAGATCTTTTTGGTGGTTGTTCATTTTCTCTTTTCCAGAAAACCCGTGTCCTAAAAGA
194 CATGGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTAAAAGA
* *
1636391 TCATAACTACTATC-TTAGAACATTATTTGCA-TGTATGATACA
259 TCATAACTACTATCTTTA-AACATTACTTGCATTGCATG-T--A
* * *
1636433 TGTGCTCTTTTG-CTGTATGTTTTGATTGCCTTGGAATTGCGTAACCTGTCCGTATTTAGAATCC
1 --TGCCCTTTTGTC-ATATGTTTTGATTGCCTTGGAATTGCATAACCT-TCCGTATTTAGAATCC
* * *
1636497 TTGATTTTTATTAGTTGTTTGGAATCTCTACGTGGCTTTGAAGACATCGGTGTGTGTG-AGGAAA
62 TTGATTTTTATTAGTTGTTTGGAAGCTCTATGTGGCTTTGAAGAC-TCGGTGTGTGTGAAGGACA
* * * *
1636561 ATGAAGGGATAATATATCTGGAAATGATGTGAAATAACCGAAGAGAACTTGGAATTTCAATGTCA
126 ATAAATGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACTTGGAATTTCAATGTCA
* *
1636626 CTACATGTGAGAGAT
191 CCACATGGGAGAGAT
1636641 ATTACTGCTG
Statistics
Matches: 425, Mismatches: 68, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
297 8 0.02
298 80 0.19
299 49 0.12
300 74 0.17
301 9 0.02
302 60 0.14
303 80 0.19
305 65 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (298 bp):
TGCCCTTTTGTCATATGTTTTGATTGCCTTGGAATTGCATAACCTTCCGTATTTAGAATCCTTGA
TTTTTATTAGTTGTTTGGAAGCTCTATGTGGCTTTGAAGACTCGGTGTGTGTGAAGGACAATAAA
TGAATAATATATCCGGAAATGATGTGAAATAACCGAAGAGAACTTGGAATTTCAATGTCACCACA
TGGGAGAGATCTTTCTGGTGATTGGTCACTTTCTCCTTTCCAGAAAACCCGTGTCCTAAAAGATC
ATAACTACTATCTTTAAACATTACTTGCATTGCATGTA
Found at i:1637547 original size:22 final size:22
Alignment explanation
Indices: 1637519--1637566 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1637509 GTTAGTGATA
1637519 TGCTTGAATAATCTCGAGTT-GG
1 TGCTTGAATAATCTCGA-TTCGG
1637541 TGCTTGAATAATCTCGATTCGG
1 TGCTTGAATAATCTCGATTCGG
1637563 TGCT
1 TGCT
1637567 ATGATTGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (22 bp):
TGCTTGAATAATCTCGATTCGG
Found at i:1641276 original size:29 final size:30
Alignment explanation
Indices: 1641239--1641306 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1641229 TAATGTACCT
*
1641239 TTTGTCCCCTGAATTTGG-TTTGATATGCAA
1 TTTG-CCCCTGAATTTGGCTTAGATATGCAA
*
1641269 TTTGCCCC-GACTTTGGCTTAGATATGCAA
1 TTTGCCCCTGAATTTGGCTTAGATATGCAA
*
1641298 TTTTCCCCT
1 TTTGCCCCT
1641307 TATTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.21
29 22 0.67
30 4 0.12
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (30 bp):
TTTGCCCCTGAATTTGGCTTAGATATGCAA
Done.