Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 142 of 213
Found at i:42528922 original size:30 final size:31
Alignment explanation
Indices: 42528886--42528966 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 31
42528876 TGACGATTTC
42528886 GCCACAAAGGCTCACATATAACAGAGAA-AA
1 GCCACAAAGGCTCACATATAACAGAGAACAA
*
42528916 GCCACAAATGCT--CATATAACAGAGAACAA
1 GCCACAAAGGCTCACATATAACAGAGAACAA
*
42528945 -CCAAAAAGGCTTTCACATATAA
1 GCCACAAAGGC--TCACATATAA
42528967 TAGATTCAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 22 0.51
29 2 0.05
30 12 0.28
32 7 0.16
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (31 bp):
GCCACAAAGGCTCACATATAACAGAGAACAA
Found at i:42530101 original size:177 final size:181
Alignment explanation
Indices: 42529794--42530143 Score: 564
Period size: 177 Copynumber: 2.0 Consensus size: 181
42529784 TTACCTAGAG
*
42529794 TTAACTAAGTTTTCTTTCAAAAATCACCTCACATAGTGCTTATAATCTTCATATCTGAAGTCAAA
1 TTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGCTTAT-ATCTTCATATCTGAAGTCAAA
42529859 CATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATGCCTAGATC
65 CATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATGCCTAGATC
* *
42529924 CAAACCAATTACTACCATTCATGATCAAACATTGAGCACAACTCACCTAAAC
130 CAAACCAATTACTACCACTCATGATCAAACAATGAGCACAACTCACCTAAAC
* * * *
42529976 TTAACTAAGTTTTCTTTCAAAATTCACATCACATGGTGC-T-T-T-TTCATCTCTTAAGTCAAAC
1 TTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGCTTATATCTTCATATCTGAAGTCAAAC
* * *
42530037 ATAGAAGCCACCATACACACACATTGAATTTGCTTACCTTGACCTCAAACACCATGCTTAGATCC
66 ATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATGCCTAGATCC
*
42530102 AAACCAATTACTATCACTCATGATCAAACAATGAGCACAACT
131 AAACCAATTACTACCACTCATGATCAAACAATGAGCACAACT
42530144 TAAGAGTTAA
Statistics
Matches: 157, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
177 118 0.75
178 1 0.01
180 1 0.01
181 1 0.01
182 36 0.23
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.28
Consensus pattern (181 bp):
TTAACTAAGTTTTCTTTCAAAAATCACATCACATAGTGCTTATATCTTCATATCTGAAGTCAAAC
ATACAAGCCACCATACACACACATTGAATTTGCTAACCTTGACCTCAAACACCATGCCTAGATCC
AAACCAATTACTACCACTCATGATCAAACAATGAGCACAACTCACCTAAAC
Found at i:42535145 original size:43 final size:43
Alignment explanation
Indices: 42535054--42535145 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
42535044 CTTTTGGGGA
* *
42535054 CACACGACTGTGTCACCAGGCCATGTGTCACACACGGCTGAGT
1 CACACGACTATGTCACCAGGCCATGTGTCACACACGGCTAAGT
* ** * * *
42535097 GACACGACTATGTTGCCAGGCCGTGTGTCACATATGGCTAAGT
1 CACACGACTATGTCACCAGGCCATGTGTCACACACGGCTAAGT
42535140 CACACG
1 CACACG
42535146 CCTGTGTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (43 bp):
CACACGACTATGTCACCAGGCCATGTGTCACACACGGCTAAGT
Found at i:42538550 original size:14 final size:14
Alignment explanation
Indices: 42538531--42538557 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42538521 GTGGTCTAGT
42538531 TGAACTGAACCGAG
1 TGAACTGAACCGAG
42538545 TGAACTGAACCGA
1 TGAACTGAACCGA
42538558 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:42548873 original size:14 final size:14
Alignment explanation
Indices: 42548854--42548880 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42548844 GTGGTCCAGT
42548854 TGAACTGAACCGAG
1 TGAACTGAACCGAG
42548868 TGAACTGAACCGA
1 TGAACTGAACCGA
42548881 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:42552206 original size:47 final size:47
Alignment explanation
Indices: 42552114--42552206 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
42552104 TTTTTGAAAG
**
42552114 TCTGAAGGATTTCTACTGATACTTAGGTGGACAAGTATCTTTAGAAC
1 TCTGAAGGATTTCTACTGATACTTAGGTGGACAAGTATCGGTAGAAC
42552161 TCTGAAGGATTTCTACTGATACTTAGGTGGACAAGTATCGGTAGAA
1 TCTGAAGGATTTCTACTGATACTTAGGTGGACAAGTATCGGTAGAA
42552207 ATCAAAATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (47 bp):
TCTGAAGGATTTCTACTGATACTTAGGTGGACAAGTATCGGTAGAAC
Found at i:42552627 original size:31 final size:31
Alignment explanation
Indices: 42552592--42552662 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
42552582 CCTCAAACAC
42552592 CATGCCAAGATCTAAACCAATTACTACCATT
1 CATGCCAAGATCTAAACCAATTACTACCATT
*
42552623 CATGCCAAGATCTAAACCAATTCCTACCATT
1 CATGCCAAGATCTAAACCAATTACTACCATT
42552654 CATGACCAA
1 CATG-CCAA
42552663 ACATTTTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.38, C:0.31, G:0.07, T:0.24
Consensus pattern (31 bp):
CATGCCAAGATCTAAACCAATTACTACCATT
Found at i:42557883 original size:20 final size:20
Alignment explanation
Indices: 42557807--42557882 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
42557797 AAACTTATGC
42557807 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
*
42557827 TAAGTAGAT-AAA-GTGAAGAG
1 TAAGTAAATGAAATG-GAA-AG
* *
42557847 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
42557867 TAAGTAAATGAAATGG
1 TAAGTAAATGAAATGG
42557883 TTCATCATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 35 0.74
21 4 0.09
22 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:42561689 original size:30 final size:30
Alignment explanation
Indices: 42561655--42561733 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
42561645 CTTGACTTAA
* *
42561655 ATAGCCACAAACGCATCCATACATCATTAG
1 ATAGCCACAAAGGCATCCACACATCATTAG
***
42561685 ATAGCCACAAAGGTGCCCACACATCATTAG
1 ATAGCCACAAAGGCATCCACACATCATTAG
* *
42561715 ATAGCAACAAGGGCATCCA
1 ATAGCCACAAAGGCATCCA
42561734 AATTCATTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.16
Consensus pattern (30 bp):
ATAGCCACAAAGGCATCCACACATCATTAG
Found at i:42562280 original size:54 final size:54
Alignment explanation
Indices: 42562218--42562324 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
42562208 GTGGCCTTTG
* * *
42562218 TTTCCCCATATGATGCCATAG-CTAATGGCTAGACCTTAGACTATATGGTCTTCT
1 TTTCCCCATATGATGCCATAGTC-AACGACTAGACCTTACACTATATGGTCTTCT
* **
42562272 TTTCCCCATTTGATGCCATAGTCAACGACTAGGGCTTACACTATATGGTCTTC
1 TTTCCCCATATGATGCCATAGTCAACGACTAGACCTTACACTATATGGTCTTC
42562325 AATTGCCACT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 45 0.98
55 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
TTTCCCCATATGATGCCATAGTCAACGACTAGACCTTACACTATATGGTCTTCT
Found at i:42568054 original size:28 final size:27
Alignment explanation
Indices: 42568002--42568070 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
42567992 TGGTTATACA
* *
42568002 TATATTATATATATGCATGATTTTATCT
1 TATATAATATATATGCATGACTTTAT-T
*
42568030 TATATAATATATATGCATGGCTTTATT
1 TATATAATATATATGCATGACTTTATT
* *
42568057 TACATAGTATATAT
1 TATATAATATATAT
42568071 TAATGGATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (27 bp):
TATATAATATATATGCATGACTTTATT
Found at i:42578179 original size:27 final size:27
Alignment explanation
Indices: 42578149--42578208 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
42578139 ATCCCAACGA
** * *
42578149 ACTACTCTGTGTTTACTGTTTCGATAG
1 ACTACTCCATGTTTACTGTTCCAATAG
* *
42578176 ACTACCCCATTTTTACTGTTCCAATAG
1 ACTACTCCATGTTTACTGTTCCAATAG
42578203 ACTACT
1 ACTACT
42578209 TCGTATTTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (27 bp):
ACTACTCCATGTTTACTGTTCCAATAG
Found at i:42582850 original size:12 final size:12
Alignment explanation
Indices: 42582833--42582858 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42582823 AGGTGGTAAC
42582833 ATTAACATATTT
1 ATTAACATATTT
42582845 ATTAACATATTT
1 ATTAACATATTT
42582857 AT
1 AT
42582859 CATATTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAACATATTT
Found at i:42590853 original size:7 final size:7
Alignment explanation
Indices: 42590843--42590869 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42590833 ATAAATCACA
42590843 AATAAAG
1 AATAAAG
42590850 AATAAAG
1 AATAAAG
42590857 AATAAAG
1 AATAAAG
42590864 AATAAA
1 AATAAA
42590870 TTAGTAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:42591482 original size:20 final size:20
Alignment explanation
Indices: 42591457--42591497 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42591447 ATTTAATCAC
*
42591457 ATAAACCTAAAAACTATGCA
1 ATAAACCTAAAAACAATGCA
42591477 ATAAACCTAAAAACAATGCA
1 ATAAACCTAAAAACAATGCA
42591497 A
1 A
42591498 GATAATAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.05, T:0.17
Consensus pattern (20 bp):
ATAAACCTAAAAACAATGCA
Found at i:42604382 original size:25 final size:26
Alignment explanation
Indices: 42604333--42604382 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
42604323 AGAAAATTCA
* *
42604333 ATTAATTATTGTAAATTAGTGCTATG
1 ATTAATTAATGTAAATTAGTACTATG
*
42604359 ATTAA-TAATGTAAATTATTACTAT
1 ATTAATTAATGTAAATTAGTACTAT
42604383 TTTTTTCGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTAATTAATGTAAATTAGTACTATG
Found at i:42604595 original size:22 final size:22
Alignment explanation
Indices: 42604565--42604614 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
42604555 ATTATTAAGT
*
42604565 TGAAAAAAATTCAATCGAATGA
1 TGAATAAAATTCAATCGAATGA
42604587 TGAATAAAATTCAATCGAATGA
1 TGAATAAAATTCAATCGAATGA
42604609 TGAATA
1 TGAATA
42604615 TATGTGTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (22 bp):
TGAATAAAATTCAATCGAATGA
Found at i:42611234 original size:16 final size:16
Alignment explanation
Indices: 42611213--42611243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42611203 AAATAAAGTA
*
42611213 AAAGAATAAAAGAAAT
1 AAAGAAGAAAAGAAAT
42611229 AAAGAAGAAAAGAAA
1 AAAGAAGAAAAGAAA
42611244 CAGAGACCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAGAAGAAAAGAAAT
Found at i:42616343 original size:25 final size:27
Alignment explanation
Indices: 42616315--42616385 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
42616305 ATAGTGATCA
*
42616315 CAGCTCACCAGGCCCACT-GCAA-CCC
1 CAGCTCACCAAGCCCACTAGCAATCCC
*
42616340 CAGCTCCCCAAGCCCACTAGCAATCCC
1 CAGCTCACCAAGCCCACTAGCAATCCC
*
42616367 TA-CTGCACCAAGCCCACTA
1 CAGCT-CACCAAGCCCACTA
42616386 ACGATCATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 16 0.41
26 6 0.15
27 17 0.44
ACGTcount: A:0.27, C:0.49, G:0.13, T:0.11
Consensus pattern (27 bp):
CAGCTCACCAAGCCCACTAGCAATCCC
Found at i:42616445 original size:27 final size:27
Alignment explanation
Indices: 42616427--42616487 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
42616417 CCCTGTTCTA
42616427 CAGGCCTTCTGGCAAACCCCAGCTCAT
1 CAGGCCTTCTGGCAAACCCCAGCTCAT
* * * *
42616454 CAGGCCTTCTGGCGAACACCAGTTCAC
1 CAGGCCTTCTGGCAAACCCCAGCTCAT
42616481 CAGGCCT
1 CAGGCCT
42616488 CAAACTCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.39, G:0.21, T:0.18
Consensus pattern (27 bp):
CAGGCCTTCTGGCAAACCCCAGCTCAT
Found at i:42621936 original size:11 final size:11
Alignment explanation
Indices: 42621920--42621959 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
42621910 ATACTTGTAT
42621920 TGGTGATATAA
1 TGGTGATATAA
42621931 TGGTGATATAA
1 TGGTGATATAA
42621942 TGGTGATATAA
1 TGGTGATATAA
42621953 TGGTGAT
1 TGGTGAT
42621960 GTATTGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (11 bp):
TGGTGATATAA
Found at i:42632645 original size:22 final size:22
Alignment explanation
Indices: 42632617--42632738 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
42632607 TTCCACATCC
42632617 ATCACATTAGCCATTCGGCCTT
1 ATCACATTAGCCATTCGGCCTT
* * * *
42632639 ATCACATATATACACTTTC-ACATT
1 ATCACAT-TA-GC-CATTCGGCCTT
*
42632663 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTAGCCATTCGGCCTT
* * *
42632686 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-TA-GCCA--TTCGGCCTT
*
42632710 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTAGCCATTCGGCCTT
42632733 ATCACA
1 ATCACA
42632739 CATACACATG
Statistics
Matches: 71, Mismatches: 17, Indels: 24
0.63 0.15 0.21
Matches are distributed among these distances:
22 26 0.37
23 13 0.18
24 12 0.17
25 20 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTAGCCATTCGGCCTT
Found at i:42632652 original size:47 final size:47
Alignment explanation
Indices: 42632589--42632811 Score: 315
Period size: 47 Copynumber: 4.7 Consensus size: 47
42632579 CCCTTCGGGA
* * * *
42632589 CTTATCACATTTATACACTTCCACATCCATCACATTAGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
42632636 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
42632683 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
42632730 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
42632777 CTTATCACATATATATACACTTTCACATTCATCAC
1 CTTATCAC--ATATATACACTTTCACATTCATCAC
42632812 TTTCCAATGA
Statistics
Matches: 159, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 136 0.86
49 21 0.13
50 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:42634671 original size:56 final size:56
Alignment explanation
Indices: 42634609--42634728 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
42634599 TATTAGTTTA
42634609 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATATTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATATTTCATGACATGTT
* *
42634665 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATATTTCATGACATGTT
42634721 TTGCCCAT
1 TTGCCCAT
42634729 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATATTTCATGACATGTT
Found at i:42635820 original size:25 final size:25
Alignment explanation
Indices: 42635783--42635834 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
42635773 AAGGAATTCG
42635783 CACACACACAGTGC-CTCTAATCATT
1 CACACACACAGTGCTCT-TAATCATT
* *
42635808 CACACACATAGTGCTCTTATTCATT
1 CACACACACAGTGCTCTTAATCATT
42635833 CA
1 CA
42635835 TTATTACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.29
Consensus pattern (25 bp):
CACACACACAGTGCTCTTAATCATT
Found at i:42636042 original size:40 final size:40
Alignment explanation
Indices: 42636010--42636353 Score: 465
Period size: 40 Copynumber: 8.6 Consensus size: 40
42636000 CCAGCATGAT
* * * * *
42636010 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*** * *
42636050 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
42636090 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
42636130 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
42636170 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
42636210 TGCTGTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
*
42636250 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* * * * * *
42636290 TGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
1 TGCTCTTCGGAACTTAGCCCGGATACA-TCACTAGCACGAA
* *
42636331 TGC-CTTCGGATCTTAGTCCGGAT
1 TGCTCTTCGGAACTTAGCCCGGAT
42636354 GTAGTCGCTT
Statistics
Matches: 272, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 260 0.96
41 12 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:42638719 original size:47 final size:47
Alignment explanation
Indices: 42638656--42638878 Score: 299
Period size: 47 Copynumber: 4.7 Consensus size: 47
42638646 CCCTTCGGGA
* * * *
42638656 CTTATCACATTTATACACT-TCCACATCCATTACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
42638703 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
* *
42638750 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* * *
42638797 CTTATCACACATACACATGTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
42638844 CTTATCACATATATATACACT-TTCACATTCATCAC
1 CTTATCAC--ATATATACA-TGTTCACATTCATCAC
42638879 TTTCCAATGA
Statistics
Matches: 159, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 136 0.86
49 21 0.13
50 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:42640583 original size:56 final size:56
Alignment explanation
Indices: 42640516--42640635 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
42640506 TATTAGTTTA
42640516 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
42640572 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
42640628 TTGCCCAT
1 TTGCCCAT
42640636 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:42642454 original size:33 final size:33
Alignment explanation
Indices: 42642411--42642483 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
42642401 TTGCCACTAT
*
42642411 GGAGAAGGCCACAAAAGGGCCAGAGGGAGATAA
1 GGAGAAGGCCACAAAAGGACCAGAGGGAGATAA
* * *
42642444 TGAGAAGGCCACAACAGGACCAGAGGGAGATGA
1 GGAGAAGGCCACAAAAGGACCAGAGGGAGATAA
42642477 GGAGAAG
1 GGAGAAG
42642484 ACTAAATCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.40, T:0.04
Consensus pattern (33 bp):
GGAGAAGGCCACAAAAGGACCAGAGGGAGATAA
Found at i:42650013 original size:50 final size:50
Alignment explanation
Indices: 42649945--42650286 Score: 380
Period size: 50 Copynumber: 6.7 Consensus size: 50
42649935 TTTCTTGTTC
* * * * ** * *
42649945 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** *
42649995 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42650045 TGCCAACGCCATGTCTCAGACATGGTCTTATATGGGACCTCTCTTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42650095 TGCCAACGCCATGTCCTAGACATGGTCTTTCATGGGACGTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42650145 TGCCAACGGCATGTCCTAGACATGGCCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42650195 TGCCAACGGCATGTCCCAGACATGGTCCTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* *
42650251 TGCCAATGACATGTCCCAGACATGGT-TTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
42650287 TCTTTTTACC
Statistics
Matches: 251, Mismatches: 35, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
50 212 0.84
53 5 0.02
55 9 0.04
56 25 0.10
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42654985 original size:21 final size:21
Alignment explanation
Indices: 42654961--42655007 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
42654951 TCTGATAGTA
42654961 TTCTCAAGCCAAAATTCTGCT
1 TTCTCAAGCCAAAATTCTGCT
42654982 TTCTCAAGCCAAAATTCTGCT
1 TTCTCAAGCCAAAATTCTGCT
42655003 TTCTC
1 TTCTC
42655008 TACATCATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.36
Consensus pattern (21 bp):
TTCTCAAGCCAAAATTCTGCT
Found at i:42656972 original size:50 final size:50
Alignment explanation
Indices: 42656839--42657130 Score: 271
Period size: 50 Copynumber: 5.7 Consensus size: 50
42656829 TACTGCTAAT
* * * ** * * *
42656839 GCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCTC-AT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGC-CAAC
**** * *
42656889 GCCATGTCCCAAGACATGGTCTTTTGGGGGACCTCTCAGCTTGGTGCCAAC
1 GCCATGTCCC-AGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
42656940 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGGTCCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * *
42656990 GCCATGTCCCAGACGTGGTCTTACATGGGACCTCTTATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * * * *
42657040 GCCATGCCCCAGACATGGTCTGACTTGGGACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTGCCAAC
* *
42657096 GCCATGTCCCAGACATGGTCTTAAATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42657131 TTACCCAAAT
Statistics
Matches: 197, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
50 119 0.60
51 35 0.18
53 5 0.03
56 38 0.19
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:42657109 original size:56 final size:50
Alignment explanation
Indices: 42656782--42657131 Score: 213
Period size: 50 Copynumber: 6.9 Consensus size: 50
42656772 TGAATATAAC
* * * * * *
42656782 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA--TGTT-TCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTTATCTCG
* * * * * ** * * *
42656829 TACTGCTAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTTATCTCG
* ***** * * *
42656881 GTGCTC-ATGCCATGTCCCAAGACATGGTCTTTTGGGGGACCTCTCAGCTTG
1 ATGC-CAATGCCATGTCCC-AGACATGGTCTGACATGGGACCTCTTATCTCG
* * * * *
42656932 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTTATCTCG
* * * * *
42656982 GTCCCAACGCCATGTCCCAGACGTGGTCTTACATGGGACCTCTTATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTTATCTCG
* * *
42657032 GTGCCAATGCCATGCCCCAGACATGGTCTGACTTGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCT--T-ATCTC---G
* * *
42657088 ATGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATCTCTT
1 ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTT
42657132 TACCCAAATG
Statistics
Matches: 240, Mismatches: 49, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.00
49 30 0.12
50 124 0.52
51 37 0.15
52 4 0.02
53 5 0.02
54 1 0.00
56 38 0.16
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTGACATGGGACCTCTTATCTCG
Found at i:42658947 original size:31 final size:31
Alignment explanation
Indices: 42658891--42658951 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
42658881 GGGGAAAAGG
* **
42658891 AAGGACAAGGTTTTCCATGTGATATATTATA
1 AAGGACAAGGTTTTACATGAAATATATTATA
*
42658922 AAGGACAAGGTTTTATATGAAATATATTAT
1 AAGGACAAGGTTTTACATGAAATATATTAT
42658952 GCGAGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (31 bp):
AAGGACAAGGTTTTACATGAAATATATTATA
Found at i:42661280 original size:19 final size:19
Alignment explanation
Indices: 42661256--42661300 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
42661246 TGAAATGTGG
42661256 GTGCATTTCAAAGCCCCAT
1 GTGCATTTCAAAGCCCCAT
*
42661275 GTGCATTTCTAAGCCCCAT
1 GTGCATTTCAAAGCCCCAT
42661294 GTGCATT
1 GTGCATT
42661301 CCCCTAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGCATTTCAAAGCCCCAT
Found at i:42661366 original size:17 final size:17
Alignment explanation
Indices: 42661344--42661376 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42661334 CACTAACATG
*
42661344 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
42661361 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
42661377 GCGTACTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:42661512 original size:14 final size:15
Alignment explanation
Indices: 42661488--42661517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42661478 TTGCACGATG
42661488 TTTCTTTCTCCTCCT
1 TTTCTTTCTCCTCCT
42661503 TTTC-TTCTCCTCCT
1 TTTCTTTCTCCTCCT
42661517 T
1 T
42661518 CTTTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTCTTTCTCCTCCT
Found at i:42670648 original size:30 final size:30
Alignment explanation
Indices: 42670612--42670668 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42670602 AATGACAAAT
42670612 GGTCGTGTCACCAAGTTGTGTCTGTCACAC
1 GGTCGTGTCACCAAGTTGTGTCTGTCACAC
* *
42670642 GGTCGTGTCGCCAAGTTGTGTGTGTCA
1 GGTCGTGTCACCAAGTTGTGTCTGTCA
42670669 TACAACCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.23, G:0.32, T:0.32
Consensus pattern (30 bp):
GGTCGTGTCACCAAGTTGTGTCTGTCACAC
Found at i:42670679 original size:30 final size:30
Alignment explanation
Indices: 42670615--42670679 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
42670605 GACAAATGGT
***
42670615 CGTGTCACCAAGTTGTGTCTGTCACACGGT
1 CGTGTCACCAAGTTGTGTCTGTCACACAAC
* * *
42670645 CGTGTCGCCAAGTTGTGTGTGTCATACAAC
1 CGTGTCACCAAGTTGTGTCTGTCACACAAC
42670675 CGTGT
1 CGTGT
42670680 AACAGCCCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.31
Consensus pattern (30 bp):
CGTGTCACCAAGTTGTGTCTGTCACACAAC
Found at i:42672498 original size:48 final size:48
Alignment explanation
Indices: 42672405--42672501 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
42672395 GTGGTGTATT
* **
42672405 TATGTTGTTTTAAGGACTGATGTTTGGTGTATTAATTTAGCAGAAAAA
1 TATGTTATTTTAAGGACTGATGTTTGGTGTATTAATGCAGCAGAAAAA
* * *
42672453 TATGTTATTTTAAGGACTGTTGTTTGTTGTATTAATGCAGTAGAAAAA
1 TATGTTATTTTAAGGACTGATGTTTGGTGTATTAATGCAGCAGAAAAA
42672501 T
1 T
42672502 TCTTGTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (48 bp):
TATGTTATTTTAAGGACTGATGTTTGGTGTATTAATGCAGCAGAAAAA
Found at i:42672638 original size:91 final size:91
Alignment explanation
Indices: 42672453--42672641 Score: 229
Period size: 91 Copynumber: 2.1 Consensus size: 91
42672443 AGCAGAAAAA
* * * * * *
42672453 TATGTTATTTTAAGGACTGTTGTTTGTTGTATTAATGCAGTAGAAAAATTCTTGTTTAGTTGTTA
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGATGTCA
* * *
42672518 ATTAATGTTGTCTAAGTGACTGTATT
66 ATAAATGTGGTCTAAGTGACTGTAAT
* * *
42672544 TATGTTGTTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAG-TAAATTGTTGTTTAGATGTCA
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGATGTCA
*
42672608 ATAAATGTGGTCTGAA-TGACTTTAAAT
66 ATAAATGTGGTCT-AAGTGACTGT-AAT
42672635 TATGTTA
1 TATGTTA
42672642 ATAATGGTCG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
90 34 0.41
91 48 0.59
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (91 bp):
TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGATGTCA
ATAAATGTGGTCTAAGTGACTGTAAT
Found at i:42675353 original size:27 final size:27
Alignment explanation
Indices: 42675319--42675370 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
42675309 GTGCAATATA
*
42675319 TGTGGCAGAGCCACCAGTAATAGTATT
1 TGTGGCAGAGCCACCAGTAACAGTATT
42675346 TGTGGCAGAGCCACCAGTAACAGTA
1 TGTGGCAGAGCCACCAGTAACAGTA
42675371 CTTCCTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (27 bp):
TGTGGCAGAGCCACCAGTAACAGTATT
Found at i:42675570 original size:26 final size:26
Alignment explanation
Indices: 42675541--42675597 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
42675531 CGGTCATTCG
* * *
42675541 ACCCTTTGGGGGTATTTCAGTGATTT
1 ACCCTTCGAGGGTATTTCAGTAATTT
* *
42675567 ACCCATCGAGGGTATTTCGGTAATTT
1 ACCCTTCGAGGGTATTTCAGTAATTT
42675593 ACCCT
1 ACCCT
42675598 ATTTCGGTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (26 bp):
ACCCTTCGAGGGTATTTCAGTAATTT
Found at i:42682651 original size:48 final size:48
Alignment explanation
Indices: 42682556--42682652 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
42682546 GTGGTGGATT
* ** *
42682556 TATGCTATTTTAAGGACTGTTGTTTTGTGTATTAATTTAGCAAAAAAA
1 TATGCTATTTTAAGGACTATTGTTTTGTGTATTAATGCAACAAAAAAA
* * *
42682604 TATGTTATTTTAAGGACTATT-TTTTGGTGTATTAATGCAATAGAAAAA
1 TATGCTATTTTAAGGACTATTGTTTT-GTGTATTAATGCAACAAAAAAA
42682652 T
1 T
42682653 TCTTGTTTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (48 bp):
TATGCTATTTTAAGGACTATTGTTTTGTGTATTAATGCAACAAAAAAA
Found at i:42682789 original size:91 final size:91
Alignment explanation
Indices: 42682604--42682792 Score: 224
Period size: 91 Copynumber: 2.1 Consensus size: 91
42682594 AGCAAAAAAA
* * * *
42682604 TATGTTATTTTAAGGACTATTTTTTGGTGTATTAATGCAATAGAAAAATTCTTGTTTAGTAGTCA
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAACAGAAAAATTCTGGTTTAGTAGTCA
* * *
42682669 ATTAATGTTGTCTAAGTGATTGTATT
66 ATAAATGTGGTCTAAGTGATTGTAAT
* * *
42682695 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAG-TAAATTGTGGTTTAG-ATGTC
1 TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAACAGAAAAATTCTGGTTTAGTA-GTC
42682758 AATAAATGTGGTCTGAA-TGACTT-TAAAT
65 AATAAATGTGGTCT-AAGTGA-TTGT-AAT
42682786 TATGTTA
1 TATGTTA
42682793 ATAATGGTCG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
89 1 0.01
90 31 0.37
91 52 0.62
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (91 bp):
TATGTTATTTTAAGGACTATTGTTTGGTGTATTAAAGCAACAGAAAAATTCTGGTTTAGTAGTCA
ATAAATGTGGTCTAAGTGATTGTAAT
Found at i:42684128 original size:36 final size:36
Alignment explanation
Indices: 42684087--42684182 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
42684077 GTATATTTGA
*
42684087 ATTGATATACTTGTGATATTATAAGTGATTTGGCCT
1 ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
* *
42684123 ATTGATATACTTGTGATATTATAAGTTATTCGGGCT
1 ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
* *
42684159 AATGATATAGTTGTGATATT-TAAG
1 ATTGATATACTTGTGATATTATAAG
42684183 AGTGATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (36 bp):
ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
Found at i:42686555 original size:33 final size:33
Alignment explanation
Indices: 42686513--42686583 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42686503 GCCACTATGA
42686513 AGAAGGCCACAAAAGGACCAGAGGGAGATAAGG
1 AGAAGGCCACAAAAGGACCAGAGGGAGATAAGG
* * *
42686546 AGAAGGCCACAACAGGACTAGAGGGAGATGAGG
1 AGAAGGCCACAAAAGGACCAGAGGGAGATAAGG
42686579 AGAAG
1 AGAAG
42686584 ACTAAATCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.14, G:0.38, T:0.04
Consensus pattern (33 bp):
AGAAGGCCACAAAAGGACCAGAGGGAGATAAGG
Found at i:42698303 original size:40 final size:40
Alignment explanation
Indices: 42698223--42698303 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
42698213 GATCAGGGGC
* *
42698223 ATCGAAGTGCAAAAAGGAGCACAGATGTGCATTTAGGGGT
1 ATCGAAGTGCAAAAAGGAGCACAAATGTGCATTTAAGGGT
* * * *
42698263 ATCGAAGTTCAAACAGGGGCATAAATGTGCATTTAAGGGT
1 ATCGAAGTGCAAAAAGGAGCACAAATGTGCATTTAAGGGT
42698303 A
1 A
42698304 CCAAAGTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (40 bp):
ATCGAAGTGCAAAAAGGAGCACAAATGTGCATTTAAGGGT
Found at i:42698859 original size:15 final size:15
Alignment explanation
Indices: 42698839--42698869 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42698829 CAATGCTAAC
42698839 TGAACTTATTTCTAT
1 TGAACTTATTTCTAT
42698854 TGAACTTATTTCTAT
1 TGAACTTATTTCTAT
42698869 T
1 T
42698870 TTAATACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (15 bp):
TGAACTTATTTCTAT
Found at i:42700931 original size:19 final size:20
Alignment explanation
Indices: 42700906--42700953 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
42700896 ATTTTACAAT
*
42700906 TTTCAAAATAATTT-TTAAAA
1 TTTCAAAAT-ATTTATAAAAA
42700926 -TTCAAAATATTTATAAAAA
1 TTTCAAAATATTTATAAAAA
42700945 TTTCAAAAT
1 TTTCAAAAT
42700954 TTATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 8 0.32
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTCAAAATATTTATAAAAA
Found at i:42700951 original size:20 final size:20
Alignment explanation
Indices: 42700894--42700953 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
42700884 ATTACACGGG
* *
42700894 TAATTTTACAATTTTCAAAA
1 TAATTTTAAAAATTTCAAAA
*
42700914 TAATTTTTAAAA-TTCAAAA
1 TAATTTTAAAAATTTCAAAA
42700933 T-ATTTATAAAAATTTCAAAA
1 TAATTT-TAAAAATTTCAAAA
42700953 T
1 T
42700954 TTATATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.12
19 13 0.38
20 17 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATTTTAAAAATTTCAAAA
Found at i:42700983 original size:26 final size:26
Alignment explanation
Indices: 42700932--42700984 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
42700922 AAAATTCAAA
*
42700932 ATATTTATAAAAATTTCAAAATTTAT
1 ATATTTATAAAAATTTCAAAAATTAT
* *
42700958 ATATTTTTAACAATTAT-AAAAATTAT
1 ATATTTATAAAAATT-TCAAAAATTAT
42700984 A
1 A
42700985 AAAAAAACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATTTATAAAAATTTCAAAAATTAT
Found at i:42701004 original size:20 final size:19
Alignment explanation
Indices: 42700974--42701038 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
42700964 TTAACAATTA
42700974 TAAAAATTATAAAAAAAACC
1 TAAAAA-TATAAAAAAAACC
* **
42700994 TAAAGAATATATAAAAAGAGT
1 TAAA-AATATA-AAAAAAACC
* *
42701015 TAAAAATCTAAAAAAACCC
1 TAAAAATATAAAAAAAACC
42701034 TAAAA
1 TAAAA
42701039 TAAAAACCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
19 10 0.29
20 13 0.37
21 12 0.34
ACGTcount: A:0.66, C:0.09, G:0.05, T:0.20
Consensus pattern (19 bp):
TAAAAATATAAAAAAAACC
Found at i:42701053 original size:15 final size:14
Alignment explanation
Indices: 42701026--42701052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42701016 AAAAATCTAA
42701026 AAAAACCCTAAAAT
1 AAAAACCCTAAAAT
42701040 AAAAACCCTAAAA
1 AAAAACCCTAAAA
42701053 AACTCTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAACCCTAAAAT
Found at i:42701083 original size:10 final size:11
Alignment explanation
Indices: 42701040--42701085 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
42701030 ACCCTAAAAT
42701040 AAAAACC-CTA
1 AAAAACCTCTA
42701050 AAAAA-CTCTA
1 AAAAACCTCTA
*
42701060 AACAAAACTCTA
1 AA-AAACCTCTA
42701072 AAAAACCT-TA
1 AAAAACCTCTA
42701082 AAAA
1 AAAA
42701086 TCCTAAACCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 1 0.03
10 16 0.50
11 8 0.25
12 7 0.22
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAACCTCTA
Found at i:42701340 original size:23 final size:23
Alignment explanation
Indices: 42701312--42701374 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
42701302 ATAAAAAATA
*
42701312 ACCAAAATGTTATAAAATTT-TTT
1 ACCAAAAT-ATATAAAATTTATTT
* *
42701335 ACCAAAATATATATATTTTATTT
1 ACCAAAATATATAAAATTTATTT
42701358 ACCAAAATATATCAAAA
1 ACCAAAATATAT-AAAA
42701375 AACAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 8 0.24
23 23 0.70
24 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (23 bp):
ACCAAAATATATAAAATTTATTT
Found at i:42701460 original size:27 final size:27
Alignment explanation
Indices: 42701430--42701482 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
42701420 GCACTGGTCA
**
42701430 TGCCAATGGCATTGGCAGCACCAATGG
1 TGCCAATACCATTGGCAGCACCAATGG
* *
42701457 TGCCAATACCTTTGGCGGCACCAATG
1 TGCCAATACCATTGGCAGCACCAATG
42701483 TATAATAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (27 bp):
TGCCAATACCATTGGCAGCACCAATGG
Found at i:42701532 original size:4 final size:4
Alignment explanation
Indices: 42701523--42701653 Score: 90
Period size: 4 Copynumber: 31.0 Consensus size: 4
42701513 GAAGGAGAGG
* *
42701523 GAAA GAAA GAAA GAAA GAAA GTAGAG GAAA GAAA GAAA AAGAA GAAAA
1 GAAA GAAA GAAA GAAA GAAA G-A-AA GAAA GAAA GAAA GA-AA G-AAA
* *
42701571 GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA
1 G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
42701616 GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
42701654 AGGAAATGAG
Statistics
Matches: 105, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
3 11 0.10
4 59 0.56
5 28 0.27
6 7 0.07
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:42701549 original size:27 final size:27
Alignment explanation
Indices: 42701522--42701601 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 27
42701512 AGAAGGAGAG
*
42701522 GGAAAGAAAGAAAGA-AAGAAAGTAGA
1 GGAAAGAAAGAAAAAGAAGAAAGTAGA
* *
42701548 GGAAAGAAAGAAAAAGAAGAAAAGAAAA
1 GGAAAGAAAGAAAAAGAAG-AAAGTAGA
*
42701576 GGAAAGGAGAAGAGAAAAAAAGAAAG
1 GGAAA-GA-AAGA-AAAAGAAGAAAG
42701602 AAAGAAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.31
27 3 0.07
28 11 0.24
29 2 0.04
30 8 0.18
31 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (27 bp):
GGAAAGAAAGAAAAAGAAGAAAGTAGA
Found at i:42701622 original size:45 final size:44
Alignment explanation
Indices: 42701550--42701686 Score: 172
Period size: 40 Copynumber: 3.4 Consensus size: 44
42701540 AAAGTAGAGG
42701550 AAAGAAAGAAA-AAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAG-AAAGAAAAGGAAAGGAGAAGAGAAAA
42701594 AAAGAAAG--A-AAGAAG-AAGAAAAGGAAAGGAG-A-AG-AAA
1 AAAGAAAGAAAGAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAA
*
42701631 AAAGAAAGAAAGAAG--GAAAGAAAAGGAAATGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAA
42701673 AAAG-AAG-AAGAAGA
1 AAAGAAAGAAAGAAGA
42701687 GGAGGGAAGG
Statistics
Matches: 84, Mismatches: 1, Indels: 19
0.81 0.01 0.18
Matches are distributed among these distances:
37 11 0.13
38 3 0.04
39 17 0.20
40 26 0.31
41 5 0.06
42 14 0.17
44 8 0.10
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (44 bp):
AAAGAAAGAAAGAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAA
Found at i:42701679 original size:34 final size:34
Alignment explanation
Indices: 42701591--42701686 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 34
42701581 GGAGAAGAGA
*
42701591 AAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAG
1 AAAAAAG-AA-AAA-AAGAAGAAAAGAAAAGGAGAAG
* *
42701628 AAAAAAGAAAGAAAGAAGGAAAGAAAAGGA-AATG
1 AAAAAAGAAAAAAAGAAGAAAAGAAAAGGAGAA-G
* *
42701662 AGAAGAGAAAAAAAGAAGAAGAAGA
1 AAAAAAGAAAAAAAGAAGAA-AAGA
42701687 GGAGGGAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
33 2 0.04
34 33 0.66
35 6 0.12
36 2 0.04
37 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (34 bp):
AAAAAAGAAAAAAAGAAGAAAAGAAAAGGAGAAG
Found at i:42701685 original size:58 final size:57
Alignment explanation
Indices: 42701523--42701686 Score: 155
Period size: 54 Copynumber: 2.9 Consensus size: 57
42701513 GAAGGAGAGG
* * * *
42701523 GAAAGAAAGAAAGAAAG-AAAGTAGAGGAAAGA-AAGAAAAAGAAGAA-AAG-AAAAG
1 GAAAGAAAGAAGGAAAGAAAAGGA-AAGAAAGAGAAGAAAAAGAAGAAGAAGAAAAAA
* * *
42701577 GAAAG-GAGAAGAGAAA-AAAA-GAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAA
1 GAAAGAAAGAAG-GAAAGAAAAGGAAAGAAAG-AGAAGAAAAAG-AAGAAGAAGAAAAAA
42701634 GAAAGAAAGAAGGAAAGAAAAGGAAATGAGAAGAGAA-AAAAAGAAGAAGAAGA
1 GAAAGAAAGAAGGAAAGAAAAGGAAA-GA-AAGAGAAGAAAAAGAAGAAGAAGA
42701687 GGAGGGAAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
52 6 0.07
53 6 0.07
54 20 0.23
55 4 0.05
56 3 0.03
57 13 0.15
58 18 0.20
59 9 0.10
60 6 0.07
61 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (57 bp):
GAAAGAAAGAAGGAAAGAAAAGGAAAGAAAGAGAAGAAAAAGAAGAAGAAGAAAAAA
Found at i:42701697 original size:79 final size:77
Alignment explanation
Indices: 42701550--42701718 Score: 218
Period size: 79 Copynumber: 2.2 Consensus size: 77
42701540 AAAGTAGAGG
42701550 AAAGAAAGAAAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAA
1 AAAGAAAG-AAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAA
42701615 AGGAAAGGAGAAGAAA
65 AGG-AAGGA-AA-AAA
* * **
42701631 AAAGAAAG-AAAGAAGGAAAGAAAAGGAAATGAGAAGAGAAAAAAAG-AAG-AAGAAGAGGAGGG
1 AAAGAAAGAAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGA--AGAA
42701693 AAGGAAGGAAAAAA
64 AAGGAAGGAAAAAA
*
42701707 AAAGAAAAAAAA
1 AAAGAAAGAAAA
42701719 TGTAATTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
76 10 0.12
77 12 0.15
78 8 0.10
79 42 0.52
81 8 0.10
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (77 bp):
AAAGAAAGAAAAGAAGAAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAA
GGAAGGAAAAAA
Found at i:42707496 original size:18 final size:18
Alignment explanation
Indices: 42707473--42707517 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
42707463 ATCCCAATGA
42707473 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
42707491 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
42707509 TCACCACCA
1 TCGCCACCA
42707518 ACCATGTCAA
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:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:42708456 original size:42 final size:42
Alignment explanation
Indices: 42708410--42708528 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 42
42708400 AATTCTCCAA
*
42708410 CCTTTTAGCGGCGATTTTCGTA-AAGCGCCACTAATGCTCTAG
1 CCTTTTAGCGACG-TTTTCGTATAAGCGCCACTAATGCTCTAG
* * * *
42708452 CC-TTTAGCGATGTTTTCTTATAAGCGCCGCTAATGCTCTGG
1 CCTTTTAGCGACGTTTTCGTATAAGCGCCACTAATGCTCTAG
* * ** *
42708493 CC-TTTAGAGGCGTTTTTTTAATAAGCTCCACTAATG
1 CCTTTTAGCGACGTTTTCGT-ATAAGCGCCACTAATG
42708529 ACTTGGTCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 7 0.11
41 41 0.64
42 16 0.25
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (42 bp):
CCTTTTAGCGACGTTTTCGTATAAGCGCCACTAATGCTCTAG
Found at i:42708477 original size:41 final size:41
Alignment explanation
Indices: 42708424--42708528 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
42708414 TTAGCGGCGA
* * *
42708424 TTTTCGTA-AAGCGCCACTAATGCTCTAGCCTTTAGCGATG
1 TTTTCTTATAAGCGCCACTAATGCTCTAGCCTTTAGAGACG
* * *
42708464 TTTTCTTATAAGCGCCGCTAATGCTCTGGCCTTTAGAGGCG
1 TTTTCTTATAAGCGCCACTAATGCTCTAGCCTTTAGAGACG
* *
42708505 TTTTTTTAATAAGCTCCACTAATG
1 TTTTCTT-ATAAGCGCCACTAATG
42708529 ACTTGGTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 7 0.13
41 33 0.61
42 14 0.26
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (41 bp):
TTTTCTTATAAGCGCCACTAATGCTCTAGCCTTTAGAGACG
Found at i:42709317 original size:7 final size:7
Alignment explanation
Indices: 42709305--42709330 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42709295 AGGGCATGAT
42709305 GTTTATG
1 GTTTATG
42709312 GTTTATG
1 GTTTATG
42709319 GTTTATG
1 GTTTATG
42709326 GTTTA
1 GTTTA
42709331 GCGTTAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
GTTTATG
Found at i:42709635 original size:27 final size:28
Alignment explanation
Indices: 42709591--42709650 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
42709581 ATAGAAAAAG
* * *
42709591 ATATA-TATGCAACGATATATATATGTT
1 ATATATTATGAAACGATATAAATATATT
42709618 ATATATTATGAAAC-ATATAAATATATT
1 ATATATTATGAAACGATATAAATATATT
42709645 A-ATATT
1 ATATATT
42709651 GTGTTAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 17 0.59
28 7 0.24
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (28 bp):
ATATATTATGAAACGATATAAATATATT
Found at i:42709748 original size:23 final size:24
Alignment explanation
Indices: 42709722--42709767 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42709712 CATTATTTGA
42709722 ATAAT-TTGAATA-ATTTATAATTT
1 ATAATGTTGAATATATTTA-AATTT
*
42709745 ATAATGTTGATTATATTTAAATT
1 ATAATGTTGAATATATTTAAATT
42709768 ATACATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
ATAATGTTGAATATATTTAAATTT
Found at i:42713371 original size:213 final size:213
Alignment explanation
Indices: 42712961--42713731 Score: 1447
Period size: 213 Copynumber: 3.6 Consensus size: 213
42712951 TATATTCACT
*
42712961 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGAAAAGATTGCTTATGTAAGCTATATTTAAATTT
1 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
**
42713026 TATTAATAATAAATTGATAACTTAAATAAGTATTA--ATATTTTTAATATTATACATATATTAAT
66 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
*
42713089 TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGCCAAATCAG
131 TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
42713154 TAACACATATACCTCTCC
196 TAACACATATACCTCTCC
42713172 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
1 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
*
42713237 TATTAATAATAAATTTCTAACTTAAATAAGTATTATTATATTTTTAATATTATACATATATTAAT
66 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
42713302 TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
131 TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
*
42713367 TAACACATAAACCTCTCC
196 TAACACATATACCTCTCC
42713385 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
1 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
*
42713450 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTAAT
66 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
* *
42713515 TTACATATGTAAGCTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
131 TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
42713580 TAACACATATACCTCTCC
196 TAACACATATACCTCTCC
42713598 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
1 ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
42713663 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
66 TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
42713728 TTAC
131 TTAC
42713732 ATAATACATA
Statistics
Matches: 547, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
211 97 0.18
213 450 0.82
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (213 bp):
ACCCATAATTCAGTGGAAGATTAGTTTAAAAGCAAAGATTGCTTATGTAAGCTATATTTAAATTT
TATTAATAATAAATTTCTAACTTAAATAAGTATTACTATATTTTTAATATTATACATATATTAAT
TTACGTATGTAAACTATATTTAAATTTTATTAATAATATTTAAACATATTTTGTTGTCAAATCAG
TAACACATATACCTCTCC
Found at i:42713736 original size:9 final size:9
Alignment explanation
Indices: 42713728--42714111 Score: 249
Period size: 9 Copynumber: 44.9 Consensus size: 9
42713718 ATATATTAAT
42713728 TTACATAA-
1 TTACATAAC
42713736 -TACATAAC
1 TTACATAAC
42713744 TTACATAAC
1 TTACATAAC
* *
42713753 CTACTTAA-
1 TTACATAAC
42713761 -TACATAAC
1 TTACATAAC
*
42713769 TTGCATAAC
1 TTACATAAC
42713778 TTACATAA-
1 TTACATAAC
*
42713786 -TACACAAC
1 TTACATAAC
*
42713794 TTACAT--G
1 TTACATAAC
*
42713801 TGTAAATAA-
1 T-TACATAAC
*
42713810 -TACACAAC
1 TTACATAAC
42713818 TTACATAAC
1 TTACATAAC
*
42713827 TTACATACC
1 TTACATAAC
* *
42713836 CTACATAAA
1 TTACATAAC
* *
42713845 TTAAATAAG
1 TTACATAAC
42713854 TTACATAA-
1 TTACATAAC
*
42713862 TAATACATACC
1 T--TACATAAC
*
42713873 CTACATAAC
1 TTACATAAC
*
42713882 TTACATAAG
1 TTACATAAC
42713891 TTACATAA-
1 TTACATAAC
*
42713899 -TACACAA-
1 TTACATAAC
** *
42713906 AAACAAAAAC
1 TTAC-ATAAC
42713916 TTACATAAC
1 TTACATAAC
42713925 TTACATAA-
1 TTACATAAC
*
42713933 -TACACAAC
1 TTACATAAC
42713941 TTACATAAC
1 TTACATAAC
*
42713950 TTATATAA-
1 TTACATAAC
*
42713958 -TACACAAC
1 TTACATAAC
42713966 TTACATAAC
1 TTACATAAC
42713975 TTACATAA-
1 TTACATAAC
* *
42713983 -TACAGAAT
1 TTACATAAC
*
42713991 TTGCATAAC
1 TTACATAAC
42714000 TTACATAA-
1 TTACATAAC
*
42714008 -GACATAAC
1 TTACATAAC
*
42714016 TTACATAAG
1 TTACATAAC
*
42714025 TTTCATAA-
1 TTACATAAC
*
42714033 -TACACAAC
1 TTACATAAC
**
42714041 TTACGCAAC
1 TTACATAAC
*
42714050 TTACACAAC
1 TTACATAAC
*
42714059 TTACACAAC
1 TTACATAAC
42714068 TTACATAAC
1 TTACATAAC
*
42714077 TTACACAAC
1 TTACATAAC
42714086 TTACATAAC
1 TTACATAAC
*
42714095 TTACACAAC
1 TTACATAAC
42714104 TTACATAA
1 TTACATAA
42714112 TGTATAACTT
Statistics
Matches: 294, Mismatches: 55, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
7 59 0.20
8 7 0.02
9 220 0.75
10 8 0.03
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.29
Consensus pattern (9 bp):
TTACATAAC
Found at i:42713762 original size:25 final size:25
Alignment explanation
Indices: 42713729--42713833 Score: 113
Period size: 25 Copynumber: 4.2 Consensus size: 25
42713719 TATATTAATT
42713729 TACATAATACATAACTTACATAACC
1 TACATAATACATAACTTACATAACC
* * *
42713754 TACTTAATACATAACTTGCATAACT
1 TACATAATACATAACTTACATAACC
* ***
42713779 TACATAATACACAACTTACAT-GTG
1 TACATAATACATAACTTACATAACC
* * *
42713803 TAAATAATACACAACTTACATAACT
1 TACATAATACATAACTTACATAACC
42713828 TACATA
1 TACATA
42713834 CCCTACATAA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
24 20 0.31
25 45 0.69
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (25 bp):
TACATAATACATAACTTACATAACC
Found at i:42713872 original size:37 final size:37
Alignment explanation
Indices: 42713828--42713900 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
42713818 TTACATAACT
42713828 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
* *
42713865 TACATACCCTACATAACTTACATAAGTTACATAATA
1 TACATACCCTACATAAATTAAATAAGTTACATAATA
42713901 CACAAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.30
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:42713941 original size:25 final size:25
Alignment explanation
Indices: 42713913--42714112 Score: 238
Period size: 25 Copynumber: 7.8 Consensus size: 25
42713903 CAAAAACAAA
42713913 AACTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
42713938 AACTTACATAACTTATATAATACAC
1 AACTTACATAACTTACATAATACAC
*
42713963 AACTTACATAACTTACATAATACAG
1 AACTTACATAACTTACATAATACAC
* * * *
42713988 AATTTGCATAACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAC
* *
42714013 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAC
** *
42714038 AACTTACGCAACTTACACAACTTACAC
1 AACTTACATAACTTACATAA--TACAC
* *
42714065 AACTTACATAACTTACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAC
*
42714092 AACTTACACAACTTACATAAT
1 AACTTACATAACTTACATAAT
42714113 GTATAACTTA
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
25 103 0.69
27 47 0.31
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:42713951 original size:34 final size:35
Alignment explanation
Indices: 42713728--42714111 Score: 202
Period size: 34 Copynumber: 10.7 Consensus size: 35
42713718 ATATATTAAT
**
42713728 TTACATAA--TACATAACTTACATAACCTACTTAA-
1 TTACATAACTTACATAACTTACATAA-CTACACAAC
*
42713761 -TACATAACTTGCATAACTTACATAA-TACACAAC
1 TTACATAACTTACATAACTTACATAACTACACAAC
* * * *
42713794 TTACATGTGTAAATAATACACAACTTACATAACTTACATACC
1 TTACA----TAACT--TACATAACTTACATAAC-TACACAAC
* * * * *
42713836 CTACATAAATTAAATAAGTTACATAA-TAATACATACC
1 TTACATAACTTACATAACTTACATAACT-ACACA-A-C
* *
42713873 CTACATAACTTACATAAGTTACATAA-TACACAA-
1 TTACATAACTTACATAACTTACATAACTACACAAC
** *
42713906 AAACAAAAACTTACATAACTTACATAA-TACACAAC
1 TTAC-ATAACTTACATAACTTACATAACTACACAAC
* * *
42713941 TTACATAACTTATATAA--TACACAACTTACATAAC
1 TTACATAACTTACATAACTTACATAAC-TACACAAC
* * *
42713975 TTACATAATACAGAATTTGCATAACTTACATAA-GACATAAC
1 TTACAT-A-AC-----TTACATAACTTACATAACTACACAAC
* * * *
42714016 TTACATAAGTTTCATAA--TACACAACTTACGCAAC
1 TTACATAACTTACATAACTTACATAAC-TACACAAC
* *
42714050 TTACACAACTTACACAACTTACATAACTTACACAAC
1 TTACATAACTTACATAACTTACATAAC-TACACAAC
*
42714086 TTACATAACTTACACAACTTACATAA
1 TTACATAACTTACATAACTTACATAA
42714112 TGTATAACTT
Statistics
Matches: 274, Mismatches: 45, Indels: 61
0.72 0.12 0.16
Matches are distributed among these distances:
32 24 0.09
33 2 0.01
34 96 0.35
35 7 0.03
36 59 0.22
37 26 0.09
38 9 0.03
39 1 0.00
40 15 0.05
41 19 0.07
42 10 0.04
43 6 0.02
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.29
Consensus pattern (35 bp):
TTACATAACTTACATAACTTACATAACTACACAAC
Found at i:42719625 original size:21 final size:21
Alignment explanation
Indices: 42719581--42719649 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
42719571 CAACAACTTA
**
42719581 AAGCAGAGGCGGCAGCAA-AGG
1 AAGCAGAGGCCACAGCAAGA-G
* * *
42719602 AAGCATAGGCTACAGCGAGAG
1 AAGCAGAGGCCACAGCAAGAG
*
42719623 AAGCAGAGGCCGCAGCAAGAG
1 AAGCAGAGGCCACAGCAAGAG
42719644 AAGCAG
1 AAGCAG
42719650 CGAGAGAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.38, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCACAGCAAGAG
Found at i:42719663 original size:12 final size:12
Alignment explanation
Indices: 42719614--42719669 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
42719604 GCATAGGCTA
42719614 CAGCGAGAGAAG
1 CAGCGAGAGAAG
**
42719626 CA--GAG-GCCG
1 CAGCGAGAGAAG
*
42719635 CAGCAAGAGAAG
1 CAGCGAGAGAAG
42719647 CAGCGAGAGAAG
1 CAGCGAGAGAAG
*
42719659 CAGCGATAGAA
1 CAGCGAGAGAA
42719670 TTAGAGGTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
9 4 0.12
10 3 0.09
11 2 0.06
12 25 0.74
ACGTcount: A:0.41, C:0.20, G:0.38, T:0.02
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:42720258 original size:42 final size:41
Alignment explanation
Indices: 42720110--42720257 Score: 165
Period size: 42 Copynumber: 3.5 Consensus size: 41
42720100 TTTGTGAAAA
* *
42720110 AAGCGCCGCTAAAGAAGACT-ACTATTAGCGGCGTTTTTGACC-
1 AAGCGCCGCTAAAGAACA-TGACT-TTAGCGGCGTTTTT-TCCT
* * * *
42720152 AAACGTCGCTATAGAACATTACTTTTAGCGGCGTTTTCTTCCT
1 AAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGTTTT-TTCCT
*
42720195 AAGCGCTGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTCCT
42720237 AAGCGCCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGA
42720258 TAAACGGCGC
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 56 0.62
43 32 0.36
44 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTCCT
Found at i:42720325 original size:42 final size:44
Alignment explanation
Indices: 42720273--42720358 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
42720263 GGCGCTAGAC
*
42720273 AACATAATCTTTAGCGACG-TTTTTTC-CTAAGCGCCGCTAAAG
1 AACATAATCTTTAGCGACGTTTTTTTCTCTAAGCGCCGCAAAAG
* * *
42720315 AACATGATCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 AACATAATCTTTAGCGACGTTTTTTTCTCTAAGCGCCGCAAAAG
42720359 TTAGCGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 17 0.45
43 7 0.18
44 14 0.37
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
AACATAATCTTTAGCGACGTTTTTTTCTCTAAGCGCCGCAAAAG
Found at i:42720473 original size:22 final size:22
Alignment explanation
Indices: 42720430--42720473 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42720420 TAGTGGCGTT
* **
42720430 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAACCTA
42720452 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
42720474 TTCTGGTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:42720774 original size:19 final size:21
Alignment explanation
Indices: 42720750--42720788 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
42720740 ACTAAAACAA
*
42720750 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
42720769 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
42720789 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:42720953 original size:27 final size:27
Alignment explanation
Indices: 42720907--42720980 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
42720897 AATACGAGTA
42720907 GTGCCGCCAAT--CAGTATGGCACCATTG
1 GTGCCGCCAATGGCA-T-TGGCACCATTG
*
42720934 GTGCCGCTAATGGCATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
*
42720961 GTGCCGCCAATGGCTTTGGC
1 GTGCCGCCAATGGCATTGGC
42720981 GTGACCAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 39 0.93
28 1 0.02
29 2 0.05
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:42721061 original size:23 final size:23
Alignment explanation
Indices: 42721034--42721079 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42721024 TTTTTTTATT
*
42721034 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTAGTAAATAAAAAAA
42721057 ATATATTTTAGTAAATAAAAAAA
1 ATATATTTTAGTAAATAAAAAAA
42721080 GTTATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
ATATATTTTAGTAAATAAAAAAA
Found at i:42723496 original size:35 final size:35
Alignment explanation
Indices: 42723457--42723526 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
42723447 TAAAAATAAA
* * *
42723457 AAATAATAATTTAATCATATT-TTAATATTATTATT
1 AAAT-ATAATTTAATAAAATTCTTAATATAATTATT
42723492 AAATATAATTTAATAAAATTCTTAATATAATTATT
1 AAATATAATTTAATAAAATTCTTAATATAATTATT
42723527 TTTATATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATATAATTTAATAAAATTCTTAATATAATTATT
Found at i:42723503 original size:23 final size:22
Alignment explanation
Indices: 42723467--42723523 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
42723457 AAATAATAAT
* **
42723467 TTAATCATATTTTAATATTATTA
1 TTAAT-ATAATTTAATAAAATTA
*
42723490 TTAAATATAATTTAATAAAATTC
1 TT-AATATAATTTAATAAAATTA
42723513 TTAATATAATT
1 TTAATATAATT
42723524 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 9 0.31
23 17 0.59
24 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATATAATTTAATAAAATTA
Found at i:42724092 original size:13 final size:14
Alignment explanation
Indices: 42724063--42724099 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42724053 CGCACATATA
*
42724063 TTTTTATGCTTATT
1 TTTTTATGTTTATT
42724077 TTTTTATGTTTATT
1 TTTTTATGTTTATT
42724091 TTTTT-TGTT
1 TTTTTATGTT
42724100 AGTAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTATGTTTATT
Found at i:42728880 original size:27 final size:26
Alignment explanation
Indices: 42728834--42729013 Score: 216
Period size: 27 Copynumber: 6.7 Consensus size: 26
42728824 AAACCCTAAA
* * *
42728834 ATAGGTATAATAACTGTAATACCCCC
1 ATAGGTAAAATGACCGTAATACCCCC
42728860 ATAGGATAAAATGACCGTAATACCCCC
1 ATAGG-TAAAATGACCGTAATACCCCC
*
42728887 ATAGGATAAAATGACTGTAATACCCCC
1 ATAGG-TAAAATGACCGTAATACCCCC
*
42728914 ATAGGGTAAAATGACCGTAATACCCCT
1 ATA-GGTAAAATGACCGTAATACCCCC
* *
42728941 GTAAGGTAAAATGACCGTAATACCCCT
1 AT-AGGTAAAATGACCGTAATACCCCC
* * *
42728968 GTAGGGTAAAATGACTGTAATACCCCT
1 ATA-GGTAAAATGACCGTAATACCCCC
*
42728995 GTAGGTAAAATGACCGTAA
1 ATAGGTAAAATGACCGTAA
42729014 CGACCCTCGA
Statistics
Matches: 141, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
26 21 0.15
27 117 0.83
28 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (26 bp):
ATAGGTAAAATGACCGTAATACCCCC
Found at i:42728905 original size:54 final size:53
Alignment explanation
Indices: 42728835--42729013 Score: 250
Period size: 54 Copynumber: 3.3 Consensus size: 53
42728825 AACCCTAAAA
* * * * **
42728835 TAGGTATAATAACTGTAATACCCCCATAGGATAAAATGACCGTAATACCCCCA
1 TAGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGACCGTAATACCCCTG
*
42728888 TAGGATAAAATGACTGTAATACCCCCATAGGGTAAAATGACCGTAATACCCCTG
1 TAGG-TAAAATGACCGTAATACCCCCATAGGGTAAAATGACCGTAATACCCCTG
** *
42728942 TAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATACCCCTG
1 T-AGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGACCGTAATACCCCTG
42728996 TAGGTAAAATGACCGTAA
1 TAGGTAAAATGACCGTAA
42729014 CGACCCTCGA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
53 21 0.18
54 91 0.79
55 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (53 bp):
TAGGTAAAATGACCGTAATACCCCCATAGGGTAAAATGACCGTAATACCCCTG
Found at i:42728984 original size:81 final size:80
Alignment explanation
Indices: 42728834--42729013 Score: 245
Period size: 81 Copynumber: 2.2 Consensus size: 80
42728824 AAACCCTAAA
* * *
42728834 ATAGGTATAATAACTGTAATACCCCCATAGGATAAAATGACCGTAATACCCCCATAGGATAAAAT
1 ATAGGTAAAATGACCGTAATACCCCCATAGGATAAAATGACCGTAATACCCCCATAGGATAAAAT
42728899 GACTGTAATACCCCC
66 GACTGTAATACCCCC
** ** *
42728914 ATAGGGTAAAATGACCGTAATACCCCTGTAAGG-TAAAATGACCGTAATACCCCTGTAGGGTAAA
1 ATA-GGTAAAATGACCGTAATACCCCCAT-AGGATAAAATGACCGTAATACCCCCATAGGATAAA
*
42728978 ATGACTGTAATACCCCT
64 ATGACTGTAATACCCCC
*
42728995 GTAGGTAAAATGACCGTAA
1 ATAGGTAAAATGACCGTAA
42729014 CGACCCTCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 19 0.22
81 66 0.75
82 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (80 bp):
ATAGGTAAAATGACCGTAATACCCCCATAGGATAAAATGACCGTAATACCCCCATAGGATAAAAT
GACTGTAATACCCCC
Found at i:42729298 original size:32 final size:32
Alignment explanation
Indices: 42729256--42729366 Score: 186
Period size: 32 Copynumber: 3.5 Consensus size: 32
42729246 TTTACTACGA
42729256 CGTTACTGATGGCTTTGTGCCGATCATATTAC
1 CGTTACTGATGGCTTTGTGCCGATCATATTAC
* *
42729288 TGTTACTGATGGCTTTGTGCCGATCATAGTAC
1 CGTTACTGATGGCTTTGTGCCGATCATATTAC
*
42729320 CCTTACTGATGGCTTTGTGCCGATCATATTAC
1 CGTTACTGATGGCTTTGTGCCGATCATATTAC
*
42729352 CGTTATTGATGGCTT
1 CGTTACTGATGGCTT
42729367 GTAGCCATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.39
Consensus pattern (32 bp):
CGTTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:42731479 original size:2 final size:2
Alignment explanation
Indices: 42731472--42731517 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
42731462 AAAATAAAAG
42731472 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42731514 GA GA
1 GA GA
42731518 AAGCTTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42732924 original size:26 final size:25
Alignment explanation
Indices: 42732879--42732929 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
42732869 TTTCATTTCC
42732879 TCTCATCATTCACTAACCTCTCATTT
1 TCTCATCATTCACTAACCTC-CATTT
42732905 TCTC-TCATTCA-TAAGCCCTCCATTT
1 TCTCATCATTCACTAA--CCTCCATTT
42732930 CCCCCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 3 0.13
25 12 0.52
26 8 0.35
ACGTcount: A:0.22, C:0.35, G:0.02, T:0.41
Consensus pattern (25 bp):
TCTCATCATTCACTAACCTCCATTT
Found at i:42740374 original size:27 final size:27
Alignment explanation
Indices: 42740336--42740934 Score: 758
Period size: 27 Copynumber: 22.2 Consensus size: 27
42740326 AGTTATGGAC
42740336 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
42740363 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
42740390 AAATGACCGAAATACACTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
42740417 AAATGACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740444 AAATGACCAAAATACCCTCGAAGGATA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740471 AAATAACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
42740498 AAATGACCGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* *
42740525 AAATGACTGAAATACGCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740552 AAATGACCAAAATACCTTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
42740579 AAATGACCCTAATACCCTCGAACGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
42740606 AAATGACTGAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
42740633 AAATGACTAAAATACCCTCGAAGGATA
1 AAATGACCGAAATACCCTCGAAGGGTA
42740660 AAATGACCGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
* *
42740687 AAATGATCGAAATACCCCCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740714 AAATGACTGAAATAACCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740741 AAATGACTGAAATAACCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
42740768 AAATGACTAAAATACCCTCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* ** *
42740795 AAATGACCAAAATA-CCTTAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* **
42740821 AAAAGATAGAAATACCC-CTGAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
*
42740848 AAATGACTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
** *
42740875 AAATGACTAAAATACCCTCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
42740902 AAATGACCGAAAGACCC-CCATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
42740929 AAATGA
1 AAATGA
42740935 TTTTTAACTC
Statistics
Matches: 502, Mismatches: 62, Indels: 16
0.87 0.11 0.03
Matches are distributed among these distances:
26 24 0.05
27 475 0.95
28 3 0.01
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:42748503 original size:20 final size:21
Alignment explanation
Indices: 42748455--42748507 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
42748445 GTTCGTGCTA
*
42748455 CGGTGCCCCTGTTTGCACATT
1 CGGTGCCCCTGTTTCCACATT
* *
42748476 -TGTACCCCTGTTTCCAC-TT
1 CGGTGCCCCTGTTTCCACATT
42748495 CGGTGCCCCTGTT
1 CGGTGCCCCTGTT
42748508 ATGCATCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.08, C:0.36, G:0.21, T:0.36
Consensus pattern (21 bp):
CGGTGCCCCTGTTTCCACATT
Found at i:42749440 original size:26 final size:28
Alignment explanation
Indices: 42749411--42749468 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
42749401 CTTTGGACAT
* *
42749411 CATTAA-AACATGTAATAAAAT-TAACA
1 CATTAATAACATGCAATAAAATAAAACA
*
42749437 CATTAATAACATGCATTAAAATAAAACA
1 CATTAATAACATGCAATAAAATAAAACA
42749465 CATT
1 CATT
42749469 TATCACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 6 0.22
27 13 0.48
28 8 0.30
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (28 bp):
CATTAATAACATGCAATAAAATAAAACA
Found at i:42749445 original size:17 final size:18
Alignment explanation
Indices: 42749412--42749445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42749402 TTTGGACATC
42749412 ATTAAAACATGTAATAAA
1 ATTAAAACATGTAATAAA
*
42749430 ATTAACACAT-TAATAA
1 ATTAAAACATGTAATAA
42749446 CATGCATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAAACATGTAATAAA
Found at i:42770422 original size:51 final size:50
Alignment explanation
Indices: 42770367--42770465 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 50
42770357 ATCGAACAAT
* *
42770367 TAATAATAAAATAGCATCAA-TGGTGAAAAACCTCGGACAACATTAAACAGA
1 TAATAATAAAACAACATCAATTGG-GAAAAACCTCGGACAACA-TAAACAGA
* * * *
42770418 TAATAATTAAACAACATCAATTGGGCAAAATCTTGGACAACATAAACA
1 TAATAATAAAACAACATCAATTGGGAAAAACCTCGGACAACATAAACA
42770466 ACAAATGACT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 6 0.15
51 32 0.78
52 3 0.07
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (50 bp):
TAATAATAAAACAACATCAATTGGGAAAAACCTCGGACAACATAAACAGA
Found at i:42770507 original size:26 final size:26
Alignment explanation
Indices: 42770478--42770565 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
42770468 AAATGACTAA
*
42770478 ACAACATTAATTGAGCAAAATCTTGG
1 ACAACATTAAATGAGCAAAATCTTGG
* * * * **
42770504 ACAACATTAAAT-AACTAATTATTAA
1 ACAACATTAAATGAGCAAAATCTTGG
* * *
42770529 AAAACATTAACTGAGAAAAATCTTGG
1 ACAACATTAAATGAGCAAAATCTTGG
42770555 ACAACATTAAA
1 ACAACATTAAA
42770566 CATGTAATGA
Statistics
Matches: 43, Mismatches: 18, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
25 17 0.40
26 26 0.60
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (26 bp):
ACAACATTAAATGAGCAAAATCTTGG
Found at i:42770555 original size:51 final size:51
Alignment explanation
Indices: 42770391--42770567 Score: 214
Period size: 51 Copynumber: 3.5 Consensus size: 51
42770381 CATCAATGGT
* * * *
42770391 GAAAAACCTCGGACAACATTAAACAGA-TAATAATTAAACAACATCAATTGG
1 GAAAAATCTTGGACAACATTAAACA-ACTAATAATTAAACAACATTAATTGA
* * * *
42770442 GCAAAATCTTGGACAACA-TAAACAACAAATGACTAAACAACATTAATTGA
1 GAAAAATCTTGGACAACATTAAACAACTAATAATTAAACAACATTAATTGA
* * * * *
42770492 GCAAAATCTTGGACAACATTAAATAACTAATTATTAAAAAACATTAACTGA
1 GAAAAATCTTGGACAACATTAAACAACTAATAATTAAACAACATTAATTGA
42770543 GAAAAATCTTGGACAACATTAAACA
1 GAAAAATCTTGGACAACATTAAACA
42770568 TGTAATGACC
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 43 0.40
51 64 0.59
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (51 bp):
GAAAAATCTTGGACAACATTAAACAACTAATAATTAAACAACATTAATTGA
Found at i:42781098 original size:52 final size:51
Alignment explanation
Indices: 42780982--42781126 Score: 157
Period size: 52 Copynumber: 2.8 Consensus size: 51
42780972 CCCTTTGTTT
* ** *
42780982 TCAAGGTGCCCTTTTTGGGTTTTCACCTTGG-CCTTTCCTTTTTTTAGGAC
1 TCAAAGTGCCCTTTGCGGGTTTTCACCTTGGTCCTCTCCTTTTTTTAGGAC
*** * *
42781032 TCAAAACACCCTTTGCGGGTTTTCACCTTGGTCGTCTCATTTTTTTTAGGAC
1 TCAAAGTGCCCTTTGCGGGTTTTCACCTTGGTCCTCTC-CTTTTTTTAGGAC
* *
42781084 TTAAAGTGCCCTTTGCGGGTTTTTACCTTGGTCCCTTCTCCTT
1 TCAAAGTGCCCTTTGCGGGTTTTCACCTTGGT-CC-TCTCCTT
42781127 CTTTAGGTGA
Statistics
Matches: 75, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
50 25 0.33
51 4 0.05
52 39 0.52
53 3 0.04
54 4 0.05
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.43
Consensus pattern (51 bp):
TCAAAGTGCCCTTTGCGGGTTTTCACCTTGGTCCTCTCCTTTTTTTAGGAC
Found at i:42781488 original size:17 final size:17
Alignment explanation
Indices: 42781466--42781503 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
42781456 CAGTAGAGGT
42781466 TTTTGTTTCTTT-TTTAG
1 TTTTG-TTCTTTGTTTAG
*
42781483 TTTTGTTCTTTGTTTTG
1 TTTTGTTCTTTGTTTAG
42781500 TTTT
1 TTTT
42781504 TTGTCCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.03, C:0.05, G:0.13, T:0.79
Consensus pattern (17 bp):
TTTTGTTCTTTGTTTAG
Found at i:42781529 original size:12 final size:12
Alignment explanation
Indices: 42781465--42781529 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
42781455 CCAGTAGAGG
*
42781465 TTTTTGTTTCTT
1 TTTTTGTTTTTT
* *
42781477 TTTTAGTTTTGT
1 TTTTTGTTTTTT
* *
42781489 TCTTTGTTTTGT
1 TTTTTGTTTTTT
42781501 TTTTTGTCCTTTGTT
1 TTTTTGT--TTT-TT
42781516 TTTTTGTTTTTT
1 TTTTTGTTTTTT
42781528 TT
1 TT
42781530 GTCCTCTACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 29 0.67
13 3 0.07
14 3 0.07
15 8 0.19
ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:42784268 original size:19 final size:20
Alignment explanation
Indices: 42784244--42784290 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
42784234 TGGTGGACTT
* *
42784244 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
42784263 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
42784283 -AATGCAAA
1 TAATGCAAA
42784291 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:42786145 original size:17 final size:18
Alignment explanation
Indices: 42786120--42786159 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42786110 TGAACGACAA
* *
42786120 ATAATCAATA-AATATAC
1 ATAAGCAATACAATACAC
42786137 ATAAGCAATACAATACAC
1 ATAAGCAATACAATACAC
42786155 ATAAG
1 ATAAG
42786160 AGCAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAAGCAATACAATACAC
Found at i:42786252 original size:21 final size:21
Alignment explanation
Indices: 42786223--42786263 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42786213 CTAGTGAAGA
*
42786223 AAGCTAATTAAAAAAAACACC
1 AAGCAAATTAAAAAAAACACC
* *
42786244 AAGCAAATTAACACAAACAC
1 AAGCAAATTAAAAAAAACAC
42786264 AAACAAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.22, G:0.05, T:0.12
Consensus pattern (21 bp):
AAGCAAATTAAAAAAAACACC
Found at i:42786395 original size:11 final size:11
Alignment explanation
Indices: 42786379--42786411 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
42786369 CGTAAGTTTG
42786379 AAATAAATAAA
1 AAATAAATAAA
42786390 AAATAAAGT-AA
1 AAATAAA-TAAA
42786401 AAATAAATAAA
1 AAATAAATAAA
42786412 TTCTATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:42789193 original size:27 final size:27
Alignment explanation
Indices: 42789062--42789193 Score: 178
Period size: 27 Copynumber: 4.9 Consensus size: 27
42789052 ATCTGCACCA
* *
42789062 AAATACCCCCATAGGGT-AAATGACCA
1 AAATACCCCCATAGGGTAAAATGATCG
*
42789088 AAATACCCCCATAAGGTAAAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
**
42789115 AAATACCTTCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
* *
42789142 AAATACCCCTATAGGATAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
42789169 AAATACCCCCATAGGGTAAAATGAT
1 AAATACCCCCATAGGGTAAAATGAT
42789194 TGTTATAACC
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 17 0.18
27 74 0.80
28 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:42789218 original size:54 final size:54
Alignment explanation
Indices: 42789062--42789222 Score: 152
Period size: 54 Copynumber: 3.0 Consensus size: 54
42789052 ATCTGCACCA
* * *
42789062 AAATACCCCCATAGGGT-AAATGACCAAAATACCCCCATA-AGG-TAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGATCGAAATA-ACCC-TAGAGGATAAAATGACTG
** * *
42789115 AAATACCTTCATAGGGTAAAATGATCGAAATACCCCTATAGGATAAAATGA-TCG
1 AAATACCCCCATAGGGTAAAATGATCGAAATAACCCTAGAGGATAAAATGACT-G
* ** *
42789169 AAATACCCCCATAGGGTAAAATGATTGTTATAACCCTAG-GAGATGAAATGACTG
1 AAATACCCCCATAGGGTAAAATGATCGAAATAACCCTAGAG-GATAAAATGACTG
42789223 TTATGGCCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
52 2 0.02
53 24 0.27
54 63 0.70
55 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (54 bp):
AAATACCCCCATAGGGTAAAATGATCGAAATAACCCTAGAGGATAAAATGACTG
Found at i:42798267 original size:27 final size:27
Alignment explanation
Indices: 42798236--42798413 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42798226 TAAATTGTAC
42798236 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42798263 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
42798289 ATGCACTAAGTGTGCAAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42798317 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42798345 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42798372 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
42798399 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
42798414 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42798404 original size:82 final size:81
Alignment explanation
Indices: 42798233--42798413 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42798223 GATTAAATTG
* *
42798233 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42798298 GTGTGCAAATTGACCA
66 GTGTGCAAATTGACCA
* * ** *
42798314 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* * **
42798378 AAGTGTGCGAGTTGATTA
64 AAGTGTGCAAATTGACCA
*
42798396 TATAGCACTAAGTGTGCG
1 TACAGCACTAAGTGTGCG
42798414 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCAAATTGACCA
Found at i:42798424 original size:27 final size:27
Alignment explanation
Indices: 42798318--42798424 Score: 72
Period size: 27 Copynumber: 3.9 Consensus size: 27
42798308 TGACCATGCG
* * * *
42798318 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
42798346 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
42798373 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
42798400 GCACTAAGTGTGCG-GACTCAATATA
1 GCACTAAGTGTGCGAG-CTCAATATA
42798425 CATTCGTGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 53 0.77
28 15 0.22
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:42803926 original size:26 final size:26
Alignment explanation
Indices: 42803870--42803926 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
42803860 GGCTTTGTGT
* *
42803870 TGGTGTATATTTAGTAGCCTTCATAC
1 TGGTGCATATTTAGAAGCCTTCATAC
* *
42803896 CGGTGCATATTTAGCAAG-CTTCATGC
1 TGGTGCATATTTAG-AAGCCTTCATAC
42803922 TGGTG
1 TGGTG
42803927 TATTCAGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (26 bp):
TGGTGCATATTTAGAAGCCTTCATAC
Found at i:42804301 original size:40 final size:40
Alignment explanation
Indices: 42804225--42804303 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
42804215 ATGTTACGTT
* *
42804225 TGGTTATATGAATCGGTTATATGAAAATATAAATATGAAA
1 TGGTTATATGAATCAGTTATATGAAAATAGAAATATGAAA
* *
42804265 TGGTTATATGAATCAGTTATATGAAAATCGATATATGAA
1 TGGTTATATGAATCAGTTATATGAAAATAGAAATATGAA
42804304 TGGATGGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (40 bp):
TGGTTATATGAATCAGTTATATGAAAATAGAAATATGAAA
Found at i:42817466 original size:14 final size:14
Alignment explanation
Indices: 42817447--42817476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42817437 ATCATTAGTA
42817447 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
42817461 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
42817475 AA
1 AA
42817477 TGTGTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:42827249 original size:15 final size:15
Alignment explanation
Indices: 42827224--42827258 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42827214 GACTCTATTT
*
42827224 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
42827238 TAATTAATATTAAGA
1 TAATTAATATTAAGA
42827253 TAATTA
1 TAATTA
42827259 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:42830953 original size:14 final size:14
Alignment explanation
Indices: 42830934--42830960 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42830924 TAGTTACATC
42830934 TGAGCTCTATATGG
1 TGAGCTCTATATGG
42830948 TGAGCTCTATATG
1 TGAGCTCTATATG
42830961 ATTATGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (14 bp):
TGAGCTCTATATGG
Found at i:42837114 original size:18 final size:18
Alignment explanation
Indices: 42837091--42837126 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42837081 GTTTTATTCA
42837091 AAGATTTCTAGGTTTTCT
1 AAGATTTCTAGGTTTTCT
* *
42837109 AAGATTTTTGGGTTTTCT
1 AAGATTTCTAGGTTTTCT
42837127 CATTCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (18 bp):
AAGATTTCTAGGTTTTCT
Found at i:42837424 original size:20 final size:18
Alignment explanation
Indices: 42837392--42837435 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
42837382 TAATTATTTC
*
42837392 TTATATATATTTTAGAGT
1 TTATATATATTTTAGAAT
*
42837410 TTATATATAATTTTTATAAT
1 TTATATAT-A-TTTTAGAAT
42837430 TTATAT
1 TTATAT
42837436 TTAGATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 1 0.05
20 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTATATATATTTTAGAAT
Found at i:42837886 original size:20 final size:21
Alignment explanation
Indices: 42837849--42837902 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
42837839 CCGGCCCATT
**
42837849 TTTTAATAAATACCAAAAATTTA
1 TTTTAA-AAATA-CAAAAAAGTA
42837872 TTTTAAAAATA-AAAAAAGTA
1 TTTTAAAAATACAAAAAAGTA
42837892 TTTTAAAAATA
1 TTTTAAAAATA
42837903 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
TTTTAAAAATACAAAAAAGTA
Found at i:42837904 original size:11 final size:11
Alignment explanation
Indices: 42837884--42837938 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
42837874 TTAAAAATAA
42837884 AAAAAGTATTTT
1 AAAAA-TATTTT
42837896 AAAAATATTTT
1 AAAAATATTTT
42837907 --AAA-A--TT
1 AAAAATATTTT
42837913 AAAAATTATTTT
1 AAAAA-TATTTT
42837925 -AAAATATTTT
1 AAAAATATTTT
42837935 AAAA
1 AAAA
42837939 TTTAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
6 2 0.06
8 4 0.11
9 3 0.08
10 7 0.19
11 13 0.36
12 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Done.