Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008489.1 Hibiscus syriacus cultivar Beakdansim tig00111331_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: 1108073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:664577 original size:103 final size:103
Alignment explanation
Indices: 664249--664569 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
664239 GTCGTGGGTC
664249 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
664314 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* *
664352 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTTAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
664417 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
664455 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
664520 TTGATCCCTAGTATATGTATACGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
664558 TATGTGGTCCTT
1 TATGTGGTCCTT
664570 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:664616 original size:23 final size:23
Alignment explanation
Indices: 664586--664671 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
664576 ATTATTATAT
664586 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
664609 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
664632 GACACT-CTGGTGCAATTATATGT
1 GGCACTAC-GGTGCAATTCTACGC
*
664655 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
664672 ATATGAGCTG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
22 1 0.02
23 54 0.96
24 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:664672 original size:23 final size:23
Alignment explanation
Indices: 664579--664676 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
664569 TATGGACATT
664579 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
664600 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* * *
664623 ATTCTACGCGACACT-CTGGTGCA
1 ATTATATGCGGCACTAC-GGTGCA
* *
664646 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
664669 ATTATATG
1 ATTATATG
664677 AGCTGTGATG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
21 5 0.08
22 1 0.02
23 59 0.89
24 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:670659 original size:103 final size:103
Alignment explanation
Indices: 670331--670651 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
670321 GTCGAGGGTC
* * * **
670331 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTAAAGTCTGGTGCGATGCATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
670396 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
670434 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
670499 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
670537 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
670602 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
670640 TATGTGGTCCTT
1 TATGTGGTCCTT
670652 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:670701 original size:23 final size:23
Alignment explanation
Indices: 670671--670753 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
670661 ATTATATGGT
*
670671 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGTGGC
670694 ACTACGGTGCAATTCTACGTGGC
1 ACTACGGTGCAATTCTACGTGGC
* * * *
670717 ACTCCGGTGCAATTATATGTGGT
1 ACTACGGTGCAATTCTACGTGGC
*
670740 ACTTCGGTGCAATT
1 ACTACGGTGCAATT
670754 ATATGAGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGTGGC
Found at i:672768 original size:22 final size:22
Alignment explanation
Indices: 672740--672783 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
672730 GATAAACCTA
*
672740 ATAACCAACTATGTTAAGCTGG
1 ATAACCAACTATGCTAAGCTGG
*
672762 ATAACCAACTATGCTGAGCTGG
1 ATAACCAACTATGCTAAGCTGG
672784 CATCCAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
ATAACCAACTATGCTAAGCTGG
Found at i:673761 original size:20 final size:20
Alignment explanation
Indices: 673736--673773 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
673726 AATATTAAAA
* *
673736 ATATTATATTAAATTATAAG
1 ATATTAAATAAAATTATAAG
673756 ATATTAAATAAAATTATA
1 ATATTAAATAAAATTATA
673774 GGTTAATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATATTAAATAAAATTATAAG
Found at i:674267 original size:15 final size:16
Alignment explanation
Indices: 674247--674279 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
674237 CGATTATAAC
674247 TAAAATAG-CCAAAAT
1 TAAAATAGTCCAAAAT
*
674262 TAAAATAGTCCTAAAT
1 TAAAATAGTCCAAAAT
674278 TA
1 TA
674280 CTATTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAATAGTCCAAAAT
Found at i:677810 original size:167 final size:166
Alignment explanation
Indices: 677534--677866 Score: 641
Period size: 167 Copynumber: 2.0 Consensus size: 166
677524 TATATTCATC
677534 CTTTATCTATCATCCTTCAAATTTTCGTAAAATTTTGGTTCTATCCGATTATCCTATTTTCTTTC
1 CTTTATCTATCATCCTTCAAATTTTCGTAAAATTTTGGTTCTATCCGATTATCCTATTTTCTTTC
677599 AGACTTTACAGCTTTATAGCTTTTAACACAAATTCTAGAACGAAATTTCAATTCCCACGAATATG
66 AGACTTTACAGCTTTATAGCTTTTAACACAAATTCTAGAACGAAATTTCAATTCCCACGAATAT-
677664 GTCATTCTTAAGGTTGAAACTATTCA-TTACGAGGTTA
130 GTCATTCTTAAGGTTG-AACTATTCATTTACGAGGTTA
677701 CTTTATCTATCATCCTTCAAATTTTCGTAAAATTTTGGTTCTATCCGATTATCCTATTTTCTTTC
1 CTTTATCTATCATCCTTCAAATTTTCGTAAAATTTTGGTTCTATCCGATTATCCTATTTTCTTTC
677766 AGACTTTACAGCTTTATAGCTTTTAACACAAATTCTAGAACGAAATTTCAATTCCCACGAATATG
66 AGACTTTACAGCTTTATAGCTTTTAACACAAATTCTAGAACGAAATTTCAATTCCCACGAATATG
677831 TCATTCTTAAGGTTGAACTATTCATTTACGAGGTTA
131 TCATTCTTAAGGTTGAACTATTCATTTACGAGGTTA
677867 AAATGCCTAA
Statistics
Matches: 165, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
165 9 0.05
166 27 0.16
167 129 0.78
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (166 bp):
CTTTATCTATCATCCTTCAAATTTTCGTAAAATTTTGGTTCTATCCGATTATCCTATTTTCTTTC
AGACTTTACAGCTTTATAGCTTTTAACACAAATTCTAGAACGAAATTTCAATTCCCACGAATATG
TCATTCTTAAGGTTGAACTATTCATTTACGAGGTTA
Found at i:682676 original size:31 final size:31
Alignment explanation
Indices: 682638--682713 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
682628 GGGACGGACC
* * **
682638 CTTGGGTAGGCTCTGTAGCCCCGATATTTTT
1 CTTGGGTAGGCTCTATAGCCCCGAGAACTTT
* * *
682669 CTTGGGTAGGCCCCATGGCCCCGAGAACTTT
1 CTTGGGTAGGCTCTATAGCCCCGAGAACTTT
682700 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
682714 CAAACCCCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGGCTCTATAGCCCCGAGAACTTT
Found at i:686574 original size:149 final size:148
Alignment explanation
Indices: 686377--686673 Score: 560
Period size: 150 Copynumber: 2.0 Consensus size: 148
686367 AGAATTACTA
686377 ATAGGCACACAATAGAAAATAAATCTAAAAACCTTTCGATGCTCATTCTTTACGAATTTCATATC
1 ATAGGCACACAATAGAAAATAAATCTAAAAACCTTTCGATGCTCATTCTTTACGAATTTCATATC
686442 ACATCATCAATG-TGACCTTAATACTTCAAATGGACCAATAAATCCCTTTTTATCCAAAATCACC
66 ACATCATCAATGTTGACCTTAATACTTCAAATGGACCAATAAATCCCTTTTTATCCAAAATCACC
686506 CAAACTTCACATAACATT
131 CAAACTTCACATAACATT
686524 ATAGGCACACAATAGAAAATAAATTCCTAAAAACCTTTCGATGCTCATTCTTTACGAATTTCATA
1 ATAGGCACACAATAGAAAATAAA-T-CTAAAAACCTTTCGATGCTCATTCTTTACGAATTTCATA
*
686589 TCACATCATCAATGTTGACCTTAATACTTCAAATTGACCAATAAATCCCTTTTTATCCAAAATCA
64 TCACATCATCAATGTTGACCTTAATACTTCAAATGGACCAATAAATCCCTTTTTATCCAAAATCA
686654 CCCAAACTTCACATAACATT
129 CCCAAACTTCACATAACATT
686674 CTTCAATTTT
Statistics
Matches: 146, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
147 23 0.16
148 1 0.01
149 53 0.36
150 69 0.47
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (148 bp):
ATAGGCACACAATAGAAAATAAATCTAAAAACCTTTCGATGCTCATTCTTTACGAATTTCATATC
ACATCATCAATGTTGACCTTAATACTTCAAATGGACCAATAAATCCCTTTTTATCCAAAATCACC
CAAACTTCACATAACATT
Found at i:693897 original size:16 final size:16
Alignment explanation
Indices: 693876--693912 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
693866 TCTAGCATGC
693876 CAACTGAAGCTGAACA
1 CAACTGAAGCTGAACA
693892 CAACTGAAGCTGAACA
1 CAACTGAAGCTGAACA
693908 CAACT
1 CAACT
693913 TCAGTTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (16 bp):
CAACTGAAGCTGAACA
Found at i:695390 original size:19 final size:19
Alignment explanation
Indices: 695366--695406 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
695356 TCCATCTCAT
695366 CTTTCATGAAAGACTCCCA
1 CTTTCATGAAAGACTCCCA
*
695385 CTTTCATGGAAGACTCCCA
1 CTTTCATGAAAGACTCCCA
695404 CTT
1 CTT
695407 GACTGAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (19 bp):
CTTTCATGAAAGACTCCCA
Found at i:699631 original size:2 final size:2
Alignment explanation
Indices: 699624--699675 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
699614 AATCATGACA
699624 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
699666 AT AT AT AT AT
1 AT AT AT AT AT
699676 GAATATTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:716112 original size:32 final size:33
Alignment explanation
Indices: 716076--716137 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
716066 GATTGCATGA
*
716076 TTCTATGAATACAAGCATAT-TGTTTATATAGT
1 TTCTATGAATACAAGAATATATGTTTATATAGT
** *
716108 TTCTATGTGTACATGAATATATGTTTATAT
1 TTCTATGAATACAAGAATATATGTTTATAT
716138 GTTATATGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 16 0.64
33 9 0.36
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (33 bp):
TTCTATGAATACAAGAATATATGTTTATATAGT
Found at i:716245 original size:15 final size:15
Alignment explanation
Indices: 716214--716251 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
716204 GTACATGTCC
*
716214 ATGTG-ATATAATTT
1 ATGTGAATATAATAT
*
716228 ATGTGAATATGATAT
1 ATGTGAATATAATAT
716243 ATGTGAATA
1 ATGTGAATA
716252 CATGTCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (15 bp):
ATGTGAATATAATAT
Found at i:716263 original size:16 final size:15
Alignment explanation
Indices: 716196--716264 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
716186 TGACTATGAG
*
716196 CTATGTGAGTACATGT
1 CTATGTGAATA-ATGT
*
716212 CCATGTGATATAAT-T
1 CTATGTGA-ATAATGT
716227 -TATGTGAAT-ATGAT
1 CTATGTGAATAATG-T
*
716241 ATATGTGAATACATGT
1 CTATGTGAATA-ATGT
716257 CTATGTGA
1 CTATGTGA
716265 CAAGTTATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 2 0.05
13 2 0.05
14 7 0.16
15 10 0.23
16 17 0.40
17 5 0.12
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (15 bp):
CTATGTGAATAATGT
Found at i:734314 original size:30 final size:30
Alignment explanation
Indices: 734280--734337 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
734270 GAACCAGCGG
** *
734280 TTCACATCGGTTTTGTCGGTTTTCAGCCGA
1 TTCACATCGGTTTTACCGGTTCTCAGCCGA
*
734310 TTCACATTGGTTTTACCGGTTCTCAGCC
1 TTCACATCGGTTTTACCGGTTCTCAGCC
734338 AGTTCTACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (30 bp):
TTCACATCGGTTTTACCGGTTCTCAGCCGA
Found at i:735001 original size:21 final size:22
Alignment explanation
Indices: 734970--735027 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
734960 GATTGTCCAT
734970 GGGATACAGATTCCCCCCCAGA
1 GGGATACAGATTCCCCCCCAGA
734992 GGGA-ACAGATTCCCCCCCAG-
1 GGGATACAGATTCCCCCCCAGA
*
735012 GGGGTATC-GATTCCCC
1 GGGATA-CAGATTCCCC
735028 GGGAACAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 25 0.76
22 5 0.15
ACGTcount: A:0.22, C:0.36, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGATACAGATTCCCCCCCAGA
Found at i:735050 original size:34 final size:35
Alignment explanation
Indices: 734992--735061 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 35
734982 CCCCCCCAGA
734992 GGGAACAGATTCCCCCCCAGGGGGTATC-GATTCCCC
1 GGGAACAGATT-CCCCCCAGGGGGTA-CAGATTCCCC
*
735028 GGGAACAGATT-CCCCCATGGGGTACAGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTACAGATTCCCC
735062 CTGCATGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.03
34 20 0.62
36 11 0.34
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.17
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTACAGATTCCCC
Found at i:735201 original size:21 final size:21
Alignment explanation
Indices: 735175--735237 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
735165 ATTTGAATAT
*
735175 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
735196 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
735217 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
735238 CCCATTCTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:738626 original size:20 final size:20
Alignment explanation
Indices: 738571--738666 Score: 96
Period size: 20 Copynumber: 5.0 Consensus size: 20
738561 ATCAGATTGT
738571 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
738591 CCAGAGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
738611 CCAGGGGGTATC-GATT---C
1 CCAGGGGGTA-CAGATTCCCC
* *
738628 CC--TGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
738646 CCAGGGGGTATAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
738666 C
1 C
738667 TGCATGGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.02
15 8 0.13
17 3 0.05
18 3 0.05
20 44 0.73
21 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:738636 original size:35 final size:35
Alignment explanation
Indices: 738596--738664 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
738586 TCCCCCCAGA
*
738596 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCT
1 GGGAACAGATTCCCCCCAGGGGGTATAGATTCCCT
738631 GGGAACAGATTCCCCCCAGGGGGTATAGATTCCC
1 GGGAACAGATTCCCCCCAGGGGGTATAGATTCCC
738665 CCTGCATGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATAGATTCCCT
Found at i:738784 original size:21 final size:21
Alignment explanation
Indices: 738758--738797 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
738748 ATTTGAATAT
*
738758 TATGAAGGGGTATCGATTCTC
1 TATGAAGGGGTACCGATTCTC
738779 TATGAAGGGGTACCGATTC
1 TATGAAGGGGTACCGATTC
738798 CCCCCATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCTC
Found at i:739840 original size:32 final size:32
Alignment explanation
Indices: 739804--739864 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
739794 AAAAATTAGG
739804 TTTTTATTTTAAAAATAAATTATAATTTTGGA
1 TTTTTATTTTAAAAATAAATTATAATTTTGGA
739836 TTTTTATTTTAAAAATAAATTATAATTTT
1 TTTTTATTTTAAAAATAAATTATAATTTT
739865 AAGTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
TTTTTATTTTAAAAATAAATTATAATTTTGGA
Found at i:739872 original size:32 final size:31
Alignment explanation
Indices: 739803--739872 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 31
739793 AAAAAATTAG
*
739803 GTTTTTATTTTAAAAATAAATTATAATTTTG
1 GTTTTTATTTTAAAAATAAATTATAATTTTA
739834 GATTTTTATTTTAAAAATAAATTATAATTTTAA
1 G-TTTTTATTTTAAAAATAAATTATAATTTT-A
739867 GTTTTT
1 GTTTTT
739873 TTAAATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 1 0.03
32 34 0.94
33 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (31 bp):
GTTTTTATTTTAAAAATAAATTATAATTTTA
Found at i:739884 original size:32 final size:32
Alignment explanation
Indices: 739805--739886 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
739795 AAAATTAGGT
* * *
739805 TTTTATTTTAAAAATAAATTATAATTTTGGAT
1 TTTTATTTAAAAAATAAATTATAATTTTGAAG
*
739837 TTTTATTTTAAAAATAAATTATAATTTT-AAG
1 TTTTATTTAAAAAATAAATTATAATTTTGAAG
739868 TTTT-TTTAAATTAAATAAA
1 TTTTATTTAAA--AAATAAA
739887 AAAGTTACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 5 0.11
31 5 0.11
32 35 0.78
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
TTTTATTTAAAAAATAAATTATAATTTTGAAG
Found at i:743501 original size:19 final size:19
Alignment explanation
Indices: 743464--743515 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
743454 TCTAAATAAT
743464 TTTTCAAAATTTC-ATTTTGA
1 TTTTCAAAA--TCAATTTTGA
*
743484 TTTTCAAAATCAATTTTGG
1 TTTTCAAAATCAATTTTGA
*
743503 CTTTCAAAATCAA
1 TTTTCAAAATCAA
743516 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 18 0.62
20 9 0.31
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (19 bp):
TTTTCAAAATCAATTTTGA
Found at i:745834 original size:21 final size:21
Alignment explanation
Indices: 745793--745834 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
745783 CTCAGAGGGA
*
745793 ACCGATTCCCCCCCAAGGGTT
1 ACCGATTCCCCCCCAACGGTT
**
745814 ACCGATTCCCCCTGAACGGTT
1 ACCGATTCCCCCCCAACGGTT
745835 TGGCTCCGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
ACCGATTCCCCCCCAACGGTT
Found at i:749395 original size:18 final size:18
Alignment explanation
Indices: 749372--749410 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
749362 CTATGTTAAA
749372 GATGGTGAAATTATAGGT
1 GATGGTGAAATTATAGGT
749390 GATGGTGAAATTATAGGT
1 GATGGTGAAATTATAGGT
749408 GAT
1 GAT
749411 CCATCAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (18 bp):
GATGGTGAAATTATAGGT
Found at i:749896 original size:62 final size:63
Alignment explanation
Indices: 749799--749925 Score: 247
Period size: 62 Copynumber: 2.0 Consensus size: 63
749789 ATCATGGATG
749799 TTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAG-AGTGTATGTGGAACAACCTCCAGGTT
1 TTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAACAACCTCCAGGTT
749861 TTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAACAACCTCCAGGTT
1 TTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAACAACCTCCAGGTT
749924 TT
1 TT
749926 GAAGATTCAA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 36 0.56
63 28 0.44
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (63 bp):
TTAAAAGTGCATTTTTAAATGGTTTTATAAAGGAAGAAGTGTATGTGGAACAACCTCCAGGTT
Found at i:751369 original size:23 final size:23
Alignment explanation
Indices: 751334--751392 Score: 111
Period size: 22 Copynumber: 2.6 Consensus size: 23
751324 CCCCATGAGA
751334 GAACCGATTCCCCCTTTGAAGGG
1 GAACCGATTCCCCCTTTGAAGGG
751357 G-ACCGATTCCCCCTTTGAAGGG
1 GAACCGATTCCCCCTTTGAAGGG
751379 GAACCGATTCCCCC
1 GAACCGATTCCCCC
751393 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 22 0.63
23 13 0.37
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (23 bp):
GAACCGATTCCCCCTTTGAAGGG
Found at i:751401 original size:21 final size:21
Alignment explanation
Indices: 751375--751414 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
751365 CCCCCTTTGA
*
751375 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
751396 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
751415 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:755836 original size:40 final size:40
Alignment explanation
Indices: 755790--755880 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
755780 ATTCAATCAG
*** *
755790 TATCGATACCAAAGGGGTTGTATATATACTGAAGGGAAGA
1 TATCGATACCAAAGGGGCCATATATATACCGAAGGGAAGA
755830 TATCGATACCAAAGGGGCCATATATATACCGAAGGGAAGA
1 TATCGATACCAAAGGGGCCATATATATACCGAAGGGAAGA
755870 TATCGATACCA
1 TATCGATACCA
755881 TTTCAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (40 bp):
TATCGATACCAAAGGGGCCATATATATACCGAAGGGAAGA
Found at i:755838 original size:20 final size:20
Alignment explanation
Indices: 755815--755879 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
755805 GGTTGTATAT
*
755815 ATACTGAAGGGAAGATATCG
1 ATACCGAAGGGAAGATATCG
* *** **
755835 ATACCAAAGGGGCCATATAT
1 ATACCGAAGGGAAGATATCG
755855 ATACCGAAGGGAAGATATCG
1 ATACCGAAGGGAAGATATCG
755875 ATACC
1 ATACC
755880 ATTTCAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (20 bp):
ATACCGAAGGGAAGATATCG
Found at i:755911 original size:17 final size:19
Alignment explanation
Indices: 755891--755932 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
755881 TTTCAAAAAA
755891 AATACAAAAAT-G-GTATC
1 AATACAAAAATAGAGTATC
*
755908 AATACCAAAATAGAGTATC
1 AATACAAAAATAGAGTATC
*
755927 AGTACA
1 AATACA
755933 TAGTATGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.21
Consensus pattern (19 bp):
AATACAAAAATAGAGTATC
Found at i:756400 original size:20 final size:20
Alignment explanation
Indices: 756375--756454 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
756365 TAATTAAAAT
756375 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
756395 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
756421 GTATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
756441 GTATGAAAGGATGC
1 GCATGAAAGGATGC
756455 CATAAACTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 28 0.57
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 13 0.27
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.25
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:756434 original size:46 final size:46
Alignment explanation
Indices: 756362--756481 Score: 177
Period size: 46 Copynumber: 2.6 Consensus size: 46
756352 TAAATCGAAT
756362 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
756408 TCATAATTAAAATGTATGAAATGATGCATTAAGGTATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
756454 CCATAAACTAGAATGCATGAAAGGATGC
1 CCAT-AATTAAAATGCATGAAAGGATGC
756482 CATAATTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
46 45 0.70
47 19 0.30
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:757944 original size:28 final size:26
Alignment explanation
Indices: 757868--757944 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 26
757858 CCAATTTATT
* *
757868 AAATATATTTTATTTTTTTA-CTTAA
1 AAATATATTTTATTATTTTATCTGAA
*
757893 AAATATATTTTGTTATTAACTTATCTCGAA
1 AAATATATTTTATTATT---TTATCT-GAA
*
757923 ATAATATATTTTATTCTTTTAT
1 A-AATATATTTTATTATTTTAT
757945 TAACTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 15 0.37
28 7 0.17
29 2 0.05
30 3 0.07
31 14 0.34
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (26 bp):
AAATATATTTTATTATTTTATCTGAA
Found at i:758757 original size:11 final size:10
Alignment explanation
Indices: 758737--758761 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
758727 ATTAAATATA
758737 TTAATTTTTT
1 TTAATTTTTT
758747 TTAATTTTTT
1 TTAATTTTTT
758757 TTAAT
1 TTAAT
758762 GAATTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTAATTTTTT
Found at i:760754 original size:12 final size:12
Alignment explanation
Indices: 760737--760761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
760727 GTTCTTAAGA
760737 GAAGATAATGAG
1 GAAGATAATGAG
760749 GAAGATAATGAG
1 GAAGATAATGAG
760761 G
1 G
760762 GTGACGGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:761525 original size:16 final size:16
Alignment explanation
Indices: 761475--761525 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
761465 ATATTTTTAA
761475 TTTAATTACT-TAACT
1 TTTAATTACTCTAACT
761490 TTTAAATTACTCCTAA--
1 TTT-AATTACT-CTAACT
*
761506 TTTAATCACTCTAACT
1 TTTAATTACTCTAACT
761522 TTTA
1 TTTA
761526 TTTTTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 14 0.47
18 3 0.10
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAATTACTCTAACT
Found at i:762068 original size:14 final size:13
Alignment explanation
Indices: 762049--762124 Score: 65
Period size: 14 Copynumber: 6.1 Consensus size: 13
762039 TCGTGAACGT
762049 TCGATTATGTTCG
1 TCGATTATGTTCG
762062 CTCGATTATGTTCG
1 -TCGATTATGTTCG
*
762076 T---TTATGTTTG
1 TCGATTATGTTCG
762086 TTCGATTATGTTCG
1 -TCGATTATGTTCG
*
762100 T---TTATGTTTG
1 TCGATTATGTTCG
762110 TTCGATTATGTTCG
1 -TCGATTATGTTCG
762124 T
1 T
762125 TTATGTTCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
10 16 0.32
11 2 0.04
13 3 0.06
14 29 0.58
ACGTcount: A:0.13, C:0.12, G:0.21, T:0.54
Consensus pattern (13 bp):
TCGATTATGTTCG
Found at i:762074 original size:24 final size:24
Alignment explanation
Indices: 762047--762145 Score: 137
Period size: 24 Copynumber: 4.1 Consensus size: 24
762037 GTTCGTGAAC
* *
762047 GTTCGATTATGTTCGCTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
762071 GTTCGTTTATGTTTGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
762095 GTTCGTTTATGTTTGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
762119 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
762143 GTT
1 GTT
762146 TAACCCAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
23 1 0.01
24 68 0.99
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:763253 original size:16 final size:16
Alignment explanation
Indices: 763228--763268 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
763218 CCAACGTTTA
763228 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
763244 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
763260 T-TT-ATTTAT
1 TGTTCATTTAT
763269 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:763355 original size:16 final size:16
Alignment explanation
Indices: 763330--763370 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
763320 AAAAAAATTT
763330 TGTTCATTTATATTCG
1 TGTTCATTTATATTCG
* *
763346 TGTTCGTTTATGTTCG
1 TGTTCATTTATATTCG
763362 T-TT-ATTTAT
1 TGTTCATTTAT
763371 TAAATGAACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 5 0.23
15 2 0.09
16 15 0.68
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATATTCG
Found at i:770526 original size:32 final size:32
Alignment explanation
Indices: 770490--770591 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
770480 TTATCATAGG
770490 TATCACAGTCATAAAATAATAATTTAGGACAA
1 TATCACAGTCATAAAATAATAATTTAGGACAA
* * * ** *
770522 TATCATTA-TCATTATATAATAATCATTA-TTCTA
1 TATCA-CAGTCATAAAATAATAAT--TTAGGACAA
770555 TATCACAGTCATAAAATAATAATTTAGGACAA
1 TATCACAGTCATAAAATAATAATTTAGGACAA
770587 TATCA
1 TATCA
770592 TTATCATTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
31 3 0.06
32 26 0.49
33 21 0.40
34 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (32 bp):
TATCACAGTCATAAAATAATAATTTAGGACAA
Found at i:770594 original size:65 final size:65
Alignment explanation
Indices: 770490--770619 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
770480 TTATCATAGG
770490 TATCACAGTCATAAAATAATAATTTAGGACAATATCATTATCATTATATAATAATCATTATTCTA
1 TATCACAGTCATAAAATAATAATTTAGGACAATATCATTATCATTATATAATAATCATTATTCTA
770555 TATCACAGTCATAAAATAATAATTTAGGACAATATCATTATCATTATATAATAATCATTATTCTA
1 TATCACAGTCATAAAATAATAATTTAGGACAATATCATTATCATTATATAATAATCATTATTCTA
770620 ATAACGAACC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (65 bp):
TATCACAGTCATAAAATAATAATTTAGGACAATATCATTATCATTATATAATAATCATTATTCTA
Found at i:771284 original size:17 final size:17
Alignment explanation
Indices: 771262--771294 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
771252 CAATTTAAGG
771262 AGAACTAGACACAAACT
1 AGAACTAGACACAAACT
771279 AGAACTAGACACAAAC
1 AGAACTAGACACAAAC
771295 AGTCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.09
Consensus pattern (17 bp):
AGAACTAGACACAAACT
Found at i:771787 original size:156 final size:156
Alignment explanation
Indices: 771578--771890 Score: 626
Period size: 156 Copynumber: 2.0 Consensus size: 156
771568 TATCATAACC
771578 ATTTTTTCGTAAAACAATTAAATATTATTTTAAAAAACGATTATGACTTTGATTTTGGAAAATTG
1 ATTTTTTCGTAAAACAATTAAATATTATTTTAAAAAACGATTATGACTTTGATTTTGGAAAATTG
771643 GTTGATTAGTAATTAAATAGAAAATGAGTCACCATCGACCTTTAGGTTAGTTAGGTTGAATAACT
66 GTTGATTAGTAATTAAATAGAAAATGAGTCACCATCGACCTTTAGGTTAGTTAGGTTGAATAACT
771708 AAAAACGTCCTTTAAAAATAATTTTA
131 AAAAACGTCCTTTAAAAATAATTTTA
771734 ATTTTTTCGTAAAACAATTAAATATTATTTTAAAAAACGATTATGACTTTGATTTTGGAAAATTG
1 ATTTTTTCGTAAAACAATTAAATATTATTTTAAAAAACGATTATGACTTTGATTTTGGAAAATTG
771799 GTTGATTAGTAATTAAATAGAAAATGAGTCACCATCGACCTTTAGGTTAGTTAGGTTGAATAACT
66 GTTGATTAGTAATTAAATAGAAAATGAGTCACCATCGACCTTTAGGTTAGTTAGGTTGAATAACT
771864 AAAAACGTCCTTTAAAAATAATTTTA
131 AAAAACGTCCTTTAAAAATAATTTTA
771890 A
1 A
771891 GAAAAATCGT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (156 bp):
ATTTTTTCGTAAAACAATTAAATATTATTTTAAAAAACGATTATGACTTTGATTTTGGAAAATTG
GTTGATTAGTAATTAAATAGAAAATGAGTCACCATCGACCTTTAGGTTAGTTAGGTTGAATAACT
AAAAACGTCCTTTAAAAATAATTTTA
Found at i:772159 original size:30 final size:30
Alignment explanation
Indices: 772125--772184 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
772115 TTAGGGAAAA
772125 TTCTTTAACTCGAAAAGAAACTTCGAAATT
1 TTCTTTAACTCGAAAAGAAACTTCGAAATT
772155 TTCTTTAACTCGAAAAGAAACTTCGAAATT
1 TTCTTTAACTCGAAAAGAAACTTCGAAATT
772185 AGCGATCCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (30 bp):
TTCTTTAACTCGAAAAGAAACTTCGAAATT
Found at i:772757 original size:30 final size:30
Alignment explanation
Indices: 772693--772848 Score: 129
Period size: 30 Copynumber: 5.2 Consensus size: 30
772683 TTGAAATTAC
* * *
772693 AAGGACCAAAATTAGCAAAAACATA-AACTCA
1 AAGGACTAAAA-TAGTAAAAACA-AGAACTTA
* * *
772724 AAGGACCAAAATAGTACAAACAAGAATTTA
1 AAGGACTAAAATAGTAAAAACAAGAACTTA
* * *
772754 AAGGACTAAAATGGCAAAAA-TAGAAACTTA
1 AAGGACTAAAATAGTAAAAACAAG-AACTTA
* * *
772784 AAGGTCTAAAATAGTAAAAACAAAAAGTTA
1 AAGGACTAAAATAGTAAAAACAAGAACTTA
* *
772814 AAGGACTAAAATAATAAAAACATA-AACTAA
1 AAGGACTAAAATAGTAAAAACA-AGAACTTA
772844 AAGGA
1 AAGGA
772849 TTGAACAACA
Statistics
Matches: 101, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
29 3 0.03
30 85 0.84
31 13 0.13
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.16
Consensus pattern (30 bp):
AAGGACTAAAATAGTAAAAACAAGAACTTA
Found at i:772795 original size:60 final size:60
Alignment explanation
Indices: 772693--772848 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 60
772683 TTGAAATTAC
* * * * *
772693 AAGGACCAAAATTAGCAAAAACATAAACTCAAAGGACCAAAATAGTACAAACAAGAATTTA
1 AAGGACTAAAA-TAGCAAAAACAGAAACTCAAAGGACCAAAATAGTAAAAACAAAAAGTTA
* * * * *
772754 AAGGACTAAAATGGCAAAAATAGAAACTTAAAGGTCTAAAATAGTAAAAACAAAAAGTTA
1 AAGGACTAAAATAGCAAAAACAGAAACTCAAAGGACCAAAATAGTAAAAACAAAAAGTTA
** * *
772814 AAGGACTAAAATAATAAAAACATAAACTAAAAGGA
1 AAGGACTAAAATAGCAAAAACAGAAACTCAAAGGA
772849 TTGAACAACA
Statistics
Matches: 78, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 68 0.87
61 10 0.13
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.16
Consensus pattern (60 bp):
AAGGACTAAAATAGCAAAAACAGAAACTCAAAGGACCAAAATAGTAAAAACAAAAAGTTA
Found at i:774102 original size:3 final size:3
Alignment explanation
Indices: 774094--774142 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
774084 GATATTGTAT
774094 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
774141 TA
1 TA
774143 TTTTTGCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:774238 original size:22 final size:23
Alignment explanation
Indices: 774204--774251 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
774194 AAAAAGGATT
*
774204 TAAAATTAATGAA-AATAAATGAA
1 TAAAATTAATGAATAAAAAAT-AA
*
774227 TAAAA-TATTGAATAAAAAATAA
1 TAAAATTAATGAATAAAAAATAA
774249 TAA
1 TAA
774252 TGATAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (23 bp):
TAAAATTAATGAATAAAAAATAA
Found at i:785094 original size:8 final size:8
Alignment explanation
Indices: 785081--785121 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
785071 CTCATTTTTA
785081 GAGAATTT
1 GAGAATTT
785089 GAGAATTT
1 GAGAATTT
*
785097 -AGAGTTT
1 GAGAATTT
*
785104 GTGAATTT
1 GAGAATTT
785112 GAGAATTT
1 GAGAATTT
785120 GA
1 GA
785122 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (8 bp):
GAGAATTT
Found at i:785368 original size:128 final size:128
Alignment explanation
Indices: 785202--785943 Score: 1209
Period size: 128 Copynumber: 5.7 Consensus size: 128
785192 ACTATTCACA
* *
785202 TGAAGGCGCGTTCCC-GGGGCGCGCCTTCTATTATTTTGTCAGAGAATATTTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
785266 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
785329 TGAAGGCGCGTTCCCGGGGGTGCGCCTTCTATTATTTTGTAAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
785394 TTATGTCACTCATGTCCCTCGGGGACACAATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
785457 TGAAGGCGCGTTCCCGGGGGGGGGGGCCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
1 TGAAGGCGCGTTCCC--GGGGGCGCG-CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
*
785522 CTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAATACCTATTATTTCTCAGGGGAC
63 CTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGAC
785587 T
128 T
* * *
785588 TGAAGGCGCGTTCTCGGGGGGGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATT
1 TGAAGGCGCGTTC-C-----CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
* * *
785653 GCCCTATTATATCACTCATGTCCCTC-GGGACACTATTAATATCAATACCTATTATTTCTCAGGG
60 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGG
785717 GACT
125 GACT
** * *
785721 TGAAGGCGCGTTCCCGGGGGAACGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGTCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
785786 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
785849 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
785914 TTATGTCACTCATGTCTCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
785944 GATGGATTGT
Statistics
Matches: 577, Mismatches: 27, Indels: 21
0.92 0.04 0.03
Matches are distributed among these distances:
127 81 0.14
128 253 0.44
130 7 0.01
131 113 0.20
132 2 0.00
133 54 0.09
134 59 0.10
135 8 0.01
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:786378 original size:34 final size:34
Alignment explanation
Indices: 786339--786445 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
786329 TAAGTTGAAA
* *
786339 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
786373 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
786407 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
786441 TTTAA
1 TTTAA
786446 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:787075 original size:21 final size:21
Alignment explanation
Indices: 786966--787080 Score: 153
Period size: 21 Copynumber: 5.5 Consensus size: 21
786956 TATGGTATAA
* *
786966 AACCCTGTGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
786987 AA-CCTGACGGGCTAGGAATGT
1 AACCCTG-CGGGCTAGGAATGT
* *
787008 AACCCTACGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
787029 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
787050 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
787071 AACCCTGCGG
1 AACCCTGCGG
787081 AGATGGCATA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
20 7 0.08
21 70 0.84
22 6 0.07
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:788728 original size:18 final size:17
Alignment explanation
Indices: 788661--788734 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
788651 TACATTATAA
* *
788661 AAAATTAAAATTAATAT
1 AAAATTAAAATAAATTT
* *
788678 -AAATTCATAATAACTTT
1 AAAATT-AAAATAAATTT
788695 AAAATTAAAATAAATTT
1 AAAATTAAAATAAATTT
* *
788712 AAATATTAATATTAATTAT
1 AAA-ATTAAAATAAATT-T
788731 AAAA
1 AAAA
788735 AATATTACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
16 5 0.11
17 19 0.42
18 17 0.38
19 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTAAAATAAATTT
Found at i:788878 original size:19 final size:19
Alignment explanation
Indices: 788854--788912 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
788844 TTAATAATTC
*
788854 TAAATAAATAATAATTATA
1 TAAATAAATAATATTTATA
*
788873 TAAAT--ATTAT-TTTA-A
1 TAAATAAATAATATTTATA
*
788888 TAAAAAAATAATATTTATA
1 TAAATAAATAATATTTATA
788907 TAAATA
1 TAAATA
788913 TATTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 5 0.16
16 3 0.10
17 8 0.26
18 4 0.13
19 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAAATAATATTTATA
Found at i:788897 original size:34 final size:31
Alignment explanation
Indices: 788854--788933 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 31
788844 TTAATAATTC
*
788854 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
*
788888 TAAAAAAATAATATTTATATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
*
788919 TATAAAATATAATAA
1 TA-AAAAAATAATAA
788934 CTATTTACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.24
33 2 0.05
34 23 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:788926 original size:15 final size:15
Alignment explanation
Indices: 788892--788929 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
788882 TTTTAATAAA
*
788892 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
788908 -AAATATATTAATAT
1 AAAATATATTAATAT
788922 AAAATATA
1 AAAATATA
788930 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:790474 original size:30 final size:29
Alignment explanation
Indices: 790396--790475 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
790386 TTTATTGTTA
790396 TTTATATTTCAGT-ATTTTAATTTTTAGT
1 TTTATATTTCAGTCATTTTAATTTTTAGT
* * * *
790424 TTTATTTATTCCGTCTTTTTATTTTTTAGCT
1 TTTATAT-TTCAGTCATTTTAATTTTTAG-T
*
790455 TTTATATTTCAGTCCTTTTAA
1 TTTATATTTCAGTCATTTTAA
790476 ATTCCAGCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 6 0.15
29 5 0.12
30 23 0.56
31 7 0.17
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTATATTTCAGTCATTTTAATTTTTAGT
Found at i:802364 original size:24 final size:23
Alignment explanation
Indices: 802300--802365 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
802290 CAATCTTATA
* *
802300 TGGCACTACGGTGCATTTCTACG
1 TGGCACTACGGTGAAATTCTACG
* **
802323 TGGCACTTCAATGCAAATTCTACG
1 TGGCACTACGGTG-AAATTCTACG
802347 TGGCACTACGGTGTAAATT
1 TGGCACTACGGTG-AAATT
802366 TATACGAGCT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGAAATTCTACG
Found at i:812650 original size:33 final size:33
Alignment explanation
Indices: 812613--812679 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
812603 ATATCTAATA
812613 TAGTGTAGGGAATCCACAACTCA-TATTTCCCTT
1 TAGTGTAGGGAATCCACAACTCAGT-TTTCCCTT
812646 TAGTGTAGGGAATCCACAACTCAGTTTTCCCTT
1 TAGTGTAGGGAATCCACAACTCAGTTTTCCCTT
812679 T
1 T
812680 TTCACTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (33 bp):
TAGTGTAGGGAATCCACAACTCAGTTTTCCCTT
Found at i:815179 original size:23 final size:23
Alignment explanation
Indices: 815153--815216 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
815143 CGGCTCGTAT
815153 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* *
815176 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACATAG
*
815199 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
815217 TATAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:816640 original size:18 final size:18
Alignment explanation
Indices: 816617--816665 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
816607 TTAGTCATGC
*
816617 ATACATACAATCAATGTA
1 ATACATATAATCAATGTA
816635 ATACATATAATCAATGTA
1 ATACATATAATCAATGTA
816653 ATACATATAATCA
1 ATACATATAATCA
816666 CATATAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (18 bp):
ATACATATAATCAATGTA
Found at i:817069 original size:21 final size:21
Alignment explanation
Indices: 817045--817089 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
817035 TTTTGTTCGT
* *
817045 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
817066 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
817087 TTG
1 TTG
817090 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:820108 original size:23 final size:23
Alignment explanation
Indices: 820082--820145 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
820072 CGGCTCGTAT
820082 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* *
820105 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACATAG
*
820128 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
820146 TATAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:821984 original size:21 final size:21
Alignment explanation
Indices: 821954--821998 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
821944 TTTTATTCGT
* *
821954 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
821975 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
821996 TTG
1 TTG
821999 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:827787 original size:18 final size:18
Alignment explanation
Indices: 827764--827799 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
827754 CCACAAGCGC
827764 AATTTAATACTATATTAT
1 AATTTAATACTATATTAT
827782 AATTTAATACTATATTAT
1 AATTTAATACTATATTAT
827800 GGCATATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAATACTATATTAT
Found at i:828555 original size:45 final size:45
Alignment explanation
Indices: 828486--828621 Score: 226
Period size: 45 Copynumber: 3.1 Consensus size: 45
828476 TAAAGTGATT
828486 AACAAGGTAGTATATATTTA-AAATAGTCTCAACTAATTGACAATA
1 AACAAGGTAGTATATA-TTAGAAATAGTCTCAACTAATTGACAATA
828531 AACAAGGTAGTATATATTAGAAATAGTCTCAACTAATTGACAATA
1 AACAAGGTAGTATATATTAGAAATAGTCTCAACTAATTGACAATA
*
828576 AACAAGGTAGTATATATT-GGAA-AGTCTCAACTAA-TGACAATA
1 AACAAGGTAGTATATATTAGAAATAGTCTCAACTAATTGACAATA
828618 AACA
1 AACA
828622 CTCATACATC
Statistics
Matches: 89, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
42 12 0.13
43 12 0.13
44 6 0.07
45 59 0.66
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (45 bp):
AACAAGGTAGTATATATTAGAAATAGTCTCAACTAATTGACAATA
Found at i:829485 original size:15 final size:15
Alignment explanation
Indices: 829464--829514 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
829454 TTGGGAGAGC
829464 TGCTGCTGTTGCTGT
1 TGCTGCTGTTGCTGT
*
829479 TGTTGCTGTTGCTGT
1 TGCTGCTGTTGCTGT
* *
829494 TGCTGCTGCTGCTGC
1 TGCTGCTGTTGCTGT
829509 TGCTGC
1 TGCTGC
829515 AAATGTGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.00, C:0.24, G:0.33, T:0.43
Consensus pattern (15 bp):
TGCTGCTGTTGCTGT
Found at i:829531 original size:3 final size:3
Alignment explanation
Indices: 829462--829514 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
829452 AGTTGGGAGA
* * * * *
829462 GCT GCT GCT GTT GCT GTT GTT GCT GTT GCT GTT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
829510 GCT GC
1 GCT GC
829515 AAATGTGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.25, G:0.34, T:0.42
Consensus pattern (3 bp):
GCT
Found at i:829555 original size:18 final size:18
Alignment explanation
Indices: 829534--829579 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
829524 AGCTGCTGTG
829534 GCTGCTGCTGCTGTTGCA
1 GCTGCTGCTGCTGTTGCA
829552 GCTG-TGGCAT-CTGTTGCA
1 GCTGCT-GC-TGCTGTTGCA
*
829570 TCTGCTGCTG
1 GCTGCTGCTG
829580 TTGATGCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 8
0.72 0.03 0.25
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.07, C:0.26, G:0.33, T:0.35
Consensus pattern (18 bp):
GCTGCTGCTGCTGTTGCA
Found at i:840081 original size:18 final size:18
Alignment explanation
Indices: 840058--840099 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
840048 AGACAAAATT
840058 TTTAAAATAAGATATT-TA
1 TTTAAAATAAGA-ATTCTA
*
840076 TTT-AAATAATAATTCTA
1 TTTAAAATAAGAATTCTA
840093 TTTAAAA
1 TTTAAAA
840100 ACATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 12 0.57
18 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAAATAAGAATTCTA
Found at i:843658 original size:3 final size:3
Alignment explanation
Indices: 843629--843686 Score: 62
Period size: 3 Copynumber: 18.0 Consensus size: 3
843619 CTTTTTTATT
**
843629 TAA TAA TATA TATA TATA TATA TAA TAA TAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
843678 TAA TAA TAA
1 TAA TAA TAA
843687 GTAAACTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 35 0.70
4 15 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:843803 original size:24 final size:24
Alignment explanation
Indices: 843756--843802 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
843746 AATAGAGCAA
843756 AGACGAATAAAGACAATAATTTTT
1 AGACGAATAAAGACAATAATTTTT
843780 AGACGAA-AAAGACAATAATTTTT
1 AGACGAATAAAGACAATAATTTTT
843803 TTCATTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AGACGAATAAAGACAATAATTTTT
Found at i:843970 original size:46 final size:46
Alignment explanation
Indices: 843858--844634 Score: 1186
Period size: 46 Copynumber: 16.8 Consensus size: 46
843848 TGTCCAGAGG
*
843858 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
843903 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
843949 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCTGAAGAT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
843995 GTTTGAAAACATCAAGCACTGGAGGGCTTATAGATGACCCGAAGGA
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
844041 TTTTGAAAACATCAGGC-CTTGAAGGGCTTACAGATGACCCGAAGG-
1 TTTTGAAAACATCAAGCAC-TGAAGGGCTTACAGATGACCCGAAGGT
844086 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
844132 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
844178 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATAACCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
844224 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACGCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
844270 TTTTGAAAACATCAAGCACTTAAGGGCTTACAGATGGCCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
844316 TTTTGTAAACATCAAGCACTGAAGGGCTTATAGATGAACTGAAGG-
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
844361 TTTTGAAAACATCAAGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTTT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG------T
*
844413 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
844459 TTTTGAAAACATCAAGCACTAAAGGGCTTACAGATGACCCGAAGGTTTT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG---T
* *
844508 TTTTGAAAACATCATGCACTGAAGGGCTTACATATGACCCGAAGG-
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
844553 TTTTGAAAACATCAAGCACTGAAGGGCTTACAAATGACCCGAAGAT
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
844599 TTTTGAAAACATCAAGCACTGAAGGTCTTACAGATG
1 TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATG
844635 TGGGAAACAA
Statistics
Matches: 670, Mismatches: 47, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
45 170 0.25
46 414 0.62
49 43 0.06
52 43 0.06
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (46 bp):
TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:844166 original size:183 final size:183
Alignment explanation
Indices: 843858--844634 Score: 1175
Period size: 183 Copynumber: 4.2 Consensus size: 183
843848 TGTCCAGAGG
* *
843858 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCAC
1 TTTTGAAAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCAC
843922 TGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
66 TGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
* * * *
843987 CTGAAGATGTTTGAAAACATCAAGCACTGGAGGGCTTATAGATGACCCGAAGGA
131 CCGAAGGT-TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGA
844041 TTTTGAAAACATCAGGC-CTTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAGCA
1 TTTTGAAAACATCAGGCAC-TGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCA
844104 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
65 CTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
* *
844169 CCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATAACCCGAAGGT
130 CCCGAAGG-TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGA
* * *
844224 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACGCGAAGGTTTTTGAAAACATCAAGCAC
1 TTTTGAAAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCAC
* * * * *
844289 TTAAGGGCTTACAGATGGCCCGAAGGTTTTTGTAAACATCAAGCACTGAAGGGCTTATAGATGAA
66 TGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
* * *
844354 CTGAAGGTTTTGAAAACATCAAGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTTT
131 CCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG------A
*
844413 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCAC
1 TTTTGAAAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCAC
* * *
844478 TAAAGGGCTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGGCTTACATAT
66 TGAAGGGCTTACAGATGACCCGAAGG---TTTTTGAAAACATCAAGCACTGAAGGGCTTACAGAT
*
844543 GACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAAATGACCCGAA-GA
128 GACCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGA
* *
844598 TTTTTGAAAACATCAAGCACTGAAGGTCTTACAGATG
1 -TTTTGAAAACATCAGGCACTGAAGGGCTTACAGATG
844635 TGGGAAACAA
Statistics
Matches: 546, Mismatches: 34, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
182 1 0.00
183 254 0.47
184 87 0.16
186 34 0.06
189 88 0.16
191 1 0.00
192 81 0.15
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (183 bp):
TTTTGAAAACATCAGGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCAC
TGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGAC
CCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGA
Found at i:845329 original size:22 final size:22
Alignment explanation
Indices: 845304--845355 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
845294 AATAAAGCTT
* *
845304 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATATA
845326 TCATCTTT---AAGAAAATATA
1 TCATCTTTGAAAAGAAAATATA
845345 TCATCTTTGAA
1 TCATCTTTGAA
845356 GAATGTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 17 0.68
22 8 0.32
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATATA
Found at i:850028 original size:6 final size:7
Alignment explanation
Indices: 850012--850065 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
850002 CTTGATTCAA
850012 TTTTCCT
1 TTTTCCT
850019 TTTTCCTT
1 TTTTCC-T
*
850027 TTTTTCT
1 TTTTCCT
850034 TTTT-CT
1 TTTTCCT
* *
850040 TATTCTT
1 TTTTCCT
850047 TTTTCCTT
1 TTTTCC-T
850055 TTTTCCT
1 TTTTCCT
850062 TTTT
1 TTTT
850066 GTTTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 5 0.13
7 21 0.54
8 13 0.33
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCCT
Found at i:850056 original size:28 final size:26
Alignment explanation
Indices: 850018--850077 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
850008 TCAATTTTCC
*
850018 TTTTTCCTTTTTTTCTTTTTCTTATTCT
1 TTTTTCCTTTTTTCCTTTTTCTT-TT-T
*
850046 TTTTTCCTTTTTTCCTTTTTGTTTTT
1 TTTTTCCTTTTTTCCTTTTTCTTTTT
850072 TTTTTC
1 TTTTTC
850078 TGATGAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.23
27 2 0.07
28 21 0.70
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTTCCTTTTTTCCTTTTTCTTTTT
Found at i:851031 original size:10 final size:10
Alignment explanation
Indices: 851018--851044 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
851008 AAAGAACAAA
851018 AAACAAGTTT
1 AAACAAGTTT
851028 AAACAAGTTT
1 AAACAAGTTT
851038 AAACAAG
1 AAACAAG
851045 ATGCTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (10 bp):
AAACAAGTTT
Found at i:852597 original size:7 final size:7
Alignment explanation
Indices: 852561--852598 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
852551 ATAAAAGTAT
852561 AAATGCA
1 AAATGCA
852568 AAATG-A
1 AAATGCA
852574 AAATTGCA
1 AAA-TGCA
852582 AAGATGCA
1 AA-ATGCA
852590 AAATGCA
1 AAATGCA
852597 AA
1 AA
852599 TGTATGTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.14
7 14 0.50
8 9 0.32
9 1 0.04
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (7 bp):
AAATGCA
Found at i:852832 original size:30 final size:30
Alignment explanation
Indices: 852797--852856 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
852787 GCTTATGGGT
* *
852797 CATATTGCTTGTCTGGACTGCAGCTTCTTC
1 CATATTGCTTATCTGGACTGCAACTTCTTC
852827 CATATTGCTTATCTGGACTGCAACTTCTTC
1 CATATTGCTTATCTGGACTGCAACTTCTTC
852857 TATGACATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.40
Consensus pattern (30 bp):
CATATTGCTTATCTGGACTGCAACTTCTTC
Found at i:854156 original size:18 final size:19
Alignment explanation
Indices: 854109--854170 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
854099 AGCGTTAATT
* *
854109 AAAATTATATATATATATA
1 AAAATAATAAATATATATA
* * *
854128 TATATATATAAATAT-TATG
1 AAAATA-ATAAATATATATA
*
854147 AAAATAATAAGTATATATA
1 AAAATAATAAATATATATA
854166 AAAAT
1 AAAAT
854171 TTTGAAAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
18 7 0.22
19 18 0.56
20 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATAATAAATATATATA
Found at i:857955 original size:21 final size:21
Alignment explanation
Indices: 857911--857968 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
857901 CCCTGTGGGA
857911 GGAATCGGTTCCCCTTCAAAGGG
1 GGAATCGGTT-CCC-TCAAAGGG
857934 GGAATCGGTTCCCTC-AAGGG
1 GGAATCGGTTCCCTCAAAGGG
* *
857954 GGGATCGATTCCCTC
1 GGAATCGGTTCCCTC
857969 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.55
21 2 0.06
22 3 0.09
23 10 0.30
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (21 bp):
GGAATCGGTTCCCTCAAAGGG
Found at i:864194 original size:32 final size:32
Alignment explanation
Indices: 864146--864208 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
864136 ACAATTATTG
* *
864146 TTAATTTATAAAATTAATCAAATAATAATAAT
1 TTAATTTATAAAATTAAACAAATAAAAATAAT
*
864178 TTAATTTA-AAATATTAAACATATAAAAATAA
1 TTAATTTATAAA-ATTAAACAAATAAAAATAA
864209 ATATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
TTAATTTATAAAATTAAACAAATAAAAATAAT
Found at i:865579 original size:3 final size:3
Alignment explanation
Indices: 865571--865638 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
865561 TCTTTTTTAT
* * * *
865571 ATA ATA ATA TATA ATA ATA ATA ATA ATA ATT ATT ATT ATT ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
865617 ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
865639 GTAAACTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
ATA
Found at i:872681 original size:18 final size:18
Alignment explanation
Indices: 872658--872692 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
872648 ACTAAATTTT
872658 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
872676 TGTCCCGAATGACCACT
1 TGTCCCAAAGGACCACT
872693 GATTGTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:878737 original size:18 final size:18
Alignment explanation
Indices: 878716--878783 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
878706 TATTTGTCCC
878716 GAAGGACCACTATGTCTT
1 GAAGGACCACTATGTCTT
878734 GAAGGACCACTGATTGT-TCT
1 GAAGGACCACT-A-TGTCT-T
* *
878754 GAAGAACCACTATGTCTC
1 GAAGGACCACTATGTCTT
878772 GAAGGACCACTA
1 GAAGGACCACTA
878784 ATAATCCCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 25 0.58
19 4 0.09
20 14 0.33
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (18 bp):
GAAGGACCACTATGTCTT
Found at i:881233 original size:15 final size:15
Alignment explanation
Indices: 881204--881244 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
881194 TACATAAATA
*
881204 ATTAT-AAACATATT
1 ATTATAAAATATATT
881218 ATTATAAAATATATT
1 ATTATAAAATATATT
*
881233 ATTTTAAAATAT
1 ATTATAAAATAT
881245 TAATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:894062 original size:23 final size:23
Alignment explanation
Indices: 894036--894096 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
894026 CGATCAGTTT
894036 GCTGGTTCTGATGTGGTTTGGAG
1 GCTGGTTCTGATGTGGTTTGGAG
*
894059 GCTGGTTTTGATGTGGTTTGGAG
1 GCTGGTTCTGATGTGGTTTGGAG
*
894082 GTTGGTTCTGATGTG
1 GCTGGTTCTGATGTG
894097 ATTATCTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.08, C:0.07, G:0.43, T:0.43
Consensus pattern (23 bp):
GCTGGTTCTGATGTGGTTTGGAG
Found at i:894529 original size:82 final size:80
Alignment explanation
Indices: 894443--894695 Score: 265
Period size: 81 Copynumber: 3.1 Consensus size: 80
894433 TAACTTTAAT
894443 GGCGTTTTTATACAAACGTCGCAATAGGTTCATCTATAGTGAAATTTTTTCAATAAACGCCTCAA
1 GGCGTTTTTATACAAACG-CGCAATAGGTTCATCTATAGTG-AATTTTTTCAATAAACGCCTCAA
*
894508 CATAGTGGTACTTTAGC
64 CATAGTAGTACTTTAGC
* * * *** * ** *
894525 GGCGTTTTTATACAAACGCCGTAATAGGGTCATCTATAGCGGCGTTTTTCAATAAATGCAGCGAC
1 GGCGTTTTTATACAAACG-CGCAATAGGTTCATCTATAGTGAATTTTTTCAATAAACGCCTCAAC
*
894590 AAAGTAGTACTTTAGC
65 ATAGTAGTACTTTAGC
* * * * *
894606 GGCATTTTTATACTAACGCTGCAATAGGATCCATCTATAGTGGCATTTTTTCAATAAACACCGT-
1 GGCGTTTTTATACAAACGC-GCAATAGG-TTCATCTATAGT-GAATTTTTTCAATAAACGCC-TC
*
894670 AATATAGTAGTACTTTAGC
62 AACATAGTAGTACTTTAGC
*
894689 AGCGTTT
1 GGCGTTT
894696 GAATGCCGCT
Statistics
Matches: 136, Mismatches: 31, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
80 1 0.01
81 54 0.40
82 46 0.34
83 35 0.26
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (80 bp):
GGCGTTTTTATACAAACGCGCAATAGGTTCATCTATAGTGAATTTTTTCAATAAACGCCTCAACA
TAGTAGTACTTTAGC
Found at i:894533 original size:41 final size:40
Alignment explanation
Indices: 894488--894614 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 40
894478 ATAGTGAAAT
894488 TTTTTCAATAAACGCCTCAACATAGTGGTACTTTAGCGGCG
1 TTTTTCAATAAACGCCTC-ACATAGTGGTACTTTAGCGGCG
* *
894529 TTTTT-ATACAAACGCCGT-A-ATAG-GGTCATCTATAGCGGCG
1 TTTTTCA-ATAAACGCC-TCACATAGTGGT-A-CTTTAGCGGCG
* ** * * *
894569 TTTTTCAATAAATGCAGCGACAAAGTAGTACTTTAGCGGCA
1 TTTTTCAATAAACGCCTC-ACATAGTGGTACTTTAGCGGCG
894610 TTTTT
1 TTTTT
894615 ATACTAACGC
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
38 3 0.04
39 5 0.07
40 23 0.34
41 29 0.43
42 5 0.07
43 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (40 bp):
TTTTTCAATAAACGCCTCACATAGTGGTACTTTAGCGGCG
Found at i:894800 original size:41 final size:41
Alignment explanation
Indices: 894700--894842 Score: 198
Period size: 40 Copynumber: 3.5 Consensus size: 41
894690 GCGTTTGAAT
* *
894700 GCCGCTATAGACTCTTACTTTAGTGGCGTTTTTATACAAAC
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
*
894741 G-CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
894781 GCCGCTAAAGACTCATACTTTAGTGTCGTTTTTATTTACAAAT
1 GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA--TACAAAC
*
894824 ACCGCTAAAGACTCGTACT
1 GCCGCTAAAGACTCGTACT
894843 GACGTTTGTG
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 39 0.42
41 30 0.33
43 23 0.25
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (41 bp):
GCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAAC
Found at i:897837 original size:15 final size:15
Alignment explanation
Indices: 897810--897848 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
897800 CGCCGCTATC
* *
897810 TTTT-GCGGTGTTAG
1 TTTTAGCGGCGTTAA
897824 TTTTAGCGGCGTTAA
1 TTTTAGCGGCGTTAA
897839 TTTTAGCGGC
1 TTTTAGCGGC
897849 ACTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.13, C:0.13, G:0.31, T:0.44
Consensus pattern (15 bp):
TTTTAGCGGCGTTAA
Found at i:898382 original size:2 final size:2
Alignment explanation
Indices: 898377--898464 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
898367 GCGACAAAAA
898377 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
898419 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
898461 AT AT
1 AT AT
898465 TGATTTGAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:903598 original size:23 final size:23
Alignment explanation
Indices: 903556--903621 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
903546 CACCACAGCT
* * *
903556 CGTATAAATGCTCCAAAGTGCCA-
1 CGTAGAAATGCACCGAAGTG-CAG
* *
903579 CGTAGAATTGCACCGTAGTGCAG
1 CGTAGAAATGCACCGAAGTGCAG
903602 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
903622 TCATATAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 2 0.06
23 33 0.94
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCAG
Found at i:907761 original size:28 final size:28
Alignment explanation
Indices: 907721--907787 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
907711 TAAACTTCAA
907721 TAGGGCATCTACGGTGAACCTTGTCTAC
1 TAGGGCATCTACGGTGAACCTTGTCTAC
*
907749 TAGGGCATCTACGGTGGACCTTGTCTAC
1 TAGGGCATCTACGGTGAACCTTGTCTAC
*
907777 TAGGACATCTA
1 TAGGGCATCTA
907788 ATCCTAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (28 bp):
TAGGGCATCTACGGTGAACCTTGTCTAC
Found at i:910246 original size:23 final size:23
Alignment explanation
Indices: 910220--910269 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
910210 TTCTTGGGAA
*
910220 TTATCATTTTATTATTTAAGATT
1 TTATCATTCTATTATTTAAGATT
*
910243 TTATCATTCTATTATTTAAGTTT
1 TTATCATTCTATTATTTAAGATT
910266 TTAT
1 TTAT
910270 TTGAAAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATCATTCTATTATTTAAGATT
Found at i:910855 original size:47 final size:47
Alignment explanation
Indices: 910786--910882 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
910776 GTTAGTCCAA
910786 ACAAGGAGTGAATTTCAAATATTGACTTAAGAATATTGATTTACTGG
1 ACAAGGAGTGAATTTCAAATATTGACTTAAGAATATTGATTTACTGG
910833 ACAAGGAGTGAATTTCAAATATTGACTTAAGAATATTGATTTACTGG
1 ACAAGGAGTGAATTTCAAATATTGACTTAAGAATATTGATTTACTGG
910880 ACA
1 ACA
910883 GAAAAGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (47 bp):
ACAAGGAGTGAATTTCAAATATTGACTTAAGAATATTGATTTACTGG
Found at i:916381 original size:18 final size:17
Alignment explanation
Indices: 916358--916391 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
916348 CCGCTATTAG
916358 TGAACCGGTCAGAACCGC
1 TGAACCGGTCA-AACCGC
*
916376 TGAACCGTTCAAACCG
1 TGAACCGGTCAAACCG
916392 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (17 bp):
TGAACCGGTCAAACCGC
Found at i:916935 original size:22 final size:21
Alignment explanation
Indices: 916910--916950 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
916900 TATAAAAAAT
916910 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
916932 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
916951 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:917234 original size:12 final size:12
Alignment explanation
Indices: 917206--917242 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
917196 TTTGGTAATC
917206 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
917219 CCCGCCCCGATA
1 CCCGCCCCGATA
*
917231 CCCGACCCGATA
1 CCCGCCCCGATA
917243 AATAGTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:917302 original size:24 final size:26
Alignment explanation
Indices: 917275--917335 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
917265 ATATATATAT
*
917275 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
917299 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
917323 AT-ATATATATATA
1 ATAATATAAATATA
917336 CCCGGCCCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 18 0.58
25 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:917317 original size:19 final size:19
Alignment explanation
Indices: 917293--917332 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
917283 AATAAATTTA
917293 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
917312 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
917331 AT
1 AT
917333 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:917382 original size:12 final size:12
Alignment explanation
Indices: 917333--917382 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
917323 ATATATATAT
*
917333 ATACCCGGCCCG
1 ATACCCGGCCCA
*
917345 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
917357 ATA-CCGACCCA
1 ATACCCGGCCCA
*
917368 ATACCCGGTCCA
1 ATACCCGGCCCA
917380 ATA
1 ATA
917383 TCCGTTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.26, C:0.44, G:0.16, T:0.14
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:918232 original size:104 final size:104
Alignment explanation
Indices: 918052--918260 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
918042 ACTTTGCATT
918052 TGAGAGATTTTGTTACACGTTATTTCGATGTTATTGGTTGGACTGTATATTTTGAAATTAAATGT
1 TGAGAGATTTTGTTACACGTTATTTCGATGTTATTGGTTGGACTGTATATTTTGAAATTAAATGT
918117 GGAACGTTTTATGAGTTGGTTTTCAAGTTCTATACCACA
66 GGAACGTTTTATGAGTTGGTTTTCAAGTTCTATACCACA
918156 TGAGAGATTTTGTTACACGTTATTTCGATGTTATTGGTTGGACTGTATATTTTGAAATTAAATGT
1 TGAGAGATTTTGTTACACGTTATTTCGATGTTATTGGTTGGACTGTATATTTTGAAATTAAATGT
918221 GGAACGTTTTATGAGTTGGTTTTCAAGTTCTATACCACA
66 GGAACGTTTTATGAGTTGGTTTTCAAGTTCTATACCACA
918260 T
1 T
918261 TTAATTTTTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (104 bp):
TGAGAGATTTTGTTACACGTTATTTCGATGTTATTGGTTGGACTGTATATTTTGAAATTAAATGT
GGAACGTTTTATGAGTTGGTTTTCAAGTTCTATACCACA
Found at i:918445 original size:19 final size:19
Alignment explanation
Indices: 918417--918459 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
918407 ACATCTTTTC
*
918417 TTGA-GATGACGTAGGGCG
1 TTGATGATGACGTAGGGCA
918435 TTGATGATGACGTAGGGCA
1 TTGATGATGACGTAGGGCA
918454 TTGATG
1 TTGATG
918460 TAGATCAGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.28
Consensus pattern (19 bp):
TTGATGATGACGTAGGGCA
Found at i:921913 original size:18 final size:19
Alignment explanation
Indices: 921878--921914 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
921868 CACGGAATCT
921878 AAGATTACCAGCGGGAATAA
1 AAGATTACCA-CGGGAATAA
921898 AAGATTACCA-GGGAATA
1 AAGATTACCACGGGAATA
921915 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (19 bp):
AAGATTACCACGGGAATAA
Found at i:922085 original size:16 final size:16
Alignment explanation
Indices: 922064--922095 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
922054 AAATTCTAAA
922064 TATTTAAATAAAAATT
1 TATTTAAATAAAAATT
*
922080 TATTTATATAAAAATT
1 TATTTAAATAAAAATT
922096 CTATATGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAAATAAAAATT
Found at i:923354 original size:67 final size:67
Alignment explanation
Indices: 923246--923380 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
923236 ATGATCACCA
923246 GCAAGAGCAACACTGTTTGCGACCCCCCTCATTCTTCTTATTTCCCTCTTTTCGGGTATTTCTGC
1 GCAAGAGCAACACTGTTTGCGACCCCCCTCATTCTTCTTATTTCCCTCTTTTCGGGTATTTCTGC
923311 AG
66 AG
923313 GCAAGAGCAACACTGTTTGCGACCCCCCTCATTCTTCTTATTTCCCTCTTTTCGGGTATTTCTGC
1 GCAAGAGCAACACTGTTTGCGACCCCCCTCATTCTTCTTATTTCCCTCTTTTCGGGTATTTCTGC
923378 AG
66 AG
923380 G
1 G
923381 TATATGCTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (67 bp):
GCAAGAGCAACACTGTTTGCGACCCCCCTCATTCTTCTTATTTCCCTCTTTTCGGGTATTTCTGC
AG
Found at i:926376 original size:37 final size:37
Alignment explanation
Indices: 926335--926411 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
926325 TTTTTATATT
926335 TTTAATTTTGTAAAAAAAATTACATAAATATTATG-AA
1 TTTAATTTTGTAAAAAAAA-TACATAAATATTATGCAA
* * * *
926372 TTTAATTTTTTAAAGAAAATATATAAATATTTTGCAA
1 TTTAATTTTGTAAAAAAAATACATAAATATTATGCAA
926409 TTT
1 TTT
926412 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATACATAAATATTATGCAA
Found at i:928250 original size:2 final size:2
Alignment explanation
Indices: 928245--928281 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
928235 ATTCAAAGCA
928245 AT AT 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 AT AT A
928282 CTTTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:931701 original size:3 final size:3
Alignment explanation
Indices: 931693--931785 Score: 116
Period size: 3 Copynumber: 31.3 Consensus size: 3
931683 TTTAATATAT
* * *
931693 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
931741 TAA TGT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
931786 GGATAAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:932280 original size:114 final size:114
Alignment explanation
Indices: 932025--932685 Score: 968
Period size: 114 Copynumber: 5.9 Consensus size: 114
932015 GCTCTTGATG
* *
932025 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CT
* * * *
932089 CTGGTAATG-TTGATCCATCAACTGATG-A-TCAAGCAAAAGGTTGAACA
65 CTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
932136 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
932201 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
932250 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
** * * * * *
932315 TGG-AAAGGGTGATCCACCAAATGATGGATTCAGGTAAAAGG-TGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
932362 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
932427 TGGAAACG-ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACA
932476 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC---ATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * *
932538 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTCGAAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTG-AACA
932588 AGTTCTTCTCATTATGAACTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* *
932652 TGG-AAACAATGATCCATCAATTTGATGAATTCAA
66 TGGAAAAGAATGATCCATCAA-GTGATGAATTCAA
932686 ATCTTTGCTA
Statistics
Matches: 499, Mismatches: 38, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
110 1 0.00
111 132 0.26
112 136 0.27
113 66 0.13
114 164 0.33
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:932428 original size:226 final size:227
Alignment explanation
Indices: 932025--932686 Score: 1011
Period size: 226 Copynumber: 2.9 Consensus size: 227
932015 GCTCTTGATG
*
932025 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * *
932089 CTGGTAATGTTGATCCATCAACTGAT-GA-TCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
65 CTGGAAAGGATGATCCATCAAATGATGGATTCAAGCAAAAGG-TGAACAAATTCTTCTCATTATG
932152 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
129 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
* *
932217 ATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
194 ATCAATTTGATGAATTCAAACAAAAGGTTGAACA
932250 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
932315 TGGAAAGGGTGATCCACCAAATGATGGATTCAGGTAAAAGGTGAACAAATTCTTCTCATTATGAA
66 TGGAAAGGATGATCCATCAAATGATGGATTCAAGCAAAAGGTGAACAAATTCTTCTCATTATGAA
* *
932380 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAACG-ATGATCCAT
131 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
*
932444 CAATTTGATGAATTCAAGCAAAAGGTTGAACA
196 CAATTTGATGAATTCAAACAAAAGGTTGAACA
*
932476 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC---ATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * * *
932538 TGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAGGTCGAAACAAGTTCTTCTCATTAT
66 TGG-AAAGGATGATCCATCAAATGATGGATTCAAGCAAAAGGT-G-AACAAATTCTTCTCATTAT
*
932603 GAACTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAACAATGATC
128 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATC
932666 CATCAATTTGATGAATTCAAA
193 CATCAATTTGATGAATTCAAA
932687 TCTTTGCTAA
Statistics
Matches: 401, Mismatches: 28, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
223 14 0.03
224 33 0.08
225 166 0.41
226 178 0.44
227 10 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (227 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAGGATGATCCATCAAATGATGGATTCAAGCAAAAGGTGAACAAATTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCCAT
CAATTTGATGAATTCAAACAAAAGGTTGAACA
Done.