Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold31
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: 2401195
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 123915 characters in sequence are not A, C, G, or T
File 5 of 16
Found at i:609454 original size:29 final size:28
Alignment explanation
Indices: 609422--609569 Score: 72
Period size: 28 Copynumber: 5.2 Consensus size: 28
609412 CCTAAAATAA
609422 TAAAAATACTAAGATGACCTTAGATAATG
1 TAAAAATACTAA-ATGACCTTAGATAATG
* * *
609451 TAAATA-ACATAAATGGCCTTAAATGAA-G
1 TAAAAATAC-TAAATGACCTTAGAT-AATG
* * ** *
609479 -GAAATTGTTAAAATGACCTTAGATCATG
1 TAAAAATACT-AAATGACCTTAGATAATG
* * *
609507 T-AAAATAGCCCAAATGACCTTAAAATTATG
1 TAAAAATA--CTAAATGACCTT-AGATAATG
**
609537 -AAAAATACTAAAATGACCTTAGATTCTG
1 TAAAAATACT-AAATGACCTTAGATAATG
609565 TAAAA
1 TAAAA
609570 TAACCTAAAA
Statistics
Matches: 87, Mismatches: 20, Indels: 24
0.66 0.15 0.18
Matches are distributed among these distances:
27 4 0.05
28 37 0.43
29 34 0.39
30 12 0.14
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (28 bp):
TAAAAATACTAAATGACCTTAGATAATG
Found at i:609579 original size:48 final size:48
Alignment explanation
Indices: 609518--609626 Score: 146
Period size: 48 Copynumber: 2.2 Consensus size: 48
609508 AAAATAGCCC
* * * * **
609518 AAATGACCTTAAAATTATGAAAAATACTAAAATGACCTTAGATTCTGTA
1 AAATAACC-TAAAATGATGAAAAATACTAAAATGACCCTAAATAATGTA
*
609567 AAATAACCTAAAATGATGAAAATTACTAAAATGACCCTAAATAATGTA
1 AAATAACCTAAAATGATGAAAAATACTAAAATGACCCTAAATAATGTA
609615 AAATAACCTAAA
1 AAATAACCTAAA
609627 TAGCCTTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 46 0.87
49 7 0.13
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (48 bp):
AAATAACCTAAAATGATGAAAAATACTAAAATGACCCTAAATAATGTA
Found at i:609617 original size:29 final size:29
Alignment explanation
Indices: 609577--609718 Score: 71
Period size: 29 Copynumber: 4.9 Consensus size: 29
609567 AAATAACCTA
*
609577 AAATGATG-AAAATTACTAAAATGACCCT
1 AAATAATGTAAAATTACTAAAATGACCCT
* *
609605 AAATAATGTAAAATAACCT-AAAT-AGCCT
1 AAATAATGTAAAATTA-CTAAAATGACCCT
** * *
609633 TTA-AATGATAGAAATTACTAAAATGATCTT
1 AAATAATG-TA-AAATTACTAAAATGACCCT
* * * * *
609663 AGATCATGTAAAATAACCCAAAA-GACCCCA
1 AAATAATGTAAAATTA-CTAAAATGA-CCCT
* *
609693 AAATGAT-TAAAATTGCTAAAATGACC
1 AAATAATGTAAAATTACTAAAATGACC
609719 TTAGATTATC
Statistics
Matches: 83, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
27 4 0.05
28 23 0.28
29 34 0.41
30 19 0.23
31 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (29 bp):
AAATAATGTAAAATTACTAAAATGACCCT
Found at i:609672 original size:164 final size:161
Alignment explanation
Indices: 609411--609725 Score: 425
Period size: 164 Copynumber: 1.9 Consensus size: 161
609401 ACCTAAATGG
* * * *
609411 ACCTAAAATAATAAAAATACTAAGATGACCTTAGATAATGTAAATAACATAAATGGCCTTAAATG
1 ACCTAAAATAATAAAAATACTAAAATGACCCTAAATAATGTAAATAACATAAATAGCCTTAAATG
** * * ** *
609476 AAGGAAATTGTTAAAATGACCTTAGATCATGTAAAATAGCCCAAATGACCTTAAAATTATGAAAA
66 AAGGAAATTACTAAAATGACCTTAGATCATGTAAAATAACCCAAAAGACCCCAAAATGATGAAAA
609541 ATACTAAAATGACCTTAGATTCTGTAAAATA
131 ATACTAAAATGACCTTAGATTCTGTAAAATA
* * *
609572 ACCTAAAATGATGAAAATTACTAAAATGACCCTAAATAATGTAAAATAACCTAAATAGCCTTTAA
1 ACCTAAAATAAT-AAAAATACTAAAATGACCCTAAATAATGT-AAATAACATAAATAGCC-TTAA
* *
609637 ATGATA-GAAATTACTAAAATGATCTTAGATCATGTAAAATAACCCAAAAGACCCCAAAATGATT
63 ATGA-AGGAAATTACTAAAATGACCTTAGATCATGTAAAATAACCCAAAAGACCCCAAAATGATG
* *
609701 AAAATTGCTAAAATGACCTTAGATT
127 AAAAATACTAAAATGACCTTAGATT
609726 ATCTAAAACA
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
161 11 0.08
162 25 0.19
163 15 0.11
164 80 0.61
165 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (161 bp):
ACCTAAAATAATAAAAATACTAAAATGACCCTAAATAATGTAAATAACATAAATAGCCTTAAATG
AAGGAAATTACTAAAATGACCTTAGATCATGTAAAATAACCCAAAAGACCCCAAAATGATGAAAA
ATACTAAAATGACCTTAGATTCTGTAAAATA
Found at i:610179 original size:46 final size:46
Alignment explanation
Indices: 610075--610231 Score: 158
Period size: 46 Copynumber: 3.4 Consensus size: 46
610065 TCACTAATCT
* * * **
610075 AACTTGTAGCTTTTACATGGATAAATTTACAAATCTTTTC--CAAAC
1 AACTTGTAGCTTTTGCATAGATAAAGTTACAAA-CCCTTCAACAAAC
* *
610120 AACTTGTAACTTTTGCATTGATAAAGTTACAAACCCTTCAACAAAC
1 AACTTGTAGCTTTTGCATAGATAAAGTTACAAACCCTTCAACAAAC
** * * * *
610166 AACTAATAGCTTTTCCACAGATAAAGCTATAAACCC-TCTAACAAAC
1 AACTTGTAGCTTTTGCATAGATAAAGTTACAAACCCTTC-AACAAAC
610212 AACTTGTAGCTTTTGCATAG
1 AACTTGTAGCTTTTGCATAG
610232 GTTCACATCT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
44 4 0.04
45 31 0.34
46 56 0.62
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (46 bp):
AACTTGTAGCTTTTGCATAGATAAAGTTACAAACCCTTCAACAAAC
Found at i:613252 original size:21 final size:20
Alignment explanation
Indices: 613227--613277 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
613217 TATGATTTGC
*
613227 ATCGATACAATTA-GTGATTGT
1 ATCGATAC-A-TAGGTGAATGT
613248 ATCGATACATAGGTGAATGT
1 ATCGATACATAGGTGAATGT
*
613268 ATCGAAACAT
1 ATCGATACAT
613278 GTCTTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATCGATACATAGGTGAATGT
Found at i:614251 original size:13 final size:13
Alignment explanation
Indices: 614233--614258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
614223 TACAAAGAAC
614233 ATGTATCGATACA
1 ATGTATCGATACA
614246 ATGTATCGATACA
1 ATGTATCGATACA
614259 TCTAGGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614272 original size:20 final size:21
Alignment explanation
Indices: 614247--614285 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
614237 ATCGATACAA
614247 TGTATCGATACA-TCTAGGTG
1 TGTATCGATACATTCTAGGTG
614267 TGTATCGATACATTCTAGG
1 TGTATCGATACATTCTAGG
614286 GTTTTAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGGTG
Found at i:614329 original size:71 final size:70
Alignment explanation
Indices: 614246--614398 Score: 288
Period size: 71 Copynumber: 2.2 Consensus size: 70
614236 TATCGATACA
614246 ATGTATCGATACATCTAGGTGTGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCA
1 ATGTATCGATACATCTAGGTGTGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCA
614311 ACTTTT
66 AC-TTT
*
614317 ATGTATCAATACATCTAGGTGTGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCA
1 ATGTATCGATACATCTAGGTGTGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCA
614382 ACTTT
66 ACTTT
614387 ATGTATCGATAC
1 ATGTATCGATAC
614399 GAATACCTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
70 14 0.17
71 66 0.82
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (70 bp):
ATGTATCGATACATCTAGGTGTGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCA
ACTTT
Found at i:614343 original size:20 final size:21
Alignment explanation
Indices: 614318--614356 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
614308 TCAACTTTTA
614318 TGTATCAATACA-TCTAGGTG
1 TGTATCAATACATTCTAGGTG
*
614338 TGTATCGATACATTCTAGG
1 TGTATCAATACATTCTAGG
614357 GTTTTAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
TGTATCAATACATTCTAGGTG
Found at i:614432 original size:70 final size:71
Alignment explanation
Indices: 614267--614418 Score: 200
Period size: 71 Copynumber: 2.2 Consensus size: 71
614257 CATCTAGGTG
* * *
614267 TGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCAACTTTTATGTATCAATACATC
1 TGTATCGATACATTCAAGGATTTTAACCTTTGTAGCTTAAGTCAACTTTTATGTATCAATACATA
** *
614332 TAGGTG
66 TACCTA
* * *
614338 TGTATCGATACATTCTAGGGTTTTAACCTTTGTAGCTTAAGTCAAC-TTTATGTATCGATACGA-
1 TGTATCGATACATTCAAGGATTTTAACCTTTGTAGCTTAAGTCAACTTTTATGTATCAATAC-AT
614401 ATACCTA
65 ATACCTA
614408 TGTATCGATAC
1 TGTATCGATAC
614419 TTTGAATTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 28 0.37
71 47 0.63
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (71 bp):
TGTATCGATACATTCAAGGATTTTAACCTTTGTAGCTTAAGTCAACTTTTATGTATCAATACATA
TACCTA
Found at i:615036 original size:22 final size:23
Alignment explanation
Indices: 615011--615053 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
615001 TACTCCCCCT
615011 AAACAAATTATC-CCCCTTTATA
1 AAACAAATTATCTCCCCTTTATA
* *
615033 AAACAACTTTTCTCCCCTTTA
1 AAACAAATTATCTCCCCTTTA
615054 ACAAATTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (23 bp):
AAACAAATTATCTCCCCTTTATA
Found at i:629115 original size:58 final size:57
Alignment explanation
Indices: 628943--629245 Score: 182
Period size: 58 Copynumber: 5.3 Consensus size: 57
628933 ATCTTTTGTA
* * * *
628943 TCATTTAGGTCATTTTCCATGATCTAGAGATTTTGGGGC-T-ATTTTATAAAGTTCGATG
1 TCATTTAGGTCATTTTTCATGATCTAGGGAATTT--GGCATAATTTTATAAA-TTTGATG
* * *
629001 TCATTTAGGTCATTTTT-AGGA-CTTAGGG-AGTTGG-ATGTAATTTTATTAATTTTGATG
1 TCATTTAGGTCATTTTTCATGATC-TAGGGAATTTGGCA--TAATTTTA-TAAATTTGATG
* *
629058 TCATTTAGGTCATTTTTCATGATCGAGGGAATTTGGCATAATTTCATGAAATTTGATG
1 TCATTTAGGTCATTTTTCATGATCTAGGGAATTTGGCATAATTTTAT-AAATTTGATG
* * * * **
629116 TCATTTAGGTTA-TTTTCCTGGATCTA--AAAGTTTTG-ATGTAATTTTATGAACGTTGATG
1 TCATTTAGGTCATTTTTCAT-GATCTAGGGAA-TTTGGCA--TAATTTTAT-AAATTTGATG
** * ***
629174 TCATTTAAATCA--TTTCATGATCTA-AGAACTTTGATGTAATTTTATAAATTTTGATG
1 TCATTTAGGTCATTTTTCATGATCTAGGGAA-TTTGGCATAATTTTATAAA-TTTGATG
*
629230 TCATGTAGGTCATTTT
1 TCATTTAGGTCATTTT
629246 CTATAATCTA
Statistics
Matches: 191, Mismatches: 34, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
54 2 0.01
55 2 0.01
56 37 0.19
57 57 0.30
58 86 0.45
59 6 0.03
60 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (57 bp):
TCATTTAGGTCATTTTTCATGATCTAGGGAATTTGGCATAATTTTATAAATTTGATG
Found at i:629256 original size:114 final size:115
Alignment explanation
Indices: 629034--629246 Score: 252
Period size: 114 Copynumber: 1.9 Consensus size: 115
629024 TAGGGAGTTG
* ** ** * *
629034 GATGTAATTTTATTAATTTTGATGTCATTTAGGTCATTTTTCATGATCGAGGGAATTTGGCATAA
1 GATGTAATTTTATGAACGTTGATGTCATTTAAATCA-TTTTCATGATCGAGAGAATTTGACATAA
* * *
629099 TTTCATGAAATTTGATGTCATTTAGGTTATTTTCCTGGATCTAAAAGTTTT
65 TTTCATGAAATTTGATGTCATGTAGGTCATTTTCCTGAATCTAAAAGTTTT
* **
629150 GATGTAATTTTATGAACGTTGATGTCATTTAAATCA-TTTCATGATCTA-AGAACTTTGATGTAA
1 GATGTAATTTTATGAACGTTGATGTCATTTAAATCATTTTCATGATCGAGAGAA-TTTGACATAA
*
629213 TTTTAT-AAATTTTGATGTCATGTAGGTCATTTTC
65 TTTCATGAAA-TTTGATGTCATGTAGGTCATTTTC
629247 TATAATCTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
113 6 0.07
114 45 0.55
116 31 0.38
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (115 bp):
GATGTAATTTTATGAACGTTGATGTCATTTAAATCATTTTCATGATCGAGAGAATTTGACATAAT
TTCATGAAATTTGATGTCATGTAGGTCATTTTCCTGAATCTAAAAGTTTT
Found at i:629274 original size:58 final size:56
Alignment explanation
Indices: 629168--629275 Score: 128
Period size: 58 Copynumber: 1.9 Consensus size: 56
629158 TTTATGAACG
* * * *
629168 TTGATGTCATTTAAATCATTTCATGATCTAAGAACTTTGATGTAATTTTATAAATT
1 TTGATGTCATGTAAATCATTTCATAATCTAAGAACTTTCATGCAATTTTATAAATT
**
629224 TTGATGTCATGTAGGTCATTTTCTATAATCTAATG-ACTTTCATGCAATTTTA
1 TTGATGTCATGTAAATCA-TTTC-ATAATCTAA-GAACTTTCATGCAATTTTA
629276 CACATCTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
56 15 0.35
57 4 0.09
58 23 0.53
59 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (56 bp):
TTGATGTCATGTAAATCATTTCATAATCTAAGAACTTTCATGCAATTTTATAAATT
Found at i:630616 original size:29 final size:29
Alignment explanation
Indices: 630579--630634 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
630569 TTTTTTAATA
* *
630579 ATATTAATATTTGTTATCATATATATTAT
1 ATATGAATATTTATTATCATATATATTAT
* *
630608 ATATGAATATTTATTATCTTATTTATT
1 ATATGAATATTTATTATCATATATATT
630635 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (29 bp):
ATATGAATATTTATTATCATATATATTAT
Found at i:632561 original size:28 final size:28
Alignment explanation
Indices: 632526--632605 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
632516 AATATTTTAA
632526 ATTT-TTTTACTAATTTAAAAATAAAAT
1 ATTTATTTTACTAATTTAAAAATAAAAT
632553 ATTTATTTTA-T-ATTATAAAAAATAAAAT
1 ATTTATTTTACTAATT-T-AAAAATAAAAT
632581 ATTTATTTTAAACTAA-TTAAAAATA
1 ATTTATTTT--ACTAATTTAAAAATA
632606 CAATCCGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
26 3 0.07
27 6 0.13
28 25 0.54
29 7 0.15
30 2 0.04
31 2 0.04
32 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTATTTTACTAATTTAAAAATAAAAT
Found at i:632746 original size:21 final size:20
Alignment explanation
Indices: 632718--632763 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
632708 AATTAAAGAA
* *
632718 AAATTAAAATGAATTTAAATTT
1 AAATAAAAAT-AA-TTAAAATT
632740 AAATAAAAATAATTAAAATT
1 AAATAAAAATAATTAAAATT
632760 AAAT
1 AAAT
632764 TAATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 2 0.09
22 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAAAAATAATTAAAATT
Found at i:632757 original size:31 final size:32
Alignment explanation
Indices: 632697--632776 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
632687 ACTTAAATCA
*
632697 AAATCAAA-TTAAATTAAAGAAAAATTAAAATG
1 AAATTAAATTTAAA-TAAAGAAAAATTAAAATG
* * *
632729 AATTTAAATTTAAATAAA-AATAATTAAAATT
1 AAATTAAATTTAAATAAAGAAAAATTAAAATG
* *
632760 AAATTAATTTTTAATAA
1 AAATTAAATTTAAATAA
632777 TTTTTTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 25 0.62
32 10 0.25
33 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (32 bp):
AAATTAAATTTAAATAAAGAAAAATTAAAATG
Found at i:633074 original size:16 final size:15
Alignment explanation
Indices: 633046--633089 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
633036 AAAATGTTAA
633046 TATTATTTTTTAAAAT
1 TATT-TTTTTTAAAAT
*
633062 TTTTTTATTTTAAAAT
1 TATTTT-TTTTAAAAT
633078 TATTTTTTTTAA
1 TATTTTTTTTAA
633090 TGTTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTTTAAAAT
Found at i:633117 original size:9 final size:9
Alignment explanation
Indices: 633099--633177 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
633089 ATGTTAATTA
633099 TTTATAATAT
1 TTTAT-ATAT
633109 TTTATATAT
1 TTTATATAT
633118 ATTTA-AT-T
1 -TTTATATAT
* *
633126 TTTAAATTT
1 TTTATATAT
633135 TTTATAT-T
1 TTTATATAT
633143 TTTAATATAT
1 TTT-ATATAT
*
633153 TTTATGAGAT
1 TTTAT-ATAT
*
633163 ATTTATATTT
1 -TTTATATAT
633173 TTTAT
1 TTTAT
633178 TAATATATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
7 4 0.07
8 7 0.12
9 24 0.41
10 18 0.31
11 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTATATAT
Found at i:633134 original size:24 final size:25
Alignment explanation
Indices: 633098--633148 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
633088 AATGTTAATT
633098 ATTTATAATATTTTATATATATTTA
1 ATTTATAATATTTTATATATATTTA
* * *
633123 ATTTTTAA-ATTTTTTATATTTTTA
1 ATTTATAATATTTTATATATATTTA
633147 AT
1 AT
633149 ATATTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTTATAATATTTTATATATATTTA
Found at i:633586 original size:20 final size:20
Alignment explanation
Indices: 633539--633586 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
633529 TTGATTTGAT
* *
633539 AATAATTT-GATTAAATTTT
1 AATAATTTAAATTAAATTTA
**
633558 AATTTTTTAAATTAAATTTA
1 AATAATTTAAATTAAATTTA
633578 AATAATTTA
1 AATAATTTA
633587 TAAATATAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AATAATTTAAATTAAATTTA
Found at i:637445 original size:22 final size:22
Alignment explanation
Indices: 637386--637451 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
637376 AAAACTTACG
*
637386 ATAGAGTAAAAACTATAAGTAC
1 ATAGAGTAAAAACTATATGTAC
* *
637408 ATATAGT-ATAACTATATGTAC
1 ATAGAGTAAAAACTATATGTAC
637429 ATAGAGTAAAAACTATATGTAC
1 ATAGAGTAAAAACTATATGTAC
637451 A
1 A
637452 AATAGCTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (22 bp):
ATAGAGTAAAAACTATATGTAC
Found at i:637631 original size:30 final size:35
Alignment explanation
Indices: 637547--637623 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
637537 CAATAAGTAG
*
637547 ATATAATACAGCTATATGTACATATAGTAAAAATA
1 ATATAATACAGTTATATGTACATATAGTAAAAATA
637582 ATATAATACAGTTATATGTACATATAGTAAAAATA
1 ATATAATACAGTTATATGTACATATAGTAAAAATA
637617 ATATAAT
1 ATATAAT
637624 TATATGTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (35 bp):
ATATAATACAGTTATATGTACATATAGTAAAAATA
Found at i:638061 original size:21 final size:21
Alignment explanation
Indices: 638005--638077 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
637995 TAAATTTGAT
* *
638005 AAAGGTTGGTTCTCTTAGTGT
1 AAAGGTTGATTCTCTTAGTGA
*
638026 GAAGGAATT-AGTTCTCTTAGTGA
1 AAAGG--TTGA-TTCTCTTAGTGA
*
638049 AAAGGTTGATTCTCTTTGTGA
1 AAAGGTTGATTCTCTTAGTGA
638070 AAAGGTTG
1 AAAGGTTG
638078 GCTCTCATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 25 0.58
22 1 0.02
23 17 0.40
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.38
Consensus pattern (21 bp):
AAAGGTTGATTCTCTTAGTGA
Found at i:638083 original size:21 final size:21
Alignment explanation
Indices: 638038--638083 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
638028 AGGAATTAGT
*
638038 TCTCTTAGTGAAAAGGTTGAT
1 TCTCTTAGTGAAAAGGTTGAC
* *
638059 TCTCTTTGTGAAAAGGTTGGC
1 TCTCTTAGTGAAAAGGTTGAC
638080 TCTC
1 TCTC
638084 ATATTATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TCTCTTAGTGAAAAGGTTGAC
Found at i:639284 original size:42 final size:43
Alignment explanation
Indices: 639237--639321 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
639227 AATTGATATG
*
639237 TACATATACCTTAAAATTAATAAAAAT-AATAA-ACACAAATTT
1 TACATATACCTCAAAATTAATAAAAATCAA-AATACACAAATTT
* *
639279 TACATATATCTCAAAATTGATAAAAATCAAAATACACAAATTT
1 TACATATACCTCAAAATTAATAAAAATCAAAATACACAAATTT
639322 AAGAAAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 26 0.68
43 12 0.32
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (43 bp):
TACATATACCTCAAAATTAATAAAAATCAAAATACACAAATTT
Found at i:640995 original size:4 final size:4
Alignment explanation
Indices: 640986--641011 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
640976 ATCTTTTTAC
640986 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
641012 ACTCAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:641302 original size:19 final size:20
Alignment explanation
Indices: 641262--641311 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
641252 TAATAATTAT
641262 TTAAAATAAAATTTTAAATA
1 TTAAAATAAAATTTTAAATA
641282 TTAAAA-AATAATTTT-AATA
1 TTAAAATAA-AATTTTAAATA
641301 TTAAATATAAA
1 TTAAA-ATAAA
641312 TAATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 11 0.41
20 14 0.52
21 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAATAAAATTTTAAATA
Found at i:641593 original size:11 final size:10
Alignment explanation
Indices: 641578--641701 Score: 61
Period size: 10 Copynumber: 12.6 Consensus size: 10
641568 GTATATTTTT
641578 TATATTATAA
1 TATATTATAA
641588 TTATATT-TAAA
1 -TATATTAT-AA
*
641599 TATTTTATAA
1 TATATTATAA
641609 -ATA-TATAA
1 TATATTATAA
641617 -A-ATT-TAA
1 TATATTATAA
641624 TATATTAATAA
1 TATATT-ATAA
641635 TTTATATTATAA
1 --TATATTATAA
*
641647 -ATATTTTAA
1 TATATTATAA
641656 TATATT-T-A
1 TATATTATAA
641664 TATATTTATATCA
1 TATA-TTATA--A
* *
641677 TATTTTATAT
1 TATATTATAA
*
641687 TATATTTTAA
1 TATATTATAA
641697 T-TATT
1 TATATT
641702 TTTTATTCGT
Statistics
Matches: 90, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
7 4 0.04
8 13 0.14
9 20 0.22
10 22 0.24
11 12 0.13
12 9 0.10
13 10 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
TATATTATAA
Found at i:641636 original size:16 final size:16
Alignment explanation
Indices: 641608--641671 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
641598 ATATTTTATA
641608 AATATA-TAA-AATTT
1 AATATATTAATAATTT
641622 AATATATTAATAATTT
1 AATATATTAATAATTT
* *
641638 -ATATTATAAATATTTT
1 AATA-TATTAATAATTT
*
641654 AATATATTTATATATTT
1 AATATATTAATA-ATTT
641671 A
1 A
641672 TATCATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 21 0.52
17 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATATTAATAATTT
Found at i:641662 original size:10 final size:10
Alignment explanation
Indices: 641637--641703 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 10
641627 ATTAATAATT
*
641637 TATATTATAA
1 TATATTTTAA
641647 -ATATTTTAA
1 TATATTTTAA
641656 TATA-TTT-A
1 TATATTTTAA
641664 TATA-TTTATA
1 TATATTTTA-A
641674 TCATATTTTATA
1 T-ATATTTTA-A
641686 TTATATTTTAA
1 -TATATTTTAA
641697 T-TATTTT
1 TATATTTT
641704 TTATTCGTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
8 8 0.16
9 17 0.34
10 6 0.12
11 4 0.08
12 14 0.28
13 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATTTTAA
Found at i:641662 original size:25 final size:24
Alignment explanation
Indices: 641583--641666 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 24
641573 TTTTTTATAT
*
641583 TATAATTATATTTAAATATTTTATA
1 TATATTTATATTTAAATATTTTA-A
* * * *
641608 AATATATAAAATTT-AATATATTAA
1 TATAT-TTATATTTAAATATTTTAA
641632 TA-ATTTATATTATAAATATTTTAA
1 TATATTTATATT-TAAATATTTTAA
641656 TATATTTATAT
1 TATATTTATAT
641667 ATTTATATCA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 5 0.11
23 3 0.07
24 13 0.28
25 19 0.41
26 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTTATATTTAAATATTTTAA
Found at i:641679 original size:19 final size:17
Alignment explanation
Indices: 641657--641691 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
641647 ATATTTTAAT
641657 ATATTTATATATTTATATC
1 ATATTT-TATA-TTATATC
641676 ATATTTTATATTATAT
1 ATATTTTATATTATAT
641692 TTTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTATATTATATC
Found at i:641685 original size:40 final size:41
Alignment explanation
Indices: 641570--641702 Score: 106
Period size: 40 Copynumber: 3.4 Consensus size: 41
641560 AATAATTCGT
*
641570 ATATTTT-TTATATTATAATTATATT--TAA-ATATTTTATAA
1 ATATTTTAATATATT-TAA-TATATTAATAATATATTTTATAA
* * *
641609 ATA-TATAA-A-ATTTAATATATTAATAATTTATATTATAA
1 ATATTTTAATATATTTAATATATTAATAATATATTTTATAA
* *
641647 ATATTTTAATATATTT-ATATATTTAT-ATCATATTTTATATT
1 ATATTTTAATATATTTAATATATTAATAAT-ATATTTTATA-A
641688 ATATTTTAAT-TATTT
1 ATATTTTAATATATTT
641703 TTTATTCGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
35 6 0.08
36 3 0.04
37 6 0.08
38 15 0.20
39 9 0.12
40 23 0.30
41 14 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (41 bp):
ATATTTTAATATATTTAATATATTAATAATATATTTTATAA
Found at i:641705 original size:11 final size:12
Alignment explanation
Indices: 641656--641707 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
641646 AATATTTTAA
641656 TATATTTATATATT
1 TATA-TTATAT-TT
*
641670 TATATCATATTT
1 TATATTATATTT
641682 TATATTATATTT
1 TATATTATATTT
*
641694 TA-ATTATTTTT
1 TATATTATATTT
641705 TAT
1 TAT
641708 TCGTGCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.29
12 15 0.44
13 5 0.15
14 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATATTT
Found at i:642027 original size:22 final size:22
Alignment explanation
Indices: 641977--642027 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
641967 ATTTTAATTC
641977 AATTTA-TAAGTTGATATTAAA
1 AATTTATTAAGTTGATATTAAA
* * *
641998 AATATATTAATTTGATATTTAA
1 AATTTATTAAGTTGATATTAAA
*
642020 ATTTTATT
1 AATTTATT
642028 TTATTAAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (22 bp):
AATTTATTAAGTTGATATTAAA
Found at i:642932 original size:24 final size:23
Alignment explanation
Indices: 642891--642938 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
642881 CGATATAATT
* *
642891 ATATGATATAAAAAATAATTAAA
1 ATATGACATAAAAAATAAATAAA
642914 ATATGACATGAAAAAATAAATAAA
1 ATATGACAT-AAAAAATAAATAAA
642938 A
1 A
642939 AAATTACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (23 bp):
ATATGACATAAAAAATAAATAAA
Found at i:642939 original size:25 final size:24
Alignment explanation
Indices: 642891--642948 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
642881 CGATATAATT
* *
642891 ATATGATAT-AAAAAATAATTAAA
1 ATATGACATGAAAAAATAATAAAA
642914 ATATGACATGAAAAAATAAATAAAA
1 ATATGACATGAAAAAAT-AATAAAA
* *
642939 AAATTACATG
1 ATATGACATG
642949 GATACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.28
24 7 0.24
25 14 0.48
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (24 bp):
ATATGACATGAAAAAATAATAAAA
Found at i:651445 original size:2 final size:2
Alignment explanation
Indices: 651438--651471 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
651428 ATGAATATGC
651438 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
651472 CTGAAAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:659047 original size:51 final size:51
Alignment explanation
Indices: 658887--659057 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
658877 GAAATAACGA
* * *
658887 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
658939 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
658992 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
659043 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
659058 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:659103 original size:27 final size:28
Alignment explanation
Indices: 659040--659115 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
659030 AAAATAAAGT
*
659040 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
659068 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
659095 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
659116 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:661608 original size:13 final size:13
Alignment explanation
Indices: 661590--661615 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
661580 ACAAAGATCC
661590 ATGTATCGATACA
1 ATGTATCGATACA
661603 ATGTATCGATACA
1 ATGTATCGATACA
661616 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:661611 original size:33 final size:33
Alignment explanation
Indices: 661569--661635 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
661559 AAAATTTCCA
***
661569 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
661602 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
661635 A
1 A
661636 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:661679 original size:19 final size:18
Alignment explanation
Indices: 661655--661722 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
661645 CAGTAGCTAA
661655 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
661674 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
661689 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
661706 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
661723 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:661695 original size:13 final size:13
Alignment explanation
Indices: 661677--661701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
661667 ACAATACTTA
661677 TGTATCGATACAT
1 TGTATCGATACAT
661690 TGTATCGATACA
1 TGTATCGATACA
661702 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:661699 original size:32 final size:32
Alignment explanation
Indices: 661658--661720 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
661648 TAGCTAATTA
*
661658 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
661690 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
661721 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:661802 original size:21 final size:21
Alignment explanation
Indices: 661778--661834 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
661768 CATTTGTAGG
661778 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
661799 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
661820 ATGTATCGATACATT
1 ATGTATCGATACATT
661835 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:661863 original size:21 final size:21
Alignment explanation
Indices: 661837--661876 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
661827 GATACATTTA
661837 AATTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTC
661858 AATTTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTTT
661877 CAAACACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (21 bp):
AATTTTTTTTTTTTTTTTTTC
Found at i:661865 original size:20 final size:20
Alignment explanation
Indices: 661840--661879 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
661830 ACATTTAAAT
661840 TTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTCAA
661860 TTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTCAA
661880 ACACTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTCAA
Found at i:663865 original size:16 final size:18
Alignment explanation
Indices: 663836--663877 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
663826 AATCGTACAT
*
663836 AAAATTATGTATTTA-TA
1 AAAATTTTGTATTTATTA
663853 AAAATTTTG-ATTTATTA
1 AAAATTTTGTATTTATTA
*
663870 ATAATTTT
1 AAAATTTT
663878 AATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
AAAATTTTGTATTTATTA
Found at i:664246 original size:16 final size:16
Alignment explanation
Indices: 664225--664255 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
664215 TTTAATAACA
664225 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
664241 AATAAATATTTAATA
1 AATAAATATTAAATA
664256 AAAATTTAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:666445 original size:2 final size:2
Alignment explanation
Indices: 666440--666478 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
666430 ATCCGCGCGC
666440 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
666479 GAATACCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:667124 original size:2 final size:2
Alignment explanation
Indices: 667117--667151 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
667107 CTGCTTCAGA
667117 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 A
667152 AGCAAGTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:667679 original size:1 final size:1
Alignment explanation
Indices: 667673--667703 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
667663 TTCATCTCTT
667673 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
667704 TCTTTCATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:672146 original size:34 final size:34
Alignment explanation
Indices: 672107--672174 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
672097 AACCTCTCAT
672107 AAATTCAATAAAATGACAGCCTAATGTCAATCAG
1 AAATTCAATAAAATGACAGCCTAATGTCAATCAG
*
672141 AAATTCAATAAAATGACAGCCTAATGTCCATCAG
1 AAATTCAATAAAATGACAGCCTAATGTCAATCAG
672175 GAAGCATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (34 bp):
AAATTCAATAAAATGACAGCCTAATGTCAATCAG
Found at i:672531 original size:205 final size:209
Alignment explanation
Indices: 672141--672605 Score: 771
Period size: 205 Copynumber: 2.2 Consensus size: 209
672131 TGTCAATCAG
* *
672141 AAATTCAATAAAATGACAGCCTAATGTCCATCAGGAAGC-ATTCATAACAATTACAAAGAAACAA
1 AAATTCAATAAAATGACAGCCTAATGTCGATCACGAAGCAATTCATAACAATTACAAAGAAACAA
672205 TAAAATCAGAAAAATTCATAACATACAAAGAAACCAACTAGTCACAGATTTAATCAGAAAATTTC
66 TAAAATCAGAAAAATTCATAACATACAAAGAAACCAACTAGTCACAGATTTAATCAGAAAATTTC
* * *
672270 TCACAATGTTATTTCAAAGCATCCAACTTGCTCGACGTTAGACTTGTTTGCAATCCCGCAAAACG
131 TCACAATGTTATTTCAAAGCATCCAACTTGCTCCACATTAGACTTCTTTGCAATCCCG-AAAACG
672335 GATTAAACTTCTT-A
195 GATTAAACTTCTTAA
*
672349 AAATTCAATAAAATGACAGCCTAAT-TCGATCACGAAGCAATTCATACCAATTACAAAGAAACAA
1 AAATTCAATAAAATGACAGCCTAATGTCGATCACGAAGCAATTCATAACAATTACAAAGAAACAA
672413 TAAAATCAGAAAAATTCAT-A-ATACAAAGAAACCAACTAG-CACAGATTTAATCAGAAAATTTC
66 TAAAATCAGAAAAATTCATAACATACAAAGAAACCAACTAGTCACAGATTTAATCAGAAAATTTC
*
672475 TCACAATGTTATTTCAAAGCATCCAACTTGCTCCACATTAGACTTCTTTTCAATCCCGAAAACGG
131 TCACAATGTTATTTCAAAGCATCCAACTTGCTCCACATTAGACTTCTTTGCAATCCCGAAAACGG
672540 ATTAAACTTCTTAA
196 ATTAAACTTCTTAA
* * * * *
672554 AAATTCTATAAAACGACAGCCTGATGTCGATCACAAAGCATTTCATAACAAT
1 AAATTCAATAAAATGACAGCCTAATGTCGATCACGAAGCAATTCATAACAAT
672606 ATTACTCAAT
Statistics
Matches: 241, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
204 19 0.08
205 100 0.41
206 42 0.17
207 12 0.05
208 68 0.28
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (209 bp):
AAATTCAATAAAATGACAGCCTAATGTCGATCACGAAGCAATTCATAACAATTACAAAGAAACAA
TAAAATCAGAAAAATTCATAACATACAAAGAAACCAACTAGTCACAGATTTAATCAGAAAATTTC
TCACAATGTTATTTCAAAGCATCCAACTTGCTCCACATTAGACTTCTTTGCAATCCCGAAAACGG
ATTAAACTTCTTAA
Found at i:673549 original size:2 final size:2
Alignment explanation
Indices: 673542--673577 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
673532 TTATAGGCAA
*
673542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
673578 GCATATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673794 original size:21 final size:23
Alignment explanation
Indices: 673740--673794 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
673730 AATATTTAAA
*
673740 AAATTATTTTTATATTAAATATT
1 AAATAATTTTTATATTAAATATT
*
673763 -TATATATTTTTA-ATTAAAT-TT
1 AAATA-ATTTTTATATTAAATATT
673784 AAATAATTTTT
1 AAATAATTTTT
673795 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 8 0.30
22 12 0.44
23 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATAATTTTTATATTAAATATT
Found at i:674365 original size:28 final size:28
Alignment explanation
Indices: 674311--674372 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
674301 ATTTAATACA
* *
674311 TTTTTATATATATTATATTTATCTTAT-
1 TTTTTATATATATCATATTTATATTATG
674338 TTTTTATATTATATCATATATTA-ATTATG
1 TTTTTATA-TATATCATAT-TTATATTATG
674367 TTTTTA
1 TTTTTA
674373 ATAACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.27
28 13 0.43
29 9 0.30
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTTATATATATCATATTTATATTATG
Found at i:674753 original size:12 final size:11
Alignment explanation
Indices: 674710--674787 Score: 53
Period size: 12 Copynumber: 7.5 Consensus size: 11
674700 TATTATTCAA
* *
674710 ATTAATGATCT
1 ATTAATTATAT
*
674721 ATTTATTAATAT
1 ATTAATT-ATAT
674733 ATTAATTATAT
1 ATTAATTATAT
674744 ATATAATTATA-
1 AT-TAATTATAT
674755 A--AATTATAT
1 ATTAATTATAT
*
674764 A-AAATTA-AT
1 ATTAATTATAT
674773 -TTAATT-TAT
1 ATTAATTATAT
674782 ATTAAT
1 ATTAAT
674788 ATAAACAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.13
9 9 0.16
10 10 0.18
11 12 0.22
12 17 0.31
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (11 bp):
ATTAATTATAT
Found at i:675263 original size:21 final size:20
Alignment explanation
Indices: 675234--675307 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
675224 CTTTTAAATT
*
675234 ATTTGAATTTATGTTATTTTAA
1 ATTT-AATTTAT-TAATTTTAA
675256 ATTTAATTTATTAATTTTAAA
1 ATTTAATTTATTAATTTT-AA
* * *
675277 ATTAAATATT-TTAAATTGAA
1 ATTTAAT-TTATTAATTTTAA
675297 A-TTAATTTATT
1 ATTTAATTTATT
675308 TTTTGAATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.05
19 6 0.14
20 9 0.20
21 21 0.48
22 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
ATTTAATTTATTAATTTTAA
Found at i:676696 original size:22 final size:22
Alignment explanation
Indices: 676630--676695 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
676620 ATTATTCATA
* **
676630 TTTATTATTAATAAATAAA-AT
1 TTTATAATTAATATTTAAATAT
*
676651 TTTAT-ATTAATATTTATATAT
1 TTTATAATTAATATTTAAATAT
676672 TTTATAATTAA-ATTTAAATAT
1 TTTATAATTAATATTTAAATAT
676693 TTT
1 TTT
676696 TTTAATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.26
21 24 0.62
22 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATAATTAATATTTAAATAT
Found at i:676701 original size:22 final size:22
Alignment explanation
Indices: 676650--676703 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
676640 ATAAATAAAA
*
676650 TTTTATATTAATATTTATATATT
1 TTTTA-ATTAATATTTAAATATT
*
676673 TTATAATTAA-ATTTAAATATTT
1 TTTTAATTAATATTTAAATA-TT
676695 TTTTAATTA
1 TTTTAATTA
676704 TTAAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTAATTAATATTTAAATATT
Found at i:676902 original size:24 final size:25
Alignment explanation
Indices: 676860--676906 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
676850 ACCTTATCAA
676860 CTCTCTTTCAATTTCATGCATTAAT
1 CTCTCTTTCAATTTCATGCATTAAT
676885 CTCTCTTTC-ATTTCATGCATTA
1 CTCTCTTTCAATTTCATGCATTA
676907 CCCAAAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.21, C:0.26, G:0.04, T:0.49
Consensus pattern (25 bp):
CTCTCTTTCAATTTCATGCATTAAT
Found at i:677077 original size:2 final size:2
Alignment explanation
Indices: 677072--677135 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
677062 CTTGTGTGTG
677072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
677114 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
677136 GTTTTGAAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:679212 original size:21 final size:23
Alignment explanation
Indices: 679172--679229 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
679162 ATTAATAAAA
*
679172 TAATAATA-TAATAA-ATTTA-T
1 TAATAATATTAAAAATATTTATT
679192 TAA-AATATTAAAAATATTTATT
1 TAATAATATTAAAAATATTTATT
*
679214 TAATAATATTCAAAAT
1 TAATAATATTAAAAAT
679230 CTAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 8 0.25
21 5 0.16
22 4 0.12
23 11 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATATTAAAAATATTTATT
Found at i:679407 original size:53 final size:53
Alignment explanation
Indices: 679290--679492 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 53
679280 TTTTATAAAA
* * * **
679290 TTTAAATAGTAATT-TAGGATTTAATATAAAATAGTTTTTGAATTTTTA-T-TT
1 TTTAAATAGTTATTCGA-GATTTAATATAAAATATTTTTTTTATTTTTATTATT
*
679341 TTTAAATAGTTATTCGGGATTTAATATAAAATATTTTTTTTATTTTTATTATT
1 TTTAAATAGTTATTCGAGATTTAATATAAAATATTTTTTTTATTTTTATTATT
* * * * **
679394 TTTAAATAATTATTTGAGATTTAACATTGAATTTAATATAAATTTTTTAAATTTATTATT
1 TTTAAATAGTTATTCGAGATTTAATA-T-AA---AATAT--TTTTTTTATTTTTATTATT
*
679454 TTTAAATAGTAATTCGAGATTTAATATAAAATATTTTTT
1 TTTAAATAGTTATTCGAGATTTAATATAAAATATTTTTT
679493 AATTATTTGC
Statistics
Matches: 124, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
51 41 0.33
52 1 0.01
53 28 0.23
54 1 0.01
55 7 0.06
58 7 0.06
59 1 0.01
60 38 0.31
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.54
Consensus pattern (53 bp):
TTTAAATAGTTATTCGAGATTTAATATAAAATATTTTTTTTATTTTTATTATT
Found at i:679799 original size:6 final size:6
Alignment explanation
Indices: 679781--679826 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
679771 TTAAAAAGTT
* * * *
679781 TTATAA TTCTAA TTATAA TTATAA TAATAA TAATAA TAATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
679827 TACGTTAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
TTATAA
Found at i:679809 original size:3 final size:3
Alignment explanation
Indices: 679790--679823 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
679780 TTTATAATTC
* *
679790 TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
679824 TATTACGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:683019 original size:52 final size:51
Alignment explanation
Indices: 682934--683057 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
682924 ATATGAAAAG
* *
682934 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
682985 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
683037 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
683058 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:683070 original size:51 final size:50
Alignment explanation
Indices: 682934--683077 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
682924 ATATGAAAAG
* *
682934 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
682986 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
683037 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
683078 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:683084 original size:13 final size:13
Alignment explanation
Indices: 683066--683090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
683056 CAAAGATCAG
683066 TGTATCGATACAA
1 TGTATCGATACAA
683079 TGTATCGATACA
1 TGTATCGATACA
683091 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:683178 original size:33 final size:33
Alignment explanation
Indices: 683136--683200 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
683126 GTAGCTTAAA
683136 TTGTATCGATACAAAAAAATATGTATCGATACC
1 TTGTATCGATACAAAAAAATATGTATCGATACC
* ***
683169 TTGTATCGATACAACATTTTATGTATCGATAC
1 TTGTATCGATACAAAAAAATATGTATCGATAC
683201 AAATCGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACAAAAAAATATGTATCGATACC
Found at i:684237 original size:171 final size:171
Alignment explanation
Indices: 683999--684398 Score: 647
Period size: 171 Copynumber: 2.3 Consensus size: 171
683989 TTTTAGAGAT
* *
683999 GATGAAGGTGCCAATATGCTGATTCAAGGCCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 GATGAAGATGCCAATATGCTGATTCAAGGCC-A-G-C-G--ATATTGGACTTAAAAATGAAGATG
*
684064 AGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTGAAGATGAGAA
60 AGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAA
684129 AAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
125 AAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
*
684176 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAA
*
684241 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
684306 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
684347 GATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAA
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
684399 GGTGCTAATG
Statistics
Matches: 212, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
171 135 0.64
172 4 0.02
173 1 0.00
174 40 0.19
175 1 0.00
176 1 0.00
177 30 0.14
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:684400 original size:22 final size:21
Alignment explanation
Indices: 684375--684442 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
684365 ATGCTGATTT
684375 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
684397 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
684418 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
684440 AAG
1 AAG
684443 ATGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:684483 original size:49 final size:49
Alignment explanation
Indices: 684247--684990 Score: 777
Period size: 49 Copynumber: 15.1 Consensus size: 49
684237 AAAAGTGATA
* * * * *
684247 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G
* ** * *
684298 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
* *
684352 AAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTT-AA-A-G
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
684400 --G-TGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
684446 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G
* ** * *
684497 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
*
684551 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
684599 --G-TGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
684645 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * * *
684691 --G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
684737 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * * *
684786 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
* *
684836 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATA
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * * *
684887 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* *
684936 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
684985 ATGATG
1 AAGATG
684991 AGAAAAGTGA
Statistics
Matches: 580, Mismatches: 78, Indels: 69
0.80 0.11 0.09
Matches are distributed among these distances:
43 102 0.18
44 7 0.01
45 3 0.01
46 4 0.01
47 1 0.00
48 7 0.01
49 250 0.43
50 5 0.01
51 9 0.02
52 110 0.19
54 6 0.01
55 76 0.13
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
Found at i:684543 original size:55 final size:52
Alignment explanation
Indices: 684409--685927 Score: 1090
Period size: 49 Copynumber: 30.7 Consensus size: 52
684399 GGTGCTAATG
684409 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * **
684458 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-AAAA-GATGCCAATA
*
684513 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG-TGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAA-GATGCCAATA
* * *
684565 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G----G-TGCTAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
684608 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * *
684657 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G----G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
684700 TGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * *
684749 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
684798 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * *
684850 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT---AAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
*
684899 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * * **
684948 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAAT-G--ATGATGAGAA-A
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * * * * **
684996 AG-TGA-TAAAGATGCCAATATGTTGATTCA-TGG-C-CAACGATATTGGGCTTAAAGATGAGAA
1 TGCTGATTCAAG--GCC---A-GCT-A--CATTGGACTTAA--AGA-T-GG--AAAAGATGCCAA
*
685056 AA
51 TA
* * * * ** *
685058 AG--GATGTCAACGTG-CTGATTCAAGGCCAGCTACATTGAACTTA-AAGATGGAAAATG-TGCC
1 TGCTGAT-TCAA-G-GCCAGCTACATTG---G--AC-TT-AA---AGATG--G-AAAA-GATGCC
685118 AATA
49 AATA
* * * *
685122 TGCTGATTTAAGGCCAGCTATATTGGACTT-AA-A--G----G-TGCTAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
685165 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * **
685214 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-AAAA-GATGCCAATA
*
685269 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATG-TGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAA-GATGCCAATA
* * *
685321 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G----G-TGCTAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
685364 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * *
685413 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G----G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
685456 TGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * *
685505 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
685554 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * *
685606 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT---AAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
*
685655 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * * *
685704 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
685753 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* * *
685802 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A--G----G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
685845 TGCTGATTCAAGACCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
* *
685894 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
685928 GGTCGCCACC
Statistics
Matches: 1221, Mismatches: 151, Indels: 196
0.78 0.10 0.12
Matches are distributed among these distances:
43 207 0.17
44 15 0.01
45 6 0.00
46 11 0.01
47 6 0.00
48 19 0.02
49 614 0.50
50 4 0.00
51 7 0.01
52 159 0.13
53 14 0.01
54 11 0.01
55 86 0.07
56 2 0.00
57 1 0.00
58 4 0.00
59 3 0.00
61 12 0.01
62 5 0.00
63 7 0.01
64 16 0.01
65 8 0.01
66 4 0.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGATGCCAATA
Found at i:684587 original size:199 final size:191
Alignment explanation
Indices: 684314--685927 Score: 1507
Period size: 199 Copynumber: 8.2 Consensus size: 191
684304 GATGTCAACG
* *
684314 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AA-GTGCCAATATGCTGATTCAAGG
* * * * *
684379 CCAGCTATATTGGACTT-AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
62 CCAGCTACATTGGACTTAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * * *
684443 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGT
127 ATGAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G--AAAGG-TGC
**
684508 CAACG
187 CAATA
*
684513 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AA-GTGCCAATATGCTGATTCAAGG
* * * * *
684578 CCAGCTATATTGGACTT-AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
62 CCAGCTACATTGGACTTAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
* * * *
684642 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-AAAGGTGCCAATG
127 ATGAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATA
* *
684700 TGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG-TGCCAATATGCTGATTCAAGGCCA
* * * * * *
684765 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
65 GCTACATTGGACTT--A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
* * *
684830 AGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-AAAGGTGC
125 AGAT-G--AAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGC
*
684894 CAATG
187 CAATA
*
684899 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG-TGCCAATATGCTGATTCAAGGCCA
* * ** *
684964 GCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGC
65 GCTACATTGGACTT-AAAA-G--G-T--G-CCA---AT----ATG-C-------TGATTCAAGGC
* * * *
685029 CAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATT
107 CAGCGATATTGGACTTAAAGAT--G---AA-GATGCCAATGTGCTGATTCAAGGCCAGCTACATT
* *
685094 GAACTTAAAGATGGAAAATGTGCCAATA
166 GGACTTAAAGAT-G-AAAGGTGCCAATA
* * * *
685122 TGCTGATTTAAGGCCAGCTATATTGGACTT-AA-A-G--GTGCTAATGTGCTGATTCAAGGCCAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATATGCTGATTCAAGGCCAG
685182 CTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
66 CTACATTGGACTTAAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
* * * *
685247 GATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAT
126 GAT--G---AA-GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAG
685312 GTGCCAATA
183 GTGCCAATA
* * *
685321 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--GTGCTAATGTGCTGATTCAAGGCCAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATATGCTGATTCAAGGCCAG
685381 CTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA
66 CTACATTGGACTTAAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
* * *
685445 -A-G--G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGATG-AAGATGCCAAT
126 GATGAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAAT
685504 A
191 A
* * * *
685505 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA-GTGCCAATATGCTGATTCAAGGCCA
*
685570 GCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
65 GCTACATTGGAC-T-----T--AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
* * * *
685635 TAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGATGC
122 TAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGC
685699 CAATA
187 CAATA
* * * *
685704 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA-GTGCCAATATGCTGATTCAAGGCCA
685769 GCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
65 GCTACATTGGACTT----A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
*
685833 A-A-G--G-TGCCAATGTGCTGATTCAAGACCAGCTACATTGGACTTAAAGAT-AAAGGTGCCAA
125 AGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAA
685892 TA
190 TA
* *
685894 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
685928 GGTCGCCACC
Statistics
Matches: 1283, Mismatches: 63, Indels: 147
0.86 0.04 0.10
Matches are distributed among these distances:
183 1 0.00
184 78 0.06
185 2 0.00
186 3 0.00
187 79 0.06
188 7 0.01
190 168 0.13
191 3 0.00
193 77 0.06
194 6 0.00
195 7 0.01
196 45 0.04
197 3 0.00
198 11 0.01
199 619 0.48
201 1 0.00
202 1 0.00
205 2 0.00
206 1 0.00
207 3 0.00
209 2 0.00
210 1 0.00
211 2 0.00
214 1 0.00
215 1 0.00
216 3 0.00
217 68 0.05
218 2 0.00
219 4 0.00
220 41 0.03
221 1 0.00
222 2 0.00
223 38 0.03
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (191 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATATGCTGATTCAAGGCCAG
CTACATTGGACTTAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA
AGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATA
Found at i:684599 original size:22 final size:21
Alignment explanation
Indices: 684574--684641 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
684564 ATGCTGATTC
684574 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
684596 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
684617 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
684639 AAG
1 AAG
684642 ATGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:685156 original size:22 final size:21
Alignment explanation
Indices: 685131--685198 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
685121 ATGCTGATTT
685131 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
685153 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
685174 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
685196 AAG
1 AAG
685199 ATGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:685355 original size:22 final size:21
Alignment explanation
Indices: 685330--685397 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
685320 ATGCTGATTC
685330 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
685352 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
685373 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
685395 AAG
1 AAG
685398 ATGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:685593 original size:756 final size:756
Alignment explanation
Indices: 684142--685741 Score: 3173
Period size: 756 Copynumber: 2.1 Consensus size: 756
684132 GGATGTCAAC
* *
684142 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
684207 AGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGG
66 AGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGG
684272 CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACAT
131 CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACAT
684337 TGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGT
196 TGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGT
684402 GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
261 GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
684467 AAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
326 AAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
684532 ACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
391 ACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
684597 AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
456 AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
684662 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGA
521 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGA
684727 CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
586 CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
684792 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
651 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
684857 TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAAT
716 TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAAT
684898 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
684963 AGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGG
66 AGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGG
685028 CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACAT
131 CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACAT
685093 TGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGT
196 TGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGT
685158 GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
261 GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
685223 AAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
326 AAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
685288 ACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
391 ACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
685353 AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
456 AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
685418 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGA
521 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGA
685483 CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
586 CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
685548 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
651 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
685613 TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAAT
716 TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAAT
685654 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
685719 AGCGATATTGGACTTAAAGATGA
66 AGCGATATTGGACTTAAAAATGA
685742 AGGTGCCAAT
Statistics
Matches: 841, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
756 841 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (756 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGG
CCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACAT
TGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGT
GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCT
ACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTAGA
CTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGAT
TCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAAT
Found at i:686068 original size:32 final size:32
Alignment explanation
Indices: 685924--686124 Score: 280
Period size: 33 Copynumber: 6.2 Consensus size: 32
685914 TATTGGACTT
*
685924 AAAGGGTCGCCACCGACTTGTGTGGGCTTTAG
1 AAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * * *
685956 AGAATGGTTGTCACCAACTTGTGTGTGCTTTGG
1 A-AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
685989 AAGAAGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AA-AGGGTTGCCACCGACTTGTGTGGGCTTTAG
686021 AAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AAAG--GGTTGCCACCGACTTGTGTGGGCTTTAG
686055 AAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
686086 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 A-AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
686119 AAAGGG
1 AAAGGG
686125 AGAAAGATGC
Statistics
Matches: 151, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.02
32 65 0.43
33 78 0.52
34 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (32 bp):
AAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:686165 original size:34 final size:34
Alignment explanation
Indices: 686107--686966 Score: 1023
Period size: 34 Copynumber: 25.3 Consensus size: 34
686097 CACCGACTTG
* *
686107 TGTGGGCTTTAGAAAGGGAGAAAGATGCCACGGAGT
1 TGTGGGCTTTA-AAA-GGAAAAAGGTGCCACGGAGT
* *
686143 TGTGGAC-TTAAAAGGGAAAAAGAGTTCCACGGAGT
1 TGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGT
*
686178 TGTGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
* * *
686212 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGGTGCCACGGAGT
*
686246 TGTGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
* *
686280 TGTGGGCTTTGAAAA-GAAGACGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
686314 TGTGGGCTTT-AAAGG-AAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
*
686346 TGTGGGCTTTAAAA-GAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
686379 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGT
686416 TGTGGGCTTTAAACA-GAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGGTGCCACGGAGT
* * *
686450 TGTGGAC-TTAAAAGGGAAAAAAAGTTCCACGGAGT
1 TGTGGGCTTTAAAA-GG-AAAAAGGTGCCACGGAGT
*
686485 TGTGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
* * *
686519 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGGTGCCACGGAGT
*
686553 TGTGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
* *
686587 TGTGGGCTTTGAAAA-GAAGACGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
*
686621 TGTGGGCTTT-AAAGG-AAAAGGTGCCACGAAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
*
686653 TGTGGGCTTTAAAA-GAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
686686 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGT
686723 TGTGGGCTTTAAACA-GAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGGTGCCACGGAGT
*
686757 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
* * *
686791 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGGTGCCACGGAGT
* *
686825 TGTGGGCTTTGAAAA-GAAGAAGGCGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
*
686859 TGTGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGGTGCCACGGAGT
686893 TGTGGGCTTT-AAAGG-AAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
* *
686925 TGTGGGCTTT-GAA-GAAAAAGGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
686957 TGTGGGCTTT
1 TGTGGGCTTT
686967 GAAGAAAAAA
Statistics
Matches: 737, Mismatches: 49, Indels: 80
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.00
32 121 0.16
33 77 0.10
34 376 0.51
35 71 0.10
36 37 0.05
37 54 0.07
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGT
Found at i:686686 original size:307 final size:307
Alignment explanation
Indices: 686127--686976 Score: 1405
Period size: 307 Copynumber: 2.8 Consensus size: 307
686117 AGAAAGGGAG
* *
686127 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTTCCACGGAGTTGTGGGCTTTGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAAAGTTCCACGGAGTTGTGGGCTTTGAAA
686192 AGAAGAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
66 AGAAGAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
686257 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGTGGGCT
131 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGTGGGCT
*
686322 TTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
196 TTAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
686387 TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
261 TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
686434 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAAAGTTCCACGGAGTTGTGGGCTTTGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAAAGTTCCACGGAGTTGTGGGCTTTGAAA
686499 AGAAGAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
66 AGAAGAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
686564 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGTGGGCT
131 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGTGGGCT
686629 TTAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
196 TTAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
686694 TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
261 TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
* * * * *
686741 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AG-AAAAAGGTGCCACGGAGTTGTGGAC-TT-AA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAAAGTTCCACGGAGTTGTGGGCTTTGAA
* * * * * *
686802 AGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAA-A-GAAGAAGGCGCCACGGAGTTGTGGG
65 A-A-GAAGAAGGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAAAGTGCCACGGAGTTGTGGG
* *
686865 CTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGGAA-AAGGTGCCACGGAGTTGT
126 CTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGT
* * *
686928 GGGCTTTGAAGAAAAAGGTGCCAC-AGAGTTGTGGGCTTT-GAAGAAAAAA
191 GGGCTTTAAAGGAAAAGGTGCCACGA-AGTTGTGGGCTTTAAAAGAAAAAA
686977 TACCACTGAG
Statistics
Matches: 518, Mismatches: 19, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
303 10 0.02
304 55 0.11
305 9 0.02
306 105 0.20
307 330 0.64
308 9 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (307 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAAAGTTCCACGGAGTTGTGGGCTTTGAAA
AGAAGAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGACGGTGCCACGGAGTTGTGGGCT
TTAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
TTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAA
Found at i:687044 original size:31 final size:31
Alignment explanation
Indices: 686979--687091 Score: 133
Period size: 31 Copynumber: 3.6 Consensus size: 31
686969 AGAAAAAATA
* *
686979 CCACTGAGTCGT-GATCTTTAAAGAAAAAGA-TG
1 CCACTGAGTCGTGGA-CTTT-GAG-AAGAGATTG
*
687011 CCACTGAGT-GATGGACTTTGAGCAGAGATTG
1 CCACTGAGTCG-TGGACTTTGAGAAGAGATTG
687042 CCACTGAGTCGTGGACTTTGAGAAGAGATTG
1 CCACTGAGTCGTGGACTTTGAGAAGAGATTG
*
687073 CCACTTAGTCGTGGACTTT
1 CCACTGAGTCGTGGACTTT
687092 AAAAAGGTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
30 4 0.06
31 51 0.71
32 15 0.21
33 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
CCACTGAGTCGTGGACTTTGAGAAGAGATTG
Found at i:689872 original size:77 final size:78
Alignment explanation
Indices: 689740--689941 Score: 230
Period size: 77 Copynumber: 2.6 Consensus size: 78
689730 GAGATAATAA
* * * * * *
689740 CGGGGTTGGAGTGTTCC-CTTGAAAATAACGGGGCTGGAGTATCCCCAGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-
*
689804 A-TTAGAAAAAAAAT
64 ATTTAGAAAAAAAAC
*
689818 C-GGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGAAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
* * * *
689882 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* *
689896 CGGGGTTGGAGTATCCTCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCC
689942 GATGAAATAA
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
76 4 0.04
77 50 0.48
78 10 0.10
79 41 0.39
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:689936 original size:28 final size:28
Alignment explanation
Indices: 689896--689969 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
689886 GGAATAAAGC
*
689896 CGGGGTTGGAGTATCCTCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCTC-CGAGAAATAA
689924 CGGGGTTGGAGTATCC-CCGATGAAATAA
1 CGGGGTTGGAGTATCCTCCGA-GAAATAA
*
689952 CGAGGTTGGAGTATCCTC
1 CGGGGTTGGAGTATCCTC
689970 GATTGTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 37 0.90
29 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCCGAGAAATAA
Found at i:690116 original size:55 final size:54
Alignment explanation
Indices: 689955--690179 Score: 204
Period size: 55 Copynumber: 4.3 Consensus size: 54
689945 GAAATAACGA
*
689955 GGTTGGAGTATCCTCGATTGTG----AAAAATTAGTGTTTTTGGAAATAAAA-TCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTG-TTTT-GAAATAAAACT-GG
* * * *
690007 AGTTGGAGTATCCCCGA-T-T-AAAGAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTG-AAATAAAACTGG
*
690059 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCAATAAAACTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTT-GAAATAAAACTGG
* * ** * *
690114 GGTTGGAGTATCCCTGATTATGAAAAATCAA-TA-T-TTTGGAAAT-AAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTGAAATAAAACT-GG
690165 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
690180 TCGGAAATAA
Statistics
Matches: 145, Mismatches: 17, Indels: 23
0.78 0.09 0.12
Matches are distributed among these distances:
50 5 0.03
51 22 0.15
52 48 0.33
53 12 0.08
54 3 0.02
55 54 0.37
56 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (54 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTGAAATAAAACTGG
Found at i:690167 original size:106 final size:104
Alignment explanation
Indices: 689955--690179 Score: 267
Period size: 106 Copynumber: 2.1 Consensus size: 104
689945 GAAATAACGA
* *
689955 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCGGAGTTGGAGTATCC
*** *
690020 CCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACCGG
66 CCGATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
* *
690059 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTG-TTTTAGCAATAAAA-CTGGGGTTGGAG
1 GGTTGGAGTATCCCCGATTGTG----AAAAATTAGTGTTTTTAGAAATAAAATC-GGAGTTGGAG
* * * **
690122 TATCCCTGATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
61 TATCCCCGATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
690165 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
690180 TCGGAAATAA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
104 21 0.20
106 40 0.39
107 31 0.30
108 11 0.11
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCGGAGTTGGAGTATCC
CCGATTAAAGAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:690168 original size:266 final size:266
Alignment explanation
Indices: 689846--690346 Score: 799
Period size: 266 Copynumber: 1.9 Consensus size: 266
689836 CGAAAATAAC
* *
689846 GGGGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATC
1 GGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
* * * *
689911 CTCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTCGGAAATAACGGGATTGGAGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGT
* *
689976 GAA-AAATTAGTG-TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAAATTGG
130 GAAGAAATTAGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGACTAAAG-AAAATTAG
* *
690039 TGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCA
194 TGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCA
690104 ATAAAACT
259 ATAAAACT
* ** *
690112 GGGGTTGGAGTATCCCTGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATC
1 GGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
* *
690177 CCCTCGGAAATAACGGGATTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTG
66 CCCTCGGAAATAACGGGATTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTG
* *
690242 AAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGACTATAGAAAATTAGTG
131 AAGAAATTAGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGACTAAAGAAAATTAGTG
*
690307 TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
196 TTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTG
690347 GAGAATTGAG
Statistics
Matches: 214, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
265 29 0.14
266 145 0.68
267 40 0.19
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (266 bp):
GGGGTTGAAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
CCCTCGGAAATAACGGGATTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTG
AAGAAATTAGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGACTAAAGAAAATTAGTG
TTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGAAAAAAAAATTAGTGTTTTAGCAAT
AAAACT
Found at i:690225 original size:27 final size:28
Alignment explanation
Indices: 690162--690237 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
690152 GAAATAAAGT
***
690162 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
690190 CGGGATTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
690217 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
690238 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:690323 original size:51 final size:52
Alignment explanation
Indices: 689955--690343 Score: 258
Period size: 51 Copynumber: 7.4 Consensus size: 52
689945 GAAATAACGA
* * *
689955 GGTTGGAGTATCCTCGATTGT-GAAAAATTAGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTG-TTTTGAAAATAAAATCGG
* * * *
690007 AGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* * *
690059 GGTTGGAGTATCCCCGATTGTGAAAAAAAAATTAGTGTTTT-AGCAATAAAA-CTGG
1 GGTTGGAGTATCCCCGA-T-T-ATAGAAAAATTAGTGTTTTGA-AAATAAAATC-GG
* * * * * *
690114 GGTTGGAGTATCCCTGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* *** * *** ** *
690165 GGTTGGAGTATCCCCTCGGA-AATA-ACGGGATTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTAT-CCC-C-GATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGG
* * *
690220 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGG
* *
690274 AGTTGGAGTATCCCCGACTATAG-AAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* *
690325 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
690344 GTGGAGAATT
Statistics
Matches: 257, Mismatches: 56, Indels: 49
0.71 0.15 0.14
Matches are distributed among these distances:
51 67 0.26
52 59 0.23
53 33 0.13
54 33 0.13
55 57 0.22
56 5 0.02
57 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:692712 original size:21 final size:21
Alignment explanation
Indices: 692686--692742 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
692676 GTAAACTTCC
692686 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
692707 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
692728 -AAATGTATCGATACA
1 TAGATGTATCGATACA
692743 TTCCCTTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:692786 original size:19 final size:17
Alignment explanation
Indices: 692760--692830 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 17
692750 GGTAGTAGCT
692760 AATTATGTATCGATACA
1 AATTATGTATCGATACA
692777 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
692795 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
692809 ACATTTATGTATCGATACA
1 A-A-TTATGTATCGATACA
692828 AAT
1 AAT
692831 CGCTGAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.24
14 1 0.02
16 2 0.04
17 2 0.04
18 3 0.07
19 27 0.59
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (17 bp):
AATTATGTATCGATACA
Found at i:692802 original size:13 final size:13
Alignment explanation
Indices: 692784--692808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
692774 ACAATACTTA
692784 TGTATCGATACAT
1 TGTATCGATACAT
692797 TGTATCGATACA
1 TGTATCGATACA
692809 ACATTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:692806 original size:32 final size:32
Alignment explanation
Indices: 692765--692827 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
692755 TAGCTAATTA
*
692765 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
692797 TGTATCGATACAACATTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
692828 AATCGCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:693421 original size:55 final size:54
Alignment explanation
Indices: 693332--693696 Score: 451
Period size: 55 Copynumber: 6.8 Consensus size: 54
693322 ATAAAGTGTA
* * * *
693332 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
693387 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
693442 TCCTGCTCTTTGAGGATTGGAAAATGCTACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
693497 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
693552 TCCTACTCTTTGA-G---G--A-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
693599 CCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
693654 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGG
693697 AGGAAATGCC
Statistics
Matches: 271, Mismatches: 23, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
47 39 0.14
48 3 0.01
49 1 0.00
51 1 0.00
52 1 0.00
54 17 0.06
55 203 0.75
56 6 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:693590 original size:47 final size:47
Alignment explanation
Indices: 693521--693614 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
693511 GACTGAAAGG
*
693521 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTACTCTTTGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGCCCTACTCTTTGAGGA
*
693568 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTGCTCTTTGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTACTCTTTGAGGA
693615 CTGGAAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 42 0.95
48 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (47 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTACTCTTTGAGGA
Found at i:693631 original size:157 final size:161
Alignment explanation
Indices: 693332--693696 Score: 526
Period size: 157 Copynumber: 2.3 Consensus size: 161
693322 ATAAAGTGTA
* * * * *
693332 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAGGCGTCCTACTCTT
1 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTT
* *
693397 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGATTGG
66 TGAGGA--G-AA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGCCCTGCTCTTTGAGGACTGG
* * *
693462 AAAATGCTACCAACTTGTGTGGGCTTTGAAAGGTG
127 AAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
*
693497 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTACTCT
1 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTACTCT
693561 TTGA-G-G-A-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGCCCTGCTCTTTGAGGACTGGAA
65 TTGAGGAGAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGCCCTGCTCTTTGAGGACTGGAA
693621 AATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
129 AATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
*
693654 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGG
1 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGG
693697 AGGAAATGCC
Statistics
Matches: 186, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
157 120 0.65
158 2 0.01
159 1 0.01
161 1 0.01
164 3 0.02
165 59 0.32
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (161 bp):
TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTT
TGAGGAGAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGCCCTGCTCTTTGAGGACTGGAAAA
TGCCACCAACTTGTGTGGGCTTCGAAAGGGG
Found at i:693657 original size:102 final size:102
Alignment explanation
Indices: 693465--693665 Score: 307
Period size: 102 Copynumber: 2.0 Consensus size: 102
693455 GGATTGGAAA
* * * *
693465 ATGCTACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAA
1 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTGCTCTTTGAGGACTGAAAGATGCCACCAA
* *
693530 CTTGTGTGGGCTTTAAGAGGTGTCCTACTCTTTGAGG
66 CTTGTGTGGGCTTGAAGAGGGGTCCTACTCTTTGAGG
693567 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTGCTCTTTGAGGACTGGAAA-ATGCCACCA
1 ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTGCTCTTTGAGGACT-GAAAGATGCCACCA
*
693631 ACTTGTGTGGGCTTCGAA-AGGGGTCCTGCTCTTTG
65 ACTTGTGTGGGCTT-GAAGAGGGGTCCTACTCTTTG
693666 GGGACTGAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 84 0.93
103 6 0.07
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (102 bp):
ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGCCCTGCTCTTTGAGGACTGAAAGATGCCACCAA
CTTGTGTGGGCTTGAAGAGGGGTCCTACTCTTTGAGG
Found at i:694627 original size:10 final size:10
Alignment explanation
Indices: 694624--694668 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
694614 TTTTTCTTTG
*
694624 TTTTGGTTT-
1 TTTTGTTTTT
694633 TTTTGTTTTT
1 TTTTGTTTTT
694643 TTTTGTTTTT
1 TTTTGTTTTT
694653 TTTTGGTTTTT
1 TTTT-GTTTTT
694664 TTTTG
1 TTTTG
694669 AAAAAGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 8 0.24
10 15 0.45
11 10 0.30
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:694636 original size:18 final size:18
Alignment explanation
Indices: 694613--694654 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
694603 CTTTTCTTTC
694613 TTTTTTCTTTGTTTTGGT
1 TTTTTTCTTTGTTTTGGT
* * *
694631 TTTTTTGTTTTTTTTTGT
1 TTTTTTCTTTGTTTTGGT
694649 TTTTTT
1 TTTTTT
694655 TTGGTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (18 bp):
TTTTTTCTTTGTTTTGGT
Found at i:694644 original size:11 final size:11
Alignment explanation
Indices: 694630--694667 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
694620 TTTGTTTTGG
694630 TTTTTTTG-TT
1 TTTTTTTGTTT
694640 TTTTTTTGTTT
1 TTTTTTTGTTT
*
694651 TTTTTTGGTTT
1 TTTTTTTGTTT
694662 TTTTTT
1 TTTTTT
694668 GAAAAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:694646 original size:29 final size:29
Alignment explanation
Indices: 694604--694665 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
694594 CAGATTTTTC
694604 TTTTCTTTCTTTTT-TCTTTGTTTTGGTTT
1 TTTTCTTTCTTTTTGT-TTTGTTTTGGTTT
* * *
694633 TTTTGTTTTTTTTTGTTTTTTTTTGGTTT
1 TTTTCTTTCTTTTTGTTTTGTTTTGGTTT
694662 TTTT
1 TTTT
694666 TTGAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (29 bp):
TTTTCTTTCTTTTTGTTTTGTTTTGGTTT
Found at i:694668 original size:11 final size:10
Alignment explanation
Indices: 694630--694668 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
694620 TTTGTTTTGG
694630 TTTTTTTGTT
1 TTTTTTTGTT
694640 TTTTTTTGTT
1 TTTTTTTGTT
694650 TTTTTTTGGTT
1 TTTTTTT-GTT
694661 TTTTTTTG
1 TTTTTTTG
694669 AAAAAGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:707177 original size:78 final size:78
Alignment explanation
Indices: 707067--707269 Score: 228
Period size: 78 Copynumber: 2.6 Consensus size: 78
707057 GAGATAATAA
* * * * * * * *
707067 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCTCTGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTTATGAGAAATCAAT-A
*
707132 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* *
707145 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTTATGAGAAATCAATA-
* * * *
707210 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* *
707224 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
707270 GATGAAATAA
Statistics
Matches: 105, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 53 0.50
79 51 0.49
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAGTTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:707264 original size:28 final size:28
Alignment explanation
Indices: 707224--707299 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
707214 GGAATAAAGC
** *
707224 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
707252 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
707280 CGAGGTTGGAATATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
707300 TTAAAGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:707287 original size:107 final size:108
Alignment explanation
Indices: 707145--707349 Score: 251
Period size: 107 Copynumber: 1.9 Consensus size: 108
707135 GAAAAAAAAT
* * *
707145 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-AGTT--ATGAGAAATTAA
1 CGGGATTGGAGTATCCCCTCGAAAATAACGAGGTTGGAATATCCCCGA-TTAAAGGA-AAATTAA
**
707207 TATTTTGGGAAT-AAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
64 TATTTTGAAAATCAAA-CCGGGGTTGGAGTATCCCCTCGGAAGTAA
* *
707252 CGGGGTTGGAGTAT-CCC-CGATGAAATAACGAGGTTGGAATATCCCCGATTAAAGGAAAATTAG
1 CGGGATTGGAGTATCCCCTCGA--AAATAACGAGGTTGGAATATCCCCGATTAAAGGAAAATTAA
*
707315 TGTTTTGAAAATCAAACCGGGGTTGGAGTATCCCC
64 TATTTTGAAAATCAAACCGGGGTTGGAGTATCCCC
707350 GATTGTGAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
105 3 0.04
106 3 0.04
107 37 0.44
108 35 0.42
109 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (108 bp):
CGGGATTGGAGTATCCCCTCGAAAATAACGAGGTTGGAATATCCCCGATTAAAGGAAAATTAATA
TTTTGAAAATCAAACCGGGGTTGGAGTATCCCCTCGGAAGTAA
Found at i:707392 original size:56 final size:53
Alignment explanation
Indices: 707283--707457 Score: 184
Period size: 56 Copynumber: 3.3 Consensus size: 53
707273 GAAATAACGA
* * * *
707283 GGTTGGAATATCCCCGATTA--AAGGAAAATTAGTGTTTT-GAAAATCAAACCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAAAATTAGTGTTTTAG-AAATAAAATCGG
* *
707335 GGTTGGAGTATCCCCGATTGTGAAAAAAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATG---AAAAAAATTAGTGTTTTAGAAATAAAATCGG
* *
707391 GGTTGGAGTATCCCCGATTATGAAAACAA-TA---TTTTAGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAAATTAGTGTTTTAGAAATAAAATCGG
707440 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
707458 GATTAACGGG
Statistics
Matches: 107, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
49 34 0.32
52 20 0.19
53 6 0.06
56 44 0.41
57 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (53 bp):
GGTTGGAGTATCCCCGATTATGAAAAAAATTAGTGTTTTAGAAATAAAATCGG
Found at i:707532 original size:130 final size:130
Alignment explanation
Indices: 707332--707588 Score: 306
Period size: 131 Copynumber: 2.0 Consensus size: 130
707322 AAAATCAAAC
* **
707332 CGGGGTTGGAGTATCCCCGATTGTGAAAAAAAAAATTAGTGTTTTAGCAATAAAATCGGGGTTGG
1 CGGGGTTGGAGTATCCCCGATTGTG---AAAAAAATTAGTGTTTTAGAAATAAAATCGAAGTTGG
* * *
707397 AGTATCCCCGATTAT-GAAAA-CAATATTTT-AGAAATAAAGTCGGGGTTGGAGTATCCCCGATG
63 AGTAT-CCCGATTATAGAAAATCAATATTTTGA-AAATAAAATCGGAGTTGGAATATCCCCGATG
707459 ATTAA
126 ATTAA
* * * *
707464 CGGGGTTGGAGTATCCTCGATTGTG-AAGAAATTGGTGTTTTTTGGAAATAAAATCGAAGTTGGA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAAAATTAGTG--TTTTAGAAATAAAATCGAAGTTGGA
* * *
707528 GTATCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGAT
64 GTATCCCGATTATAGAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCGAT
707589 TGTGGAGAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
128 10 0.09
129 9 0.08
130 30 0.28
131 33 0.31
132 25 0.23
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAAAATTAGTGTTTTAGAAATAAAATCGAAGTTGGAGT
ATCCCGATTATAGAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATGATTAA
Found at i:707565 original size:50 final size:52
Alignment explanation
Indices: 707468--707589 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 52
707458 GATTAACGGG
* * *
707468 GTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCC-CGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGAA
*
707522 GTTGGAGTATCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGAA
*
707572 GTTGGAATATCCCCGATT
1 GTTGGAGTAT-CCCGATT
707590 GTGGAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
50 26 0.43
51 9 0.15
52 8 0.13
53 6 0.10
54 12 0.20
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.34
Consensus pattern (52 bp):
GTTGGAGTATCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGAA
Found at i:709955 original size:21 final size:21
Alignment explanation
Indices: 709929--709985 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
709919 GTAAACTTCC
*
709929 TAGATGTATCAATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
709950 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
709971 -AAATGTATCGATACA
1 TAGATGTATCGATACA
709986 TTCCCTTGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:710052 original size:21 final size:21
Alignment explanation
Indices: 710026--710082 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
710016 TACAATACTT
710026 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
710047 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
710068 ATGTATCGATACATT
1 ATGTATCGATACATT
710083 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:713758 original size:20 final size:20
Alignment explanation
Indices: 713730--713804 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
713720 TTTTACCCAG
713730 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
713750 ATATATCGATTCATGTATGA
1 ATGTATCGATACATTTTTCA
* *
713770 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
713790 ATGTATCGATACATT
1 ATGTATCGATACATT
713805 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:713790 original size:40 final size:39
Alignment explanation
Indices: 713730--713807 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
713720 TTTTACCCAG
* *
713730 ATGTATCGATACATTTTTCAATATATCGATTCATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
713770 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
713808 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:714451 original size:13 final size:13
Alignment explanation
Indices: 714433--714460 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
714423 CATTACTCAA
714433 TGTATCGATACAT
1 TGTATCGATACAT
714446 TGTATCGATACAT
1 TGTATCGATACAT
714459 TG
1 TG
714461 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:714455 original size:33 final size:33
Alignment explanation
Indices: 714413--714478 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
714403 GCCAAGGAAA
714413 TGTATCGATACATT-ACTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
714446 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
714479 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Done.