Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397285.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_299.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1083202
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 21736 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:567291 original size:70 final size:71
Alignment explanation
Indices: 567102--567293 Score: 216
Period size: 70 Copynumber: 2.7 Consensus size: 71
567092 CAAGAACTTG
*
567102 ATTAAAATTGTTTAATTAAGTTA-T-GCCTAATTAATTAAATTATTTAATT-AAGTTGTTAGGCC
1 ATTAAAATTGTTTAATTAAGTTATTGGCCTAATTGATTAAATTATTTAATTAAAGTTGTTAGGCC
* *
567164 TAGTTG
66 TAATTA
** *
567170 ATTAAAATTGTTTAATTAAGCCATTAGGCTTAATTGATTAAAATT-TTTAATTAAAG-TGTTAGG
1 ATTAAAATTGTTTAATTAAGTTATT-GGCCTAATTGATT-AAATTATTTAATTAAAGTTGTTAGG
**
567233 TTTAATTA
64 CCTAATTA
* **
567241 ATT-ATATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAAATAATTAA
1 ATTAAAATTGTTTAATTAAGTTATT-GGCCTAATTGATTAAATTATTTAATTAA
567294 GTTAACTAGG
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
68 21 0.20
69 6 0.06
70 37 0.36
71 31 0.30
72 8 0.08
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (71 bp):
ATTAAAATTGTTTAATTAAGTTATTGGCCTAATTGATTAAATTATTTAATTAAAGTTGTTAGGCC
TAATTA
Found at i:578326 original size:21 final size:22
Alignment explanation
Indices: 578297--578340 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
578287 AAGTGATTAA
578297 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
578318 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
578340 T
1 T
578341 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:579005 original size:12 final size:13
Alignment explanation
Indices: 578990--579025 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
578980 AGATATTTTT
578990 GAGGCAGCAAGA-
1 GAGGCAGCAAGAG
579002 GAGGCAGCAA-AG
1 GAGGCAGCAAGAG
579014 GAGGCAGCAAGA
1 GAGGCAGCAAGA
579026 AACAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GAGGCAGCAAGAG
Found at i:582149 original size:33 final size:33
Alignment explanation
Indices: 582086--582149 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
582076 ATGATGTACT
*
582086 TTGGAGACATTAGAGATGATGATATACCCCTCA
1 TTGGAGACATTAGAGAGGATGATATACCCCTCA
* * *
582119 TTGGAGACCTTACGA-AGGATGGTATGCCCCT
1 TTGGAGACATTA-GAGAGGATGATATACCCCT
582150 ATGGTTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 24 0.92
34 2 0.08
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (33 bp):
TTGGAGACATTAGAGAGGATGATATACCCCTCA
Found at i:592858 original size:76 final size:77
Alignment explanation
Indices: 592778--592938 Score: 227
Period size: 76 Copynumber: 2.1 Consensus size: 77
592768 ATTTCCTAAT
* * * *
592778 TTAAAATACTATCTTTAATTTTAGGAATTTCTTTTAAAATA-AGAAACAATTTCCTA-TTTTTAT
1 TTAAAATACTAACCTTAATTTTAGGAATTACCTTTAAAATAGA-AAACAATTTCCTATTTTTTAT
*
592841 GAATCACCCAAAA
65 GAATCAACCAAAA
* *
592854 TTAAAATTCTAACCTTAATTTTAGGAATTACCTTTAAACTAGAAAACAATTTCCTATTTTTTATG
1 TTAAAATACTAACCTTAATTTTAGGAATTACCTTTAAAATAGAAAACAATTTCCTATTTTTTATG
*
592919 AATCAACTAAAA
66 AATCAACCAAAA
592931 TTAAAATA
1 TTAAAATA
592939 AATGGTATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
76 48 0.65
77 26 0.35
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (77 bp):
TTAAAATACTAACCTTAATTTTAGGAATTACCTTTAAAATAGAAAACAATTTCCTATTTTTTATG
AATCAACCAAAA
Found at i:611958 original size:22 final size:22
Alignment explanation
Indices: 611933--611975 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
611923 GTAGTTTAAA
611933 CTAAATAACAA-AAACATAAAAG
1 CTAAATAA-AATAAACATAAAAG
* *
611955 CTAACTAAAATAAACTTAAAA
1 CTAAATAAAATAAACATAAAA
611976 ACACAAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (22 bp):
CTAAATAAAATAAACATAAAAG
Found at i:622433 original size:15 final size:15
Alignment explanation
Indices: 622415--622451 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
622405 GAAATAAAAT
622415 TTTCCATTTTAAGAC
1 TTTCCATTTTAAGAC
**
622430 TTTCCATTTTAATTC
1 TTTCCATTTTAAGAC
622445 TTTCCAT
1 TTTCCAT
622452 AATTAAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTCCATTTTAAGAC
Found at i:622842 original size:77 final size:76
Alignment explanation
Indices: 622711--622952 Score: 304
Period size: 77 Copynumber: 3.1 Consensus size: 76
622701 TGAATTTCTC
* * * * * * *
622711 AAATTAAAATACTATCCTTAATTTTAAGAATTTCTTTTAAAGCAGAAAAAAATTTCCTATTCTTT
1 AAATTAAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTT
*
622776 ATAAATCATCCA
66 ATGAATCA-CCA
* * * *
622788 AAATTAAAATTCTATCCTTGATTTTAGGAATTAATTTTAATGTAGGAAACAATTTTCTATTTTTT
1 AAATTAAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTT
622853 ATGAATCACCCA
66 ATGAATCA-CCA
* * * *
622865 AAATTAAAATTCTGTCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAACAATTTCTTTTTTTTT
1 AAATTAAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGTAGGAAACAATTTC-CTATTTTT
622930 TATGAATCACCAA
65 TATGAATCACC-A
622943 AAATTAAAAT
1 AAATTAAAAT
622953 AGATGGCATT
Statistics
Matches: 142, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
77 116 0.82
78 26 0.18
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (76 bp):
AAATTAAAATTCTATCCTTAATTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTTTTT
ATGAATCACCA
Found at i:635533 original size:76 final size:77
Alignment explanation
Indices: 635406--635568 Score: 265
Period size: 76 Copynumber: 2.1 Consensus size: 77
635396 AATACCATCT
* *
635406 ATTTTAATTTTGGATGATCCATAAAAAATAGGAAATTGTTTCCTACTTTAAAAGCAATTCCTAAA
1 ATTTTAATTTTGGATGATCCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCCTAAA
635471 ATTAAGGATAAA
66 ATTAAGGATAAA
* * *
635483 ATTTTAATTTTGGGTGATTCAT-AAAAATAGGAAATTATTTCCTATTTTAAAAGAAATTCCTAAA
1 ATTTTAATTTTGGATGATCCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCCTAAA
*
635547 ATTAAGGATAAT
66 ATTAAGGATAAA
635559 ATTTTAATTT
1 ATTTTAATTT
635569 GGGAAATTGA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 60 0.75
77 20 0.25
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (77 bp):
ATTTTAATTTTGGATGATCCATAAAAAATAGGAAATTATTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGGATAAA
Found at i:642188 original size:16 final size:15
Alignment explanation
Indices: 642163--642197 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
642153 TGAAACCAAA
*
642163 TTTTGGGTTTTGATT
1 TTTTGAGTTTTGATT
642178 CTTTTGAGTTTTGATT
1 -TTTTGAGTTTTGATT
642194 TTTT
1 TTTT
642198 ATTTATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.69
Consensus pattern (15 bp):
TTTTGAGTTTTGATT
Found at i:642373 original size:21 final size:20
Alignment explanation
Indices: 642345--642383 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
642335 AACATTTTGT
642345 TTCAAATGTATCGATACATG
1 TTCAAATGTATCGATACATG
*
642365 TTCATAATGTATTGATACA
1 TTCA-AATGTATCGATACA
642384 ATTTTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TTCAAATGTATCGATACATG
Found at i:643541 original size:69 final size:69
Alignment explanation
Indices: 643415--643578 Score: 156
Period size: 69 Copynumber: 2.4 Consensus size: 69
643405 GCTCTAGTCA
* * * * * ** *
643415 GTGTGGGGGTAAGAGTACCACAAGATTAGGTTAGGCATTGTACCATTTCTTCCCTCTTTATGAGT
1 GTGTAGGGGTAAGAATACCATAAGGTTAGGTTAGGCATCGTACCATACCTTCCCTCTTTATAAGT
643480 CCTG
66 CCTG
*
643484 GTGTAGGGGTAAGAATACCATACGGTTAGGTTAGGCATCGTA-C-TACCTTCCAACTCTTTATAA
1 GTGTAGGGGTAAGAATACCATAAGGTTAGGTTAGGCATCGTACCATACCTTCC--CTCTTTATAA
**
643547 GTTTTG
64 GTCCTG
* * *
643553 GTG-A-GGGTTAGAATATCATAGGGTTA
1 GTGTAGGGGTAAGAATACCATAAGGTTA
643579 AACTTGGCCA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
67 25 0.32
68 2 0.03
69 52 0.66
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (69 bp):
GTGTAGGGGTAAGAATACCATAAGGTTAGGTTAGGCATCGTACCATACCTTCCCTCTTTATAAGT
CCTG
Found at i:646117 original size:19 final size:21
Alignment explanation
Indices: 646095--646133 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
646085 ATAGTGTTCA
*
646095 TCATCTTTCC-ATT-TCATCC
1 TCATCATTCCTATTCTCATCC
646114 TCATCATTCCTATTCTCATC
1 TCATCATTCCTATTCTCATC
646134 TTTGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.46
Consensus pattern (21 bp):
TCATCATTCCTATTCTCATCC
Found at i:647059 original size:17 final size:17
Alignment explanation
Indices: 647033--647066 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
647023 TCTTTTCCCT
* *
647033 ATAAAGCTTAGGTTGTC
1 ATAAACCTTAAGTTGTC
647050 ATAAACCTTAAGTTGTC
1 ATAAACCTTAAGTTGTC
647067 CAAGTATCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (17 bp):
ATAAACCTTAAGTTGTC
Found at i:648545 original size:36 final size:36
Alignment explanation
Indices: 648504--648574 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
648494 TTAATAGAGA
* *
648504 CATGTCTAATGTTG-AAGTAGCTAACAGAATAATAGT
1 CATGTCTAATG-TGAAAGCAACTAACAGAATAATAGT
648540 CATGTCTAATGTGAAAGCAACTAACAGAATAATAG
1 CATGTCTAATGTGAAAGCAACTAACAGAATAATAG
648575 AGCCACTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
CATGTCTAATGTGAAAGCAACTAACAGAATAATAGT
Found at i:650175 original size:21 final size:21
Alignment explanation
Indices: 650151--650238 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
650141 TCAAAATTGC
* *
650151 TTGAATGGTCTTTGAACTTGT
1 TTGAATGGTTTTTAAACTTGT
* * * * *
650172 TTGATTGATTTTTGAAGTTAT
1 TTGAATGGTTTTTAAACTTGT
650193 TTGAATGAGTTTTTTAAACTTGT
1 TTGAATG-G-TTTTTAAACTTGT
* *
650216 TTGAATTGTTCTTAAACTTGT
1 TTGAATGGTTTTTAAACTTGT
650237 TT
1 TT
650239 AAATAAGGCT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 36 0.68
22 1 0.02
23 16 0.30
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.53
Consensus pattern (21 bp):
TTGAATGGTTTTTAAACTTGT
Found at i:650968 original size:64 final size:65
Alignment explanation
Indices: 650895--651018 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 65
650885 AAAAAAGAAA
* * * *
650895 AAGTTATACCTTAGCCC-CTAAAAGGTAGTATTTAGAGGTTGCGCTTGATCTTT-AAAAGGCATA
1 AAGTTATACCTTAGCCCTC-AAAAGGTAATATTTAAAGGTTGCGCTTAAACTTTGAAAAGGCATA
650958 G
65 G
* * *
650959 AAGTTATACCTTAGCCTTCAAAAGGTAATGTTTAAAGGTTGTGCTTAAACTTTGAAAAGG
1 AAGTTATACCTTAGCCCTCAAAAGGTAATATTTAAAGGTTGCGCTTAAACTTTGAAAAGG
651019 AAATGGTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 44 0.86
65 7 0.14
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (65 bp):
AAGTTATACCTTAGCCCTCAAAAGGTAATATTTAAAGGTTGCGCTTAAACTTTGAAAAGGCATAG
Found at i:651072 original size:28 final size:28
Alignment explanation
Indices: 651000--651072 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
650990 TTAAAGGTTG
* * *
651000 TGCTTAAACTTTGAAAAGGAAATGGTTA
1 TGCTTGAACCTTGAAAAGGAAATGATTA
* **
651028 TGCTTGATCCTCAAAAAGGAAATGATTA
1 TGCTTGAACCTTGAAAAGGAAATGATTA
651056 TGCTTGAACCTTGAAAA
1 TGCTTGAACCTTGAAAA
651073 AGCATTGTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (28 bp):
TGCTTGAACCTTGAAAAGGAAATGATTA
Found at i:653363 original size:22 final size:21
Alignment explanation
Indices: 653306--653391 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
653296 TCAAAATTAC
* *
653306 TTGAATGA-TCTTTAAACATGT
1 TTGAATGAGT-TTTGAACTTGT
*
653327 TTGAATGA-TTTTGAAGTTGT
1 TTGAATGAGTTTTGAACTTGT
*
653347 TTGAATGAGTTTTTGAACTTCT
1 TTGAATGAG-TTTTGAACTTGT
*
653369 TTGAAT-AGGTTTTAAACTTGT
1 TTGAATGA-GTTTTGAACTTGT
653390 TT
1 TT
653392 ATTTAAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 16 0.29
21 22 0.40
22 17 0.31
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.49
Consensus pattern (21 bp):
TTGAATGAGTTTTGAACTTGT
Found at i:653768 original size:21 final size:21
Alignment explanation
Indices: 653729--653768 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
653719 AGTGAGTTAT
* * *
653729 TTTAATTTTATGATTATTTCC
1 TTTAATTTGATCATAATTTCC
653750 TTTAATTTGATCATAATTT
1 TTTAATTTGATCATAATTT
653769 ATTAGTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTAATTTGATCATAATTTCC
Found at i:662785 original size:12 final size:12
Alignment explanation
Indices: 662768--662792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
662758 CCTTTACATG
662768 TTATATATATAT
1 TTATATATATAT
662780 TTATATATATAT
1 TTATATATATAT
662792 T
1 T
662793 CAAAGTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATATATAT
Found at i:664184 original size:19 final size:19
Alignment explanation
Indices: 664135--664182 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
664125 TTAATATTTT
*
664135 AATAATATTTTATTCATAA
1 AATATTATTTTATTCATAA
*
664154 AATATTATTTTATTTA-AA
1 AATATTATTTTATTCATAA
*
664172 AATATTCTTTT
1 AATATTATTTT
664183 TACCTATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:669154 original size:20 final size:20
Alignment explanation
Indices: 669129--669188 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
669119 GATACATCTC
669129 CAAAATGTATCAATACATTT
1 CAAAATGTATCAATACATTT
* * *
669149 CAAAATATATCGATACATTC
1 CAAAATGTATCAATACATTT
669169 CAAAATGTAT-AGATACATTT
1 CAAAATGTATCA-ATACATTT
669189 GGTCTAGAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (20 bp):
CAAAATGTATCAATACATTT
Found at i:669185 original size:40 final size:41
Alignment explanation
Indices: 669108--669188 Score: 130
Period size: 40 Copynumber: 2.0 Consensus size: 41
669098 TAGTTCTACC
*
669108 CAAAATATATGGATACATCTCCAAAATGTATCAATACATTT
1 CAAAATATATCGATACATCTCCAAAATGTATCAATACATTT
669149 CAAAATATATCGATACAT-TCCAAAATGTAT-AGATACATTT
1 CAAAATATATCGATACATCTCCAAAATGTATCA-ATACATTT
669189 GGTCTAGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
39 1 0.03
40 20 0.53
41 17 0.45
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (41 bp):
CAAAATATATCGATACATCTCCAAAATGTATCAATACATTT
Found at i:669715 original size:28 final size:28
Alignment explanation
Indices: 669693--669761 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
669683 GTGCTTAAAA
669693 CTTGAAAAGGCAATGGTTATGCTTGATC
1 CTTGAAAAGGCAATGGTTATGCTTGATC
* * *
669721 CTTGAAAAAAGCAATGGCTATACTTGATC
1 CTTG-AAAAGGCAATGGTTATGCTTGATC
669750 CTTGAAAAGGCA
1 CTTGAAAAGGCA
669762 TTATATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (28 bp):
CTTGAAAAGGCAATGGTTATGCTTGATC
Found at i:683231 original size:20 final size:20
Alignment explanation
Indices: 683206--683262 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
683196 TTTCTCTATG
*
683206 ATGTATCGATACATTTAGAA
1 ATGTATCGATACATCTAGAA
*
683226 ATGTATCGATACATCTAGCA
1 ATGTATCGATACATCTAGAA
683246 ATGTATCGATACATCTA
1 ATGTATCGATACATCTA
683263 CCCTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATCTAGAA
Found at i:685183 original size:21 final size:21
Alignment explanation
Indices: 685158--685201 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
685148 TCAAAATTAC
*
685158 TTGAATGACCTTTGAATTTGT
1 TTGAATGACCTTTGAAGTTGT
**
685179 TTGAATGATTTTTGAAGTTGT
1 TTGAATGACCTTTGAAGTTGT
685200 TT
1 TT
685202 AAATAAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (21 bp):
TTGAATGACCTTTGAAGTTGT
Found at i:685212 original size:21 final size:22
Alignment explanation
Indices: 685168--685259 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 22
685158 TTGAATGACC
* * *
685168 TTTGAATTTGTTTGAATGA-TT
1 TTTGAAGTTGTTTAAATAAGTT
685189 TTTGAAGTTGTTTAAATAAGTT
1 TTTGAAGTTGTTTAAATAAGTT
*
685211 TTTGAA-TGTGTTTGAAT-AGTT
1 TTTGAAGT-TGTTTAAATAAGTT
* * *
685232 TTTAAACTTGTTTAATTAAG-T
1 TTTGAAGTTGTTTAAATAAGTT
685253 TTTGAAG
1 TTTGAAG
685260 ATCCTAAGTG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
21 39 0.67
22 19 0.33
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.52
Consensus pattern (22 bp):
TTTGAAGTTGTTTAAATAAGTT
Found at i:685216 original size:43 final size:43
Alignment explanation
Indices: 685168--685255 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
685158 TTGAATGACC
* * *
685168 TTTGAATTTGTTTGAAT-GATTTTTGAAGTTGTTTAAATAAGTT
1 TTTGAATGTGTTTGAATAG-TTTTTAAACTTGTTTAAATAAGTT
*
685211 TTTGAATGTGTTTGAATAGTTTTTAAACTTGTTTAATTAAGTT
1 TTTGAATGTGTTTGAATAGTTTTTAAACTTGTTTAAATAAGTT
685254 TT
1 TT
685256 GAAGATCCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 39 0.98
44 1 0.03
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.55
Consensus pattern (43 bp):
TTTGAATGTGTTTGAATAGTTTTTAAACTTGTTTAAATAAGTT
Found at i:685283 original size:139 final size:138
Alignment explanation
Indices: 685125--685376 Score: 348
Period size: 139 Copynumber: 1.8 Consensus size: 138
685115 CTAAATTGTA
* *
685125 TAAGTGTTTCCATGTGAAAA-TGATCAAAATTACTTGAATGACCTTTGAATTTGTTTGAATGATT
1 TAAGTGTTTCCATGTGAAAAGT-ATCAAAATTACTTGAATGACCTTTGAAATTGCTTGAATGATT
* * *
685189 TTTGAAGTTGTTTAAATAAGTTTTTGAA-TGTGTTTGAA-TAGTTTTTAAACTTGTTTAATTAAG
65 TTTGAACTTGTTTAAAT-AGTTTTTAAACT-TGTTTAAATTAG-TTTTAAACTTGTTTAATTAAG
685252 TTTTGAAGATCC
127 TTTTGAAGATCC
* * * **
685264 TAAGTGTTTCCATGTGAAAAGTTTTAAAATTGCTTGAATGAGTTTTGAAATTGCTTGAATGATTT
1 TAAGTGTTTCCATGTGAAAAGTATCAAAATTACTTGAATGACCTTTGAAATTGCTTGAATGATTT
*
685329 TTGAACTTGTTTGAATAGTTTTTAAACTTGTTTAAATTAGTTTTAAAC
66 TTGAACTTGTTTAAATAGTTTTTAAACTTGTTTAAATTAGTTTTAAAC
685377 CTCCCTTGCA
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
138 24 0.24
139 74 0.75
140 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (138 bp):
TAAGTGTTTCCATGTGAAAAGTATCAAAATTACTTGAATGACCTTTGAAATTGCTTGAATGATTT
TTGAACTTGTTTAAATAGTTTTTAAACTTGTTTAAATTAGTTTTAAACTTGTTTAATTAAGTTTT
GAAGATCC
Found at i:685376 original size:21 final size:21
Alignment explanation
Indices: 685283--685376 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
685273 CCATGTGAAA
*
685283 AGTTTTAAAATTGCTTGAATG
1 AGTTTTAAACTTGCTTGAATG
685304 AGTTTTGAAA-TTGCTTGAATG
1 AGTTTT-AAACTTGCTTGAATG
* * *
685325 ATTTTTGAACTTGTTTGAAT-
1 AGTTTTAAACTTGCTTGAATG
* * *
685345 AGTTTTTAAACTTGTTTAAATT
1 AG-TTTTAAACTTGCTTGAATG
685367 AGTTTTAAAC
1 AGTTTTAAAC
685377 CTCCCTTGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.05
21 55 0.87
22 5 0.08
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
AGTTTTAAACTTGCTTGAATG
Found at i:685540 original size:21 final size:21
Alignment explanation
Indices: 685516--685564 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
685506 ATGATTCTAC
685516 CCAAAATGTATGGATACATTT
1 CCAAAATGTATGGATACATTT
* *
685537 CCAAAATATATTGATACATTT
1 CCAAAATGTATGGATACATTT
685558 -CAAAATG
1 CCAAAATG
685565 CCTCAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
CCAAAATGTATGGATACATTT
Found at i:691328 original size:50 final size:49
Alignment explanation
Indices: 691253--691350 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
691243 CAACTACTCG
* * * *
691253 TGGGAACTTCCCATACCACCAAATATAAGTTC-GGGCTTCAAGTGCCCCTT
1 TGGGAAATCCCCACACCACCAAATATAAG-TCAGGGATTCAAGT-CCCCTT
691303 TGGGAAATCCCCACACCACCAAATATAAGTCAGGGATTCAAGTCCCCT
1 TGGGAAATCCCCACACCACCAAATATAAGTCAGGGATTCAAGTCCCCT
691351 CCAGAATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 7 0.16
50 36 0.84
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (49 bp):
TGGGAAATCCCCACACCACCAAATATAAGTCAGGGATTCAAGTCCCCTT
Found at i:695046 original size:28 final size:28
Alignment explanation
Indices: 695003--695078 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
694993 TGTTTAAAGA
695003 TTGTGCTTGAACCTTGAAAAAGCAATGG
1 TTGTGCTTGAACCTTGAAAAAGCAATGG
** *
695031 TTGTGCTTGATTCTTGAAAAGGCAATGG
1 TTGTGCTTGAACCTTGAAAAAGCAATGG
* * *
695059 TTATACTTGAACCTTTAAAA
1 TTGTGCTTGAACCTTGAAAA
695079 GGCATTGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (28 bp):
TTGTGCTTGAACCTTGAAAAAGCAATGG
Found at i:703820 original size:155 final size:157
Alignment explanation
Indices: 703657--703942 Score: 495
Period size: 155 Copynumber: 1.8 Consensus size: 157
703647 AATTTGAGAT
* * *
703657 GAAGTATTTTACAACATTATTTCAAACTTTAATATTGTGGATAAATAATAATCCTAAGAAAAGAT
1 GAAGTATTTTACAACATTATTTCAAACTTCAATACTGTGGATAAATAATAATCCTAAGAAAAAAT
* *
703722 TGTCTTATTGATGAAACATTTTCACAATGTTAACTATCAAATAATG-A-AGCAAATTTAAAAAAA
66 TGTCTTATTGATGAAACATTTTCACAATATCAACTATCAAATAATGAAGAGCAAATTTAAAAAAA
703785 AAAAAAATTATAGTGTTTGACACAGAG
131 AAAAAAATTATAGTGTTTGACACAGAG
*
703812 GAAGTATTTTACAACATTATTTCAAACTTCAATACTGTGTATAAATAATAATCCTAAGAAAAAAT
1 GAAGTATTTTACAACATTATTTCAAACTTCAATACTGTGGATAAATAATAATCCTAAGAAAAAAT
*
703877 TGTCTTATTGATGAAACATTTTCACAATATCAACTATCAAATAATGAAGAGCAAATTTTAAAAAA
66 TGTCTTATTGATGAAACATTTTCACAATATCAACTATCAAATAATGAAGAGCAAATTTAAAAAAA
703942 A
131 A
703943 TATAGTAGAA
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
155 105 0.86
156 1 0.01
157 16 0.13
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (157 bp):
GAAGTATTTTACAACATTATTTCAAACTTCAATACTGTGGATAAATAATAATCCTAAGAAAAAAT
TGTCTTATTGATGAAACATTTTCACAATATCAACTATCAAATAATGAAGAGCAAATTTAAAAAAA
AAAAAAATTATAGTGTTTGACACAGAG
Found at i:708596 original size:15 final size:16
Alignment explanation
Indices: 708571--708607 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
708561 CGATAACAAG
708571 TAAAA-AAAATATT-T
1 TAAAATAAAATATTAT
708585 TAAAATAAAATATTAT
1 TAAAATAAAATATTAT
708601 TAAAATA
1 TAAAATA
708608 TTAATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATAAAATATTAT
Found at i:710339 original size:19 final size:18
Alignment explanation
Indices: 710301--710348 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
710291 ATTAATTTTT
*
710301 AATAATATTTTATTCAAAA
1 AATATTATTTTATTC-AAA
**
710320 AATATTATTTTATTTTAA
1 AATATTATTTTATTCAAA
*
710338 AATATTCTTTT
1 AATATTATTTT
710349 TACTTGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTATTTTATTCAAA
Found at i:718154 original size:2 final size:2
Alignment explanation
Indices: 718147--718202 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
718137 TTTGCAAAGG
*
718147 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
718189 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
718203 AATTATTACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:720372 original size:34 final size:37
Alignment explanation
Indices: 720303--720372 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
720293 ATTATAAAAG
720303 AATATAATTACTATTATATTTATATAGTTTTAACATA
1 AATATAATTACTATTATATTTATATAGTTTTAACATA
* *
720340 AATATATTTACT-TTCTATTT-TAT-GTTTTAACAT
1 AATATAATTACTATTATATTTATATAGTTTTAACAT
720373 TACAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 10 0.32
35 3 0.10
36 7 0.23
37 11 0.35
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (37 bp):
AATATAATTACTATTATATTTATATAGTTTTAACATA
Found at i:720670 original size:25 final size:26
Alignment explanation
Indices: 720621--720679 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
720611 AATTTATAAG
720621 AAATATATTTACTATTATATATACTA
1 AAATATATTTACTATTATATATACTA
* * *
720647 AAATATTTTTAGTA-TATATATACTTT
1 AAATATATTTACTATTATATATAC-TA
720673 AAATATA
1 AAATATA
720680 AGTATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATATATTTACTATTATATATACTA
Found at i:720906 original size:342 final size:340
Alignment explanation
Indices: 720323--721445 Score: 1024
Period size: 357 Copynumber: 3.2 Consensus size: 340
720313 CTATTATATT
* * * * * *
720323 TATATAGTTTTAACATAAATATATTTACTTTCTATTTTATGTTTTAACATTACAAAAATTATGAT
1 TATATACTTTAAATATAAATATATTTACTTTTTA-TTT-TGTGTTAACATTACAAAAATTATAAT
* * * * * * * ** * *
720388 TTATAAAATTATTAATTATAATACATATACCATTATTTATATAAATTTATAATGTATATACTTAA
64 TTATAAAATTATTAATTATAATATAAATACCTTTGTTAATATAAACTTAGAACATATAAACCTAA
* * * * * ** * * * *
720453 AA-AAAGCTTTTGAGATTAGAATTGTTTTG-GAACCTAACTT-T-T-TTTTTAATTTCATGAAAT
129 AAGGAAG-TTATAAAATTA-AAATAATTTGAAAACGT-AGTTATCTGTTTTTAATTTCATGTAAT
* * * * *
720513 TAAGGACAAATCATATAGTTAATTATATTAATTGATGAAACTATTATTATTAATTAACTTTTAAT
191 TAAGAACAAATCATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAAT
* * ********** * *
720578 GTCTTTCAATATATATAGTNNNNNNNNNNT-GTTAATTTATAAGAAATATATTTACTATTATATA
256 GTCTTTAAATATATATACTACATAGACATTAGTTCATTTATAAGAAATATAATTACTATTATATA
720642 TACTAAAATATTTTTAGTATA
321 TA-TAAAATATTTTTAGTATA
* * *
720663 TATATACTTTAAATATAAGTATATTTTCTTTTTATTTTGTGTTAACATTTC-AAAATTATAATTT
1 TATATACTTTAAATATAAATATATTTACTTTTTATTTTGTGTTAACATTACAAAAATTATAATTT
* * *
720727 ATAAAATTATTAATTATAATATATATATAACTTTTGTTTATATAAACTTAGAATATATAAACCT-
66 ATAAAATTATTAATTATAATATA-A-AT-ACCTTTGTTAATATAAACTTAGAACATATAAACCTA
* *
720791 AAAGTGAAGTTGTAAAATTAAAATAATTTTAAAACGTAGTTA-CTGTTTTTAATTTCATGTAATT
128 AAAG-GAAGTTATAAAATTAAAATAATTTGAAAACGTAGTTATCTGTTTTTAATTTCATGTAATT
*
720855 AAGAACAAATTCATATAGTTAATTAAATTAATTTATGAAACTATAATTATTAATTAACTTGTAAT
192 AAGAACAAA-TCATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAAT
* * * *
720920 GTCTTTTAATATATATACTTTATTTACATATATATTAAGTTCATTTATAAGGAATATAATTACTT
256 GTC-TTTAA-ATATATA---TA-CTACATAGACATT-AGTTCATTTATAAGAAATATAATTAC-T
* * *
720985 ATATATATATATATATATATGAGTGTGTATGTGTA
313 AT-TATATATATA-A-A-AT-A-TTTTTA-GTATA
* * *
721020 TATGTACTTTAAATATAAATATATTTACTTTTTATTTTGTGTCAACAATACAAAAATTATAATTT
1 TATATACTTTAAATATAAATATATTTACTTTTTATTTTGTGTTAACATTACAAAAATTATAATTT
* *
721085 ATAAAATTATTAATTATAATATAAATACCTTTGTTAATATAAACTTATAACATATAAATCTAAAA
66 ATAAAATTATTAATTATAATATAAATACCTTTGTTAATATAAACTTAGAACATATAAACCTAAAA
* * * * * * * * * *
721150 GGAAGTTATGATATTAGAATAGTTTGGAAACTTAGTTATTTTTTTTTTAATTTCTTGTCATTAA-
131 GGAAGTTATAAAATTAAAATAATTTGAAAACGTAGTTA-TCTGTTTTTAATTTCATGTAATTAAG
* * * * * * *
721214 AGATAAACCTATATAGTTAATTAAATTAATTAAAGAAACCATGATTATTAATTGACTTGCAATGT
195 A-ACAAATC-ATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAATGT
* ** *
721279 CTTTTAATATATATACTTTATAGACATTGGGTTCATTTATAAGAAATATAATTACTATTATATAT
258 CTTTAAATATATATACTACATAGACATT-AGTTCATTTATAAGAAATATAATTACTATTATATAT
*
721344 ATTAAAATACTTTTAGTATA
322 A-TAAAATATTTTTAGTATA
* * * * *
721364 TATACACTTTAAATATAAATATATTTACTTTCTATTTTGTTTTAACATTACAAAAATTATAACTA
1 TATATACTTTAAATATAAATATATTTACTTTTTATTTTGTGTTAACATTACAAAAATTATAATTT
* *
721429 ATTAATTTATTAATTAT
66 ATAAAATTATTAATTAT
721446 GTTAGAGATA
Statistics
Matches: 642, Mismatches: 108, Indels: 62
0.79 0.13 0.08
Matches are distributed among these distances:
337 34 0.05
338 12 0.02
339 17 0.03
340 68 0.11
341 29 0.05
342 54 0.08
343 4 0.01
344 83 0.13
345 3 0.00
346 1 0.00
347 4 0.01
348 3 0.00
349 9 0.01
350 27 0.04
351 37 0.06
352 11 0.02
353 1 0.00
354 2 0.00
355 67 0.10
356 16 0.02
357 124 0.19
358 36 0.06
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (340 bp):
TATATACTTTAAATATAAATATATTTACTTTTTATTTTGTGTTAACATTACAAAAATTATAATTT
ATAAAATTATTAATTATAATATAAATACCTTTGTTAATATAAACTTAGAACATATAAACCTAAAA
GGAAGTTATAAAATTAAAATAATTTGAAAACGTAGTTATCTGTTTTTAATTTCATGTAATTAAGA
ACAAATCATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAATGTCTT
TAAATATATATACTACATAGACATTAGTTCATTTATAAGAAATATAATTACTATTATATATATAA
AATATTTTTAGTATA
Found at i:722941 original size:30 final size:30
Alignment explanation
Indices: 722884--723040 Score: 189
Period size: 31 Copynumber: 5.3 Consensus size: 30
722874 AATATGTTTG
*
722884 TCTTAATTTAGACAA-AAAAATATTTTTTG
1 TCTTAATTTAGACAAGAAAAATATTTTTTA
722913 TCTTAATTTAAGACAAGAAAAATATTTTTTA
1 TCTTAATTT-AGACAAGAAAAATATTTTTTA
722944 TCTTAATTTAAGACAAGAAAAATATTTTTTA
1 TCTTAATTT-AGACAAGAAAAATATTTTTTA
* **
722975 TCTTAATCTAGATTAGAAAACATA--TTTT-
1 TCTTAATTTAGACAAGAAAA-ATATTTTTTA
* *
723003 TCTGAATATAGACAAGATAAAATA-TTTTTA
1 TCTTAATTTAGACAAGA-AAAATATTTTTTA
723033 TCTTAATT
1 TCTTAATT
723041 AAAAACTAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.14
29 20 0.18
30 21 0.19
31 55 0.49
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (30 bp):
TCTTAATTTAGACAAGAAAAATATTTTTTA
Found at i:727983 original size:21 final size:22
Alignment explanation
Indices: 727948--727991 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
727938 CTCTTAAAGT
727948 AATTTAAAATAAAATAACATAA
1 AATTTAAAATAAAATAACATAA
* *
727970 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACATAA
727991 A
1 A
727992 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACATAA
Found at i:728836 original size:23 final size:23
Alignment explanation
Indices: 728810--728858 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
728800 TATATTATAC
728810 ATAATATTATATA-AATTTTAATA
1 ATAATATTATATATAA-TTTAATA
* *
728833 ATAATTTTATTTATAATTTAATA
1 ATAATATTATATATAATTTAATA
728856 ATA
1 ATA
728859 TTAATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATATTATATATAATTTAATA
Found at i:729377 original size:14 final size:15
Alignment explanation
Indices: 729350--729379 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
729340 ATATGTTAAT
729350 TTTATATAGTATATA
1 TTTATATAGTATATA
729365 TTTATAT-GTATATA
1 TTTATATAGTATATA
729379 T
1 T
729380 AGCTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTATATAGTATATA
Found at i:730002 original size:2 final size:2
Alignment explanation
Indices: 729995--730023 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
729985 AATACAAGTT
729995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
730024 TCTATTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:730600 original size:14 final size:14
Alignment explanation
Indices: 730581--730611 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
730571 TTGGCTCCAA
730581 AAAAATTTCATTGG
1 AAAAATTTCATTGG
*
730595 AAAAATTTCGTTGG
1 AAAAATTTCATTGG
730609 AAA
1 AAA
730612 TTTGTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (14 bp):
AAAAATTTCATTGG
Found at i:734160 original size:4 final size:4
Alignment explanation
Indices: 734151--734202 Score: 52
Period size: 4 Copynumber: 12.2 Consensus size: 4
734141 TTCTAACTTA
*
734151 ATTT ATTT ATTT ACTGTT AGTT ATTTT ATTT ATTT ATTT ATGTT -TTT
1 ATTT ATTT ATTT A-T-TT ATTT A-TTT ATTT ATTT ATTT AT-TT ATTT
734198 ATTT A
1 ATTT A
734203 ATTACCAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 2 0.05
4 30 0.73
5 6 0.15
6 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:750460 original size:19 final size:20
Alignment explanation
Indices: 750427--750479 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
750417 CCTATCAAGC
*
750427 ATGTATTGTTACATT-TGCTA
1 ATGTATTGATACATTAT-CTA
750447 ATGTA-TGATACATTATCTA
1 ATGTATTGATACATTATCTA
750466 ATGTATTGATACAT
1 ATGTATTGATACAT
750480 ATAGCCTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (20 bp):
ATGTATTGATACATTATCTA
Found at i:753903 original size:11 final size:10
Alignment explanation
Indices: 753885--753916 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
753875 ATGATTAGTA
753885 AGAAAAAAAG
1 AGAAAAAAAG
753895 AGAAAAAAAG
1 AGAAAAAAAG
753905 AGAAAAAGAAG
1 AGAAAAA-AAG
753916 A
1 A
753917 AGTTCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:754847 original size:89 final size:89
Alignment explanation
Indices: 754746--755060 Score: 257
Period size: 89 Copynumber: 3.5 Consensus size: 89
754736 AGTTATGCAT
* *
754746 CCTCATAT-CAAATGAGGAG-TTGATTACTGTTTAAAGTTACATAGCCTCATTCCAAATAAGAAG
1 CCTCAT-TCCAAATGAGGAGCTT-ATTACTATTTAAAGTTACGTAGCCTCATTCCAAATAAGAAG
* *
754809 CTTATTCTTTCTTTAAAGCTACATAG
64 CTTATTCATTCTTTAAAGATACATAG
* * ** * *
754835 CCTCATTCCAAATGAGGAGCTTA-TATTTATTTAAAGTTATGTAATCTCATTCCAGATAAGGAGC
1 CCTCATTCCAAATGAGGAGCTTATTA-CTATTTAAAGTTACGTAGCCTCATTCCAAATAAGAAGC
**
754899 TTATTCATTCTTTAAAGATATGTAG
65 TTATTCATTCTTTAAAGATACATAG
* * * * * * *
754924 CGTTATTCCAAATGAGGAGCTTATT-CTTTCTTTAAAGTTACGTAGCCTCATTCTAGATGAGGAG
1 CCTCATTCCAAATGAGGAGCTTATTAC--TATTTAAAGTTACGTAGCCTCATTCCAAATAAGAAG
* *
754988 CTCATTC-TTATTTAAAG-T-CATGCAG
64 CTTATTCATTCTTTAAAGATACAT--AG
* * * * * * *
755013 TCTTATTCTAGATGAGGAGCTTATTCCATTTTTAAAGTTACATAGCCT
1 CCTCATTCCAAATGAGGAGCTTATTAC-TATTTAAAGTTACGTAGCCT
755061 TATCTAGATG
Statistics
Matches: 185, Mismatches: 32, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
87 1 0.01
88 4 0.02
89 140 0.76
90 40 0.22
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (89 bp):
CCTCATTCCAAATGAGGAGCTTATTACTATTTAAAGTTACGTAGCCTCATTCCAAATAAGAAGCT
TATTCATTCTTTAAAGATACATAG
Found at i:755067 original size:44 final size:44
Alignment explanation
Indices: 754702--755078 Score: 270
Period size: 44 Copynumber: 8.5 Consensus size: 44
754692 AGTTTCGTAA
* * *
754702 CCTTATTCTAGATGAGGAGCTTATTCCTATTTAAAGTTATGCAT--
1 CCTTATTCCAGATGAGGAGCTTATTCTTCTTTAAAGTTA--CATAG
* * *
754746 CCTCATAT-CAAATGAGGAG-TTGATTAC-TGTTTAAAGTTACATAG
1 CCTTAT-TCCAGATGAGGAGCTT-ATT-CTTCTTTAAAGTTACATAG
* * * * *
754790 CCTCATTCCAAATAAGAAGCTTATTCTTTCTTTAAAGCTACATAG
1 CCTTATTCCAGATGAGGAGCTTATTC-TTCTTTAAAGTTACATAG
* * * ** *
754835 CCTCATTCCAAATGAGGAGCTTATAT-TTATTTAAAGTTATGTAA
1 CCTTATTCCAGATGAGGAGCTTAT-TCTTCTTTAAAGTTACATAG
* * * * **
754879 TCTCATTCCAGATAAGGAGCTTATTCATTCTTTAAAGATATGTAG
1 CCTTATTCCAGATGAGGAGCTTATTC-TTCTTTAAAGTTACATAG
* * *
754924 CGTTATTCCAAATGAGGAGCTTATTCTTTCTTTAAAGTTACGTAG
1 CCTTATTCCAGATGAGGAGCTTATTC-TTCTTTAAAGTTACATAG
* * * *
754969 CCTCATTCTAGATGAGGAGCTCATTCTTATTTAAAG-T-CATGCAG
1 CCTTATTCCAGATGAGGAGCTTATTCTTCTTTAAAGTTACAT--AG
* *
755013 TCTTATTCTAGATGAGGAGCTTATTCCATT-TTTAAAGTTACATAG
1 CCTTATTCCAGATGAGGAGCTTATT-C-TTCTTTAAAGTTACATAG
*
755058 CCTTA-TCTAGATGAGGAGCTT
1 CCTTATTCCAGATGAGGAGCTT
755079 TATTTTTGAA
Statistics
Matches: 275, Mismatches: 40, Indels: 36
0.78 0.11 0.10
Matches are distributed among these distances:
42 5 0.02
43 6 0.02
44 129 0.47
45 128 0.47
46 4 0.01
47 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (44 bp):
CCTTATTCCAGATGAGGAGCTTATTCTTCTTTAAAGTTACATAG
Found at i:755082 original size:45 final size:44
Alignment explanation
Indices: 754702--755078 Score: 270
Period size: 45 Copynumber: 8.5 Consensus size: 44
754692 AGTTTCGTAA
*
754702 CCTTATTCTAGATGAGGAGCTTATTCCTATTTAAAGTTATGCAT--
1 CCTTATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTA--CATAG
* * *
754746 CCTCATATC-AAATGAGGAG-TTGATTAC-TGTTTAAAGTTACATAG
1 CCTTAT-TCTAGATGAGGAGCTT-ATT-CTTATTTAAAGTTACATAG
* * * * * * *
754790 CCTCATTCCAAATAAGAAGCTTATTCTTTCTTTAAAGCTACATAG
1 CCTTATTCTAGATGAGGAGCTTATTC-TTATTTAAAGTTACATAG
* * * ** *
754835 CCTCATTCCAAATGAGGAGCTTATAT-TTATTTAAAGTTATGTAA
1 CCTTATTCTAGATGAGGAGCTTAT-TCTTATTTAAAGTTACATAG
* * * * * * **
754879 TCTCATTCCAGATAAGGAGCTTATTCATTCTTTAAAGATATGTAG
1 CCTTATTCTAGATGAGGAGCTTATTC-TTATTTAAAGTTACATAG
* * * * *
754924 CGTTATTCCAAATGAGGAGCTTATTCTTTCTTTAAAGTTACGTAG
1 CCTTATTCTAGATGAGGAGCTTATTC-TTATTTAAAGTTACATAG
* *
754969 CCTCATTCTAGATGAGGAGCTCATTCTTATTTAAAG-T-CATGCAG
1 CCTTATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTACAT--AG
*
755013 TCTTATTCTAGATGAGGAGCTTATTCCATT-TTTAAAGTTACATAG
1 CCTTATTCTAGATGAGGAGCTTATT-C-TTATTTAAAGTTACATAG
755058 CCTTA-TCTAGATGAGGAGCTT
1 CCTTATTCTAGATGAGGAGCTT
755079 TATTTTTGAA
Statistics
Matches: 276, Mismatches: 39, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
42 5 0.02
43 7 0.03
44 128 0.46
45 129 0.47
46 4 0.01
47 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (44 bp):
CCTTATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTACATAG
Found at i:755082 original size:134 final size:131
Alignment explanation
Indices: 754690--755078 Score: 435
Period size: 134 Copynumber: 2.9 Consensus size: 131
754680 AAGATGTAAA
* * * *
754690 AAAGTTTCGTAACCTTATTCTAGATGAGGAGCTTATTCCTATTTAAAGTTATGCATCCTCATATC
1 AAAGTTACGTAGCCTCATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTATGCAT-CTCAT-TC
* * * * *
754755 AAATGAGGAG-TTGATT-ACTGTTTAAAGTTACATAGCCTCATTCCAAATAAGAAGCTTATTCTT
64 AGATGAGGAGCTT-ATTCA-TTTTTAAAGTTACATAGCCTTATTCCAAATGAGGAGCTTATTCTT
754818 TCTTT
127 TCTTT
* * * * *
754823 AAAGCTACATAGCCTCATTCCAAATGAGGAGCTTATAT-TTATTTAAAGTTATGTAATCTCATTC
1 AAAGTTACGTAGCCTCATTCTAGATGAGGAGCTTAT-TCTTATTTAAAGTTATG-CATCTCATT-
* * ** *
754887 CAGATAAGGAGCTTATTCATTCTTTAAAGATATGTAGCGTTATTCCAAATGAGGAGCTTATTCTT
63 CAGATGAGGAGCTTATTCATT-TTTAAAGTTACATAGCCTTATTCCAAATGAGGAGCTTATTCTT
754952 TCTTT
127 TCTTT
* * *
754957 AAAGTTACGTAGCCTCATTCTAGATGAGGAGCTCATTCTTATTTAAAGTCATGCAGTCTTATTCT
1 AAAGTTACGTAGCCTCATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTATGCA-TCTCATTC-
* *
755022 AGATGAGGAGCTTATTCCATTTTTAAAGTTACATAGCCTTA-TCTAGATGAGGAGCTT
64 AGATGAGGAGCTTATT-CATTTTTAAAGTTACATAGCCTTATTCCAAATGAGGAGCTT
755079 TATTTTTGAA
Statistics
Matches: 212, Mismatches: 34, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
132 1 0.00
133 78 0.37
134 129 0.61
135 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (131 bp):
AAAGTTACGTAGCCTCATTCTAGATGAGGAGCTTATTCTTATTTAAAGTTATGCATCTCATTCAG
ATGAGGAGCTTATTCATTTTTAAAGTTACATAGCCTTATTCCAAATGAGGAGCTTATTCTTTCTT
T
Found at i:758200 original size:3 final size:3
Alignment explanation
Indices: 758192--758227 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
758182 CAAACATAGT
* *
758192 TAC TAC TAC TAC TAC TAC TAC TGC TAC TAT TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
758228 CAAAGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:758924 original size:20 final size:21
Alignment explanation
Indices: 758887--758927 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
758877 TCTTGCCACT
758887 TTTTTTTTTGAAAATTTTTTA
1 TTTTTTTTTGAAAATTTTTTA
*
758908 TTTTTTTTTG-AATTTTTTTA
1 TTTTTTTTTGAAAATTTTTTA
758928 CATGTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTGAAAATTTTTTA
Found at i:760402 original size:21 final size:21
Alignment explanation
Indices: 760341--760402 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
760331 TTGAATGGTG
* * *
760341 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTGTCATGAAT
*
760362 GCATCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
* *
760383 GCATTAGTCTTTGTCGTGAA
1 GCATCAGTCTTTGTCATGAA
760403 CTACATGAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:765164 original size:28 final size:28
Alignment explanation
Indices: 765132--765296 Score: 186
Period size: 29 Copynumber: 5.7 Consensus size: 28
765122 ATGACAACTT
* *
765132 AAACATGTATGTCTTAATTTAGACAATA
1 AAACATGTTTGTCTTAATTTAGACAAGA
*
765160 AAACATGTTTGGTCTTAATTTAGACAAAA
1 AAACATGTTT-GTCTTAATTTAGACAAGA
*
765189 AAATATGTTTGTCTTAATTTAAGACAAGA
1 AAACATGTTTGTCTTAATTT-AGACAAGA
* *
765218 AAACTATGTTTTGTCTTAATCTAGATAAGA
1 AAAC-ATG-TTTGTCTTAATTTAGACAAGA
* *
765248 AAACATATTTGTCTCAATTTAGACAAGA
1 AAACATGTTTGTCTTAATTTAGACAAGA
* *
765276 TAACATATTTTTGTCTTAATT
1 -AA-ACATGTTTGTCTTAATT
765297 AAAAGAGTTG
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
28 37 0.32
29 40 0.34
30 28 0.24
31 12 0.10
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
AAACATGTTTGTCTTAATTTAGACAAGA
Found at i:765259 original size:59 final size:58
Alignment explanation
Indices: 765132--765295 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 58
765122 ATGACAACTT
* * * *
765132 AAACATGTATGTCTTAATTTAGACAATAAAAC-ATGTTTGGTCTTAATTTAGACAAAA
1 AAACATGTTTGTCTTAATTTAGACAAGAAAACTATGTTTTGTCTTAATCTAGACAAAA
* * *
765189 AAATATGTTTGTCTTAATTTAAGACAAGAAAACTATGTTTTGTCTTAATCTAGATAAGA
1 AAACATGTTTGTCTTAATTT-AGACAAGAAAACTATGTTTTGTCTTAATCTAGACAAAA
* * *
765248 AAACATATTTGTCTCAATTTAGACAAGATAACATAT-TTTTGTCTTAAT
1 AAACATGTTTGTCTTAATTTAGACAAGAAAAC-TATGTTTTGTCTTAAT
765296 TAAAAGAGTT
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 18 0.19
58 34 0.37
59 41 0.44
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (58 bp):
AAACATGTTTGTCTTAATTTAGACAAGAAAACTATGTTTTGTCTTAATCTAGACAAAA
Found at i:765465 original size:17 final size:17
Alignment explanation
Indices: 765443--765475 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
765433 GATAATAATA
765443 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
765460 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
765476 ATCAAGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:767212 original size:13 final size:13
Alignment explanation
Indices: 767194--767219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
767184 GTAAAGAAAA
767194 ACAAAAAAAAAGT
1 ACAAAAAAAAAGT
767207 ACAAAAAAAAAGT
1 ACAAAAAAAAAGT
767220 CAACATTGAA
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:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
ACAAAAAAAAAGT
Found at i:767687 original size:54 final size:53
Alignment explanation
Indices: 767611--767714 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
767601 TCATATAAAT
*
767611 TCTAAAATACAAAAATGCAAAATAAAAAGAAAAACAAACAATTATTTTATATA
1 TCTAAAATACAAAAATGCAAAATAAAAAGAAAAACAAACAATGATTTTATATA
* * * *
767664 TCTATAAATATAAAATTGCAAAATAAGAAGCAAAACAAACAATGATTTTAT
1 TCTA-AAATACAAAAATGCAAAATAAAAAGAAAAACAAACAATGATTTTAT
767715 TGATCATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.26
Consensus pattern (53 bp):
TCTAAAATACAAAAATGCAAAATAAAAAGAAAAACAAACAATGATTTTATATA
Found at i:769256 original size:17 final size:15
Alignment explanation
Indices: 769229--769276 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
769219 GAGAGAAATA
769229 AAAGGAAAAAAGAATG
1 AAAGG-AAAAAGAATG
769245 AAAGAGAGAAAAGAA-G
1 AAAG-GA-AAAAGAATG
769261 AAAGGAAAGAAGAATG
1 AAAGGAAA-AAGAATG
769277 TAATAGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 7 0.25
16 11 0.39
17 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (15 bp):
AAAGGAAAAAGAATG
Found at i:785145 original size:21 final size:20
Alignment explanation
Indices: 785124--785162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
785114 TGTTTATCCT
785124 TTGAGGAATGTATCCATACC
1 TTGAGGAATGTATCCATACC
* *
785144 TTGGGGAATGTATCGATAC
1 TTGAGGAATGTATCCATAC
785163 ATTTTCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (20 bp):
TTGAGGAATGTATCCATACC
Found at i:800278 original size:64 final size:64
Alignment explanation
Indices: 800168--800330 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
800158 TTATAAGGTC
* * * *
800168 GATGATCATGTGGCATGGCCACTAGAGTTAATTATGTATCTGTGGTGAAGCC-CTCATTATTAAT
1 GATGATTATGTGGCATGACCACTAGAGTTAATTATGTATCTATGGTGAAGCCACT-ATTATCAAT
* * * *
800232 GATGATTATGTGGCATGATCACTTGAGTTAATTATG-AGTAC-ATGGTGAGGCCACTATTATCGA
1 GATGATTATGTGGCATGACCACTAGAGTTAATTATGTA-T-CTATGGTGAAGCCACTATTATCAA
800295 T
64 T
** *
800296 GATGATTAATGTGGCACAACTACTAGAGTTAATTA
1 GATGATT-ATGTGGCATGACCACTAGAGTTAATTA
800331 CGTGTACATG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 56 0.68
65 25 0.30
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (64 bp):
GATGATTATGTGGCATGACCACTAGAGTTAATTATGTATCTATGGTGAAGCCACTATTATCAAT
Found at i:800338 original size:65 final size:65
Alignment explanation
Indices: 800187--800368 Score: 169
Period size: 65 Copynumber: 2.8 Consensus size: 65
800177 GTGGCATGGC
* * * **
800187 CACTAGAGTTAATTA-TGTATCTGTGGTGAAGCC-CTCATTATTAATGATGATT-ATGTGGCATG
1 CACTAGAGTTAATTAGTGTA-C-ATGGTGAGGCCACTCATTATTGATGATGATTAATGTGGCACA
800249 AT
64 AT
* * *
800251 CACTTGAGTTAATTATGAGTACATGGTGAGGCCACT-ATTATCGATGATGATTAATGTGGCACAA
1 CACTAGAGTTAATTA-GTGTACATGGTGAGGCCACTCATTATTGATGATGATTAATGTGGCACAA
800315 -
65 T
** * *
800315 CTACTAGAGTTAATTACGTGTACATGGCAAGGCCACTGA-TATTGATAATGATTA
1 C-ACTAGAGTTAATTA-GTGTACATGGTGAGGCCACTCATTATTGATGATGATTA
800369 TGAGGTGAGA
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 38 0.39
65 55 0.57
66 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (65 bp):
CACTAGAGTTAATTAGTGTACATGGTGAGGCCACTCATTATTGATGATGATTAATGTGGCACAAT
Found at i:801317 original size:21 final size:22
Alignment explanation
Indices: 801288--801331 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
801278 AAGTGATTAA
801288 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
801309 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
801331 T
1 T
801332 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:801996 original size:12 final size:12
Alignment explanation
Indices: 801981--802027 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
801971 AGAGATTTTT
801981 GAGGCAGCAAGA
1 GAGGCAGCAAGA
801993 GAGGCAGCAAGA
1 GAGGCAGCAAGA
802005 GAGGCAGCAA-A
1 GAGGCAGCAAGA
802016 GGAGGCAGCAAG
1 -GAGGCAGCAAG
802028 CAACTATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.97
ACGTcount: A:0.40, C:0.17, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:815712 original size:36 final size:36
Alignment explanation
Indices: 815609--815702 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
815599 TTTGTAGATT
*
815609 GTGTAAGGGTTATTGCTTGATCCTGTGAAAAATCTA
1 GTGTAAGGGATATTGCTTGATCCTGTGAAAAATCTA
815645 GTGTAAGGGATATTGCTTGATCCTGTGAAAAATCTA
1 GTGTAAGGGATATTGCTTGATCCTGTGAAAAATCTA
815681 GTGTAAGGGATATTGCTTGATC
1 GTGTAAGGGATATTGCTTGATC
815703 TAGTTAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.35
Consensus pattern (36 bp):
GTGTAAGGGATATTGCTTGATCCTGTGAAAAATCTA
Found at i:822085 original size:36 final size:36
Alignment explanation
Indices: 822018--822087 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
822008 TTTGTAGATT
* *
822018 GTGTAAGGGTTATTGCTTGATCTTGTGAAAAAGCTG
1 GTGTAAGGGTTATTACTTGATCCTGTGAAAAAGCTG
822054 GTGTAAGGGTTATTACTTGATCCTGCT-AAAAAGC
1 GTGTAAGGGTTATTACTTGATCCTG-TGAAAAAGC
822088 AATAATCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (36 bp):
GTGTAAGGGTTATTACTTGATCCTGTGAAAAAGCTG
Found at i:840402 original size:19 final size:20
Alignment explanation
Indices: 840353--840402 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
840343 TAAGATATAT
*
840353 AATCAAGGTATTATGGAACA
1 AATCAAGATATTATGGAACA
* * *
840373 TATCAATATATTAT-GAATA
1 AATCAAGATATTATGGAACA
840392 AATCAAGATAT
1 AATCAAGATAT
840403 ATCTCCATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (20 bp):
AATCAAGATATTATGGAACA
Found at i:842779 original size:20 final size:20
Alignment explanation
Indices: 842756--842809 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
842746 AGACAGCCAG
* * *
842756 ATCTATTGATAGATGGCTTA
1 ATCTATCGATAGATGACTCA
* *
842776 ATCTATCAATAGATGACTCC
1 ATCTATCGATAGATGACTCA
842796 ATCTATCGATAGAT
1 ATCTATCGATAGAT
842810 TGCAACAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
ATCTATCGATAGATGACTCA
Found at i:860725 original size:2 final size:2
Alignment explanation
Indices: 860720--860746 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
860710 ATATATAACT
860720 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
860747 TCAAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:860835 original size:25 final size:25
Alignment explanation
Indices: 860806--860854 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
860796 CTAGTTCATG
*
860806 CTTTCCAC-AATAATAGTTTATAAAT
1 CTTT-CACGAATAATAGTATATAAAT
860831 CTTTCACGAATAATAGTATATAAA
1 CTTTCACGAATAATAGTATATAAA
860855 ACATCATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (25 bp):
CTTTCACGAATAATAGTATATAAAT
Found at i:867745 original size:12 final size:12
Alignment explanation
Indices: 867728--867784 Score: 69
Period size: 12 Copynumber: 4.6 Consensus size: 12
867718 AGGTACATGT
*
867728 AAAAAAATTTGA
1 AAAAAAATTTCA
*
867740 AAAAAAAATTCA
1 AAAAAAATTTCA
*
867752 AAAAAAGTTTCA
1 AAAAAAATTTCA
867764 AAAAAGAATTTCA
1 AAAAA-AATTTCA
867777 AAACAAAA
1 AAA-AAAA
867785 AATTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
12 25 0.66
13 11 0.29
14 2 0.05
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAAAAATTTCA
Found at i:867746 original size:13 final size:12
Alignment explanation
Indices: 867728--867795 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
867718 AGGTACATGT
867728 AAAAAAATTTGAA
1 AAAAAAATTT-AA
*
867741 AAAAAAA-TTCA
1 AAAAAAATTTAA
*
867752 AAAAAAGTTTCAA
1 AAAAAAATTT-AA
*
867765 AAAAGAATTTCAA
1 AAAAAAATTT-AA
*
867778 AACAAAAAATTAA
1 AA-AAAAATTTAA
867791 AAAAA
1 AAAAA
867796 TGTGGTAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.16
12 7 0.16
13 25 0.56
14 6 0.13
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAAAAATTTAA
Found at i:869599 original size:9 final size:9
Alignment explanation
Indices: 869585--869616 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
869575 CACTTTATCT
869585 CTAGTAGTA
1 CTAGTAGTA
869594 CTAGTAGTA
1 CTAGTAGTA
869603 CTAGTAGTA
1 CTAGTAGTA
*
869612 GTAGT
1 CTAGT
869617 TAGTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (9 bp):
CTAGTAGTA
Found at i:871845 original size:12 final size:12
Alignment explanation
Indices: 871828--871854 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
871818 TTAAGCTTTG
871828 AATCTCACTCTT
1 AATCTCACTCTT
871840 AATCTCACTCTT
1 AATCTCACTCTT
871852 AAT
1 AAT
871855 AGATTTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (12 bp):
AATCTCACTCTT
Found at i:880493 original size:20 final size:20
Alignment explanation
Indices: 880476--880520 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
880466 ACATCTATGG
880476 ATAGATAACAAGATCTATCC
1 ATAGATAACAAGATCTATCC
* * *
880496 ATAGATAGCAAGCTCTATCA
1 ATAGATAACAAGATCTATCC
880516 ATAGA
1 ATAGA
880521 AGGCCTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
ATAGATAACAAGATCTATCC
Found at i:881231 original size:14 final size:14
Alignment explanation
Indices: 881212--881243 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
881202 TTGCTCATAT
881212 ATATATGTATATAA
1 ATATATGTATATAA
*
881226 ATATATGTATATAT
1 ATATATGTATATAA
881240 ATAT
1 ATAT
881244 TGTTGTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
ATATATGTATATAA
Found at i:881507 original size:12 final size:12
Alignment explanation
Indices: 881490--881514 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
881480 AGTGCTTTCA
881490 AAAATTGTTTAC
1 AAAATTGTTTAC
881502 AAAATTGTTTAC
1 AAAATTGTTTAC
881514 A
1 A
881515 GTAAGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTGTTTAC
Found at i:882498 original size:30 final size:30
Alignment explanation
Indices: 882463--882533 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
882453 ATAACTCTAT
882463 GAAAAGGTAGTGAAGGGTATGCTTCCACTA
1 GAAAAGGTAGTGAAGGGTATGCTTCCACTA
*
882493 GAAAAGGTAGTGAAGGGTATGCTTCCGCTA
1 GAAAAGGTAGTGAAGGGTATGCTTCCACTA
*
882523 GAAAATGTAGT
1 GAAAAGGTAGT
882534 AATGGTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (30 bp):
GAAAAGGTAGTGAAGGGTATGCTTCCACTA
Found at i:882605 original size:35 final size:35
Alignment explanation
Indices: 882564--882662 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
882554 AAAGGTAATG
* *
882564 AGGTTATGCTTGCCTCTCTTGTAAAGGTAGTGTAA
1 AGGTTATGCTTGCCTCTCTTGAAAAGGCAGTGTAA
* *
882599 AGGTTATGC-T-CACTCCTCTTCAAAAGGCAGTGTAG
1 AGGTTATGCTTGC-CT-CTCTTGAAAAGGCAGTGTAA
*
882634 AGGTTATGCTTGCTTCTCTTGAAAAGGCA
1 AGGTTATGCTTGCCTCTCTTGAAAAGGCA
882663 CTATTTGCGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
33 1 0.02
34 3 0.06
35 47 0.87
36 2 0.04
37 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (35 bp):
AGGTTATGCTTGCCTCTCTTGAAAAGGCAGTGTAA
Found at i:885735 original size:6 final size:6
Alignment explanation
Indices: 885724--885749 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
885714 CACTCATGAT
885724 ATATAA ATATAA ATATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA AT
885750 TCTTAACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:890042 original size:21 final size:24
Alignment explanation
Indices: 890017--890068 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 24
890007 ATGTTGTTGC
890017 TTTAATTTTAATTA-AATT-AG-T
1 TTTAATTTTAATTAGAATTCAGAT
*
890038 TTTAAGTTTAATTAGAATTCAGAT
1 TTTAATTTTAATTAGAATTCAGAT
890062 TTTAATT
1 TTTAATT
890069 ATTTGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 13 0.50
22 4 0.15
23 2 0.08
24 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTAATTTTAATTAGAATTCAGAT
Found at i:890254 original size:25 final size:25
Alignment explanation
Indices: 890226--890276 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
890216 CTGCCAATCC
* *
890226 TAAATCTTTGATAATAGATTCAAGA
1 TAAATCTTGGATAATAAATTCAAGA
890251 TAAATCTTGGATAATAAATTCAAGA
1 TAAATCTTGGATAATAAATTCAAGA
890276 T
1 T
890277 GTGGATCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (25 bp):
TAAATCTTGGATAATAAATTCAAGA
Found at i:893564 original size:19 final size:18
Alignment explanation
Indices: 893535--893574 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
893525 CAAGTGGAAA
893535 ATTTTTTAATAAAATAAT
1 ATTTTTTAATAAAATAAT
*
893553 ATTTTATTAATAAAATATT
1 ATTTT-TTAATAAAATAAT
893572 ATT
1 ATT
893575 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTTAATAAAATAAT
Found at i:893571 original size:11 final size:11
Alignment explanation
Indices: 893557--893586 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
893547 AATAATATTT
893557 TATTAATAAAA
1 TATTAATAAAA
*
893568 TATTATTAAAA
1 TATTAATAAAA
893579 TATTAATA
1 TATTAATA
893587 TTGTATTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:894998 original size:25 final size:25
Alignment explanation
Indices: 894949--894998 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
894939 CGTTCTGTGA
* *
894949 TTATACGTGGCAAGGCCATGGGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
894974 TTATACGTGGCAAGGCCACGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
894999 AAATACATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCACGAGTTG
Found at i:895004 original size:25 final size:25
Alignment explanation
Indices: 894951--895004 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
894941 TTCTGTGATT
* * **
894951 ATACGTGGCAAGGCCATGGGTTGTT
1 ATACGTGGCAAGGCCACGAGTTGAA
894976 ATACGTGGCAAGGCCACGAGTTGAA
1 ATACGTGGCAAGGCCACGAGTTGAA
895001 ATAC
1 ATAC
895005 ATGATTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (25 bp):
ATACGTGGCAAGGCCACGAGTTGAA
Found at i:897512 original size:18 final size:20
Alignment explanation
Indices: 897475--897515 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
897465 ACATATGGAT
897475 AGCTTTGGTTTGTGACAATCA
1 AGCTTTGG-TTGTGACAATCA
897496 AGCTTTGG-TGT-ACAATCA
1 AGCTTTGGTTGTGACAATCA
897514 AG
1 AG
897516 TGAAGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 3 0.15
21 8 0.40
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (20 bp):
AGCTTTGGTTGTGACAATCA
Found at i:898736 original size:27 final size:27
Alignment explanation
Indices: 898692--898745 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
898682 TTAAATAATT
* * * *
898692 TTTTCTTTTTTAATCTTTTAATTTTTA
1 TTTTCTTTTTAAAACTTTAAAATTTTA
898719 TTTTCTTTTTAAAACTTTAAAATTTTA
1 TTTTCTTTTTAAAACTTTAAAATTTTA
898746 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTCTTTTTAAAACTTTAAAATTTTA
Found at i:898938 original size:8 final size:8
Alignment explanation
Indices: 898925--898963 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
898915 TATTATTGTG
898925 ATTAAAAT
1 ATTAAAAT
898933 ATTAAAAT
1 ATTAAAAT
898941 ATTAACAATT
1 ATTAA-AA-T
*
898951 TTTAAAAT
1 ATTAAAAT
898959 ATTAA
1 ATTAA
898964 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 18 0.67
9 4 0.15
10 5 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTAAAAT
Found at i:904320 original size:2 final size:2
Alignment explanation
Indices: 904313--904340 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
904303 TCAAAATTTC
904313 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
904341 GAGGATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:905390 original size:40 final size:40
Alignment explanation
Indices: 905271--905391 Score: 170
Period size: 40 Copynumber: 3.0 Consensus size: 40
905261 GTTTGGATTA
* *
905271 TTGCTATGTGATGAAACACCTAACTTTATGAACCATATAA
1 TTGCTATCTGATGAAACACCTAACTTTATGAACCATATAT
* *
905311 CTGCTATCCGATGAAACACCTAACTTTATGAACCATATAT
1 TTGCTATCTGATGAAACACCTAACTTTATGAACCATATAT
* * * *
905351 TTGCTATTTAATGAAACACTTAACTTTATCAACCATATAT
1 TTGCTATCTGATGAAACACCTAACTTTATGAACCATATAT
905391 T
1 T
905392 CACAGGAGGC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (40 bp):
TTGCTATCTGATGAAACACCTAACTTTATGAACCATATAT
Found at i:909747 original size:5 final size:5
Alignment explanation
Indices: 909716--909746 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
909706 TCCTGACCAC
*
909716 TTGAG TTGAG TTGAG TTGAG TTGAG TCGAG T
1 TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG T
909747 CATTTGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.03, G:0.39, T:0.39
Consensus pattern (5 bp):
TTGAG
Found at i:910082 original size:4 final size:4
Alignment explanation
Indices: 910073--910101 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
910063 CAGAGATTTC
910073 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
910102 TTTACTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:910256 original size:7 final size:7
Alignment explanation
Indices: 910244--910278 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
910234 GATTGGAGCT
910244 CGCAGCA
1 CGCAGCA
910251 CGCAGCA
1 CGCAGCA
910258 CGCAGCA
1 CGCAGCA
910265 CGCAGCA
1 CGCAGCA
910272 CGCAGCA
1 CGCAGCA
910279 AGCACCGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.29, T:0.00
Consensus pattern (7 bp):
CGCAGCA
Found at i:914494 original size:92 final size:92
Alignment explanation
Indices: 914335--914508 Score: 235
Period size: 92 Copynumber: 1.9 Consensus size: 92
914325 TAAGAGTAAG
* * * * * *
914335 CACTGTATTATACTTTTATCATTTCTAGGATAAATGATGAGGTAATGAATTACACTGATAGATTG
1 CACTGTACTACACTCTTATCATTTCTAAGATAAATGATGAGGTAATGAATTACACTAATAGACTG
* *
914400 TACACTTTGAAATGTTGTTAGAAAAAA
66 TACACTTTAAAAGGTTGTTAGAAAAAA
*
914427 CACTGTACTACACTCTTATCATTT-TCAAGATATATGATGAGAG-AATGAATTACACTAATAGAC
1 CACTGTACTACACTCTTATCATTTCT-AAGATAAATGATGAG-GTAATGAATTACACTAATAGAC
914490 TGTACACTTTAAAAGGTTG
64 TGTACACTTTAAAAGGTTG
914509 CCATGATTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
91 1 0.01
92 69 0.97
93 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (92 bp):
CACTGTACTACACTCTTATCATTTCTAAGATAAATGATGAGGTAATGAATTACACTAATAGACTG
TACACTTTAAAAGGTTGTTAGAAAAAA
Found at i:916537 original size:50 final size:50
Alignment explanation
Indices: 916474--916582 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
916464 TAATTCAAAT
* * *
916474 AAAA-TATATAATATAAG-AATTAGAACA-TAAAATAAGATATAAGAA-ATTA
1 AAAATTATATAATATAAGCAA-AAGAA-ATTAAAATAAAATATAA-AATATAA
*
916523 AAAATTATATAATATAGGCAAAAGAAATTAAAATAAAATATAAAATATAA
1 AAAATTATATAATATAAGCAAAAGAAATTAAAATAAAATATAAAATATAA
916573 AAAATTATAT
1 AAAATTATAT
916583 TAAAAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
49 7 0.13
50 43 0.83
51 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (50 bp):
AAAATTATATAATATAAGCAAAAGAAATTAAAATAAAATATAAAATATAA
Found at i:916567 original size:7 final size:7
Alignment explanation
Indices: 916555--916604 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
916545 AGAAATTAAA
916555 ATAAAAT
1 ATAAAAT
916562 ATAAAAT
1 ATAAAAT
*
916569 ATAAAAA
1 ATAAAAT
* *
916576 ATTATAT
1 ATAAAAT
*
916583 -TAAAAA
1 ATAAAAT
916589 ATAAAA-
1 ATAAAAT
916595 ATAAAAT
1 ATAAAAT
916602 ATA
1 ATA
916605 TAAGATTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
6 9 0.26
7 25 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAAAAT
Found at i:916586 original size:27 final size:26
Alignment explanation
Indices: 916547--916600 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
916537 TAGGCAAAAG
*
916547 AAATTAAAATAAAATATAAAATATAAA
1 AAATTAAAATAAAAAATAAAA-ATAAA
* *
916574 AAATTATATTAAAAAATAAAAATAAA
1 AAATTAAAATAAAAAATAAAAATAAA
916600 A
1 A
916601 TATATAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (26 bp):
AAATTAAAATAAAAAATAAAAATAAA
Found at i:916599 original size:33 final size:33
Alignment explanation
Indices: 916552--916634 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
916542 AAAAGAAATT
*
916552 AAAATAAAATATAAAATATAAAAAATTATATTAA
1 AAAATAAAA-ATAAAATATAAAAAATTATAATAA
* *
916586 AAAATAAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATAAAAAATTATAATAA
* *
916619 GAAATGAAAATAAAAT
1 AAAATAAAAATAAAAT
916635 GTAACATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 35 0.80
34 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAATTATAATAA
Found at i:919026 original size:19 final size:18
Alignment explanation
Indices: 918992--919027 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
918982 ATTATACATT
*
918992 AATATCTAATATATTATA
1 AATATCTAAGATATTATA
919010 AATATCTAAAGATATTAT
1 AATATCT-AAGATATTAT
919028 TTATTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
AATATCTAAGATATTATA
Found at i:921115 original size:20 final size:21
Alignment explanation
Indices: 921074--921115 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
921064 NNNNNNNNTT
*
921074 AATTTAAATGAATTATATTCA
1 AATTTAAATGAACTATATTCA
*
921095 AATTTAAATTAACTA-ATTCA
1 AATTTAAATGAACTATATTCA
921115 A
1 A
921116 TTTCATAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTTAAATGAACTATATTCA
Found at i:922178 original size:32 final size:32
Alignment explanation
Indices: 922141--922208 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
922131 TAATATTCAA
*
922141 TAAAACCAAAACAAAGCATCACATATAAAAAT
1 TAAAACCAAAACAAAGCATCACACATAAAAAT
922173 TAAAACCAAAACAAAGCATCACACATAAAAAT
1 TAAAACCAAAACAAAGCATCACACATAAAAAT
922205 TAAA
1 TAAA
922209 CATGAAGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.63, C:0.19, G:0.03, T:0.15
Consensus pattern (32 bp):
TAAAACCAAAACAAAGCATCACACATAAAAAT
Found at i:934231 original size:54 final size:54
Alignment explanation
Indices: 934148--934272 Score: 164
Period size: 54 Copynumber: 2.3 Consensus size: 54
934138 AATTCTGTGG
*
934148 GAAATTTTCCAACGGAATTTCATGAGAAATACATT-TCAAATGAAAAATTTCGTTC
1 GAAA-TTTCCAACGGAATTCCATGAGAAATAC-TTCTCAAATGAAAAATTTCGTTC
* * *
934203 GAAATTTCCAACGGAATTCCATTG-GAAATGCTTCTCCAATGAAAAATTTCGTTG
1 GAAATTTCCAACGGAATTCCA-TGAGAAATACTTCTCAAATGAAAAATTTCGTTC
*
934257 GAAATTTCCAATGGAA
1 GAAATTTCCAACGGAA
934273 CTGATACAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 2 0.03
54 55 0.87
55 6 0.10
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (54 bp):
GAAATTTCCAACGGAATTCCATGAGAAATACTTCTCAAATGAAAAATTTCGTTC
Found at i:934267 original size:26 final size:26
Alignment explanation
Indices: 934180--934269 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
934170 TGAGAAATAC
* *
934180 ATTTCAAATGAAAAATTTCGTTCGAA
1 ATTTCCAATGAAAAATTTCGTTGGAA
* * * *
934206 ATTTCCAACG--GAATTCCATTGGAA
1 ATTTCCAATGAAAAATTTCGTTGGAA
934230 ATGCTTCTCCAATGAAAAATTTCGTTGGAA
1 A---TT-TCCAATGAAAAATTTCGTTGGAA
934260 ATTTCCAATG
1 ATTTCCAATG
934270 GAACTGATAC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
24 11 0.23
26 15 0.31
27 4 0.08
28 6 0.12
30 12 0.25
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (26 bp):
ATTTCCAATGAAAAATTTCGTTGGAA
Found at i:942083 original size:40 final size:40
Alignment explanation
Indices: 942027--942275 Score: 199
Period size: 40 Copynumber: 6.3 Consensus size: 40
942017 TCATGGGGGT
* * **
942027 TGATGGGAAAGGATGCCTCAAAGATGTTTATTACATGGGC
1 TGATGGGAGAGAATGCCTCAAAGATGTTTATTATGTGGGC
* * * * *
942067 TGATGGAAGAGAATGCC-CTAGATATGTTTA-TATGGGGGT
1 TGATGGGAGAGAATGCCTC-AAAGATGTTTATTATGTGGGC
* *
942106 TGATGGGAGA-AGATGCCTTAGAGATGTTTATTATGTGGGC
1 TGATGGGAGAGA-ATGCCTCAAAGATGTTTATTATGTGGGC
* *
942146 TGATGGGAGAGAATGCC-CTAGAA-ATGTTTA-TATATAGGC
1 TGATGGGAGAGAATGCCTC-A-AAGATGTTTATTATGTGGGC
* * *
942185 TGATGGGAGA-AGCTGCCTCATATATGTTTATTATGTGGGC
1 TGATGGGAGAGA-ATGCCTCAAAGATGTTTATTATGTGGGC
* * * *
942225 TGATGGGAGAGGATGCC-CTAGATATGTTTATTATGTAGGC
1 TGATGGGAGAGAATGCCTC-AAAGATGTTTATTATGTGGGC
*
942265 TGATGGTAGAG
1 TGATGGGAGAG
942276 TCCCACAGAG
Statistics
Matches: 169, Mismatches: 27, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
38 3 0.02
39 60 0.36
40 104 0.62
41 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (40 bp):
TGATGGGAGAGAATGCCTCAAAGATGTTTATTATGTGGGC
Found at i:942150 original size:79 final size:79
Alignment explanation
Indices: 942019--942255 Score: 332
Period size: 79 Copynumber: 3.0 Consensus size: 79
942009 GGGATCTGTC
** *
942019 ATGGGGGTTGATGGGA-AAGGATGCCTCAAAGATGTTTATTACATGGGCTGATGGAAGAGAATGC
1 ATGGGGGTTGATGGGAGAA-GATGCCTCAAAGATGTTTATTATGTGGGCTGATGGGAGAGAATGC
942083 CCTAGATATGTTTAT
65 CCTAGATATGTTTAT
* *
942098 ATGGGGGTTGATGGGAGAAGATGCCTTAGAGATGTTTATTATGTGGGCTGATGGGAGAGAATGCC
1 ATGGGGGTTGATGGGAGAAGATGCCTCAAAGATGTTTATTATGTGGGCTGATGGGAGAGAATGCC
*
942163 CTAGAAATGTTTAT
66 CTAGATATGTTTAT
*** * * * * *
942177 ATATAGGCTGATGGGAGAAGCTGCCTCATATATGTTTATTATGTGGGCTGATGGGAGAGGATGCC
1 ATGGGGGTTGATGGGAGAAGATGCCTCAAAGATGTTTATTATGTGGGCTGATGGGAGAGAATGCC
942242 CTAGATATGTTTAT
66 CTAGATATGTTTAT
942256 TATGTAGGCT
Statistics
Matches: 141, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
79 139 0.99
80 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (79 bp):
ATGGGGGTTGATGGGAGAAGATGCCTCAAAGATGTTTATTATGTGGGCTGATGGGAGAGAATGCC
CTAGATATGTTTAT
Found at i:943365 original size:21 final size:21
Alignment explanation
Indices: 943339--943397 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
943329 ATGTCCCTTG
943339 ATTGATTATCCAACTAACTAC
1 ATTGATTATCCAACTAACTAC
*
943360 ATTGATTATCCAACTAACTCC
1 ATTGATTATCCAACTAACTAC
943381 ATTGATTATCCAACTAA
1 ATTGATTATCCAACTAA
943398 GAGGCTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (21 bp):
ATTGATTATCCAACTAACTAC
Found at i:952112 original size:20 final size:19
Alignment explanation
Indices: 952083--952120 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
952073 TTCAAACAAA
*
952083 ATGCTCTTAGTTGACTAAC
1 ATGCTCTTAGTAGACTAAC
952102 ATGCTTCTTAGTAGACTAA
1 ATGC-TCTTAGTAGACTAA
952121 GTCGTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (19 bp):
ATGCTCTTAGTAGACTAAC
Found at i:954222 original size:2 final size:2
Alignment explanation
Indices: 954215--954250 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
954205 TGATAATGTC
* *
954215 AT AT AT AT AT AC AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
954251 GCATGTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:963510 original size:20 final size:20
Alignment explanation
Indices: 963484--963529 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
963474 AGATGGGAGC
*
963484 CATCTATTGATAGATTTAGCT
1 CATCTATGGATAGATTT-GCT
963505 -ATCTATGGATAGATTTGCT
1 CATCTATGGATAGATTTGCT
963524 CATCTA
1 CATCTA
963530 CCCATAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
CATCTATGGATAGATTTGCT
Found at i:965724 original size:15 final size:17
Alignment explanation
Indices: 965678--965724 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
965668 ATAAATTATC
**
965678 ATAAAATAAAATAACTTA
1 ATAAAATAAGCTAA-TTA
965696 ATAAAATAAGCTAATTA
1 ATAAAATAAGCTAATTA
965713 A-AAAATAA-CTAA
1 ATAAAATAAGCTAA
965725 AATAACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 7 0.26
17 4 0.15
18 12 0.44
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAAAATAAGCTAATTA
Found at i:974364 original size:29 final size:28
Alignment explanation
Indices: 974318--974405 Score: 104
Period size: 29 Copynumber: 3.1 Consensus size: 28
974308 TAACAGTTTT
*
974318 AACATGTTTGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* * *
974346 AACATCTTTGGTCTTAATTTGGACAAAAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
974375 AATATGTTTCTCTTAATTTAAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAA
974404 AA
1 AA
974406 ATANNNNNNN
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 17 0.35
29 32 0.65
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:979336 original size:74 final size:75
Alignment explanation
Indices: 979186--979381 Score: 227
Period size: 74 Copynumber: 2.6 Consensus size: 75
979176 GTAGATTGTG
* * * **
979186 AGACAGA-AAAGACTTAGTCGACTAAGAAGCATGATTAGTCAACTAA-AAGCTCATTGTTAAAGA
1 AGACAGAGAAA-ACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAAGCTCACTGCCAAAGA
*
979249 CTTCAACTACA
65 ATTCAACTACA
* *
979260 AGACAGAGAAAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAA-CTCACTGCCAGATAA
1 AGACAGAGAAAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAAGCTCACTGCCAAAGAA
* * *
979324 TTCGATTGCA
66 TTCAACTACA
* * * *
979334 AGACAAAGAAGACTTAATCGACTAAGAAGTATGGTTACTCAACTAAGA
1 AGACAGAGAAAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGA
979382 GCACTTTGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
74 100 0.95
75 5 0.05
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (75 bp):
AGACAGAGAAAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAAGCTCACTGCCAAAGAA
TTCAACTACA
Found at i:985613 original size:29 final size:29
Alignment explanation
Indices: 985562--985618 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
985552 ACAAAGTGAG
*
985562 AAAGAGAGGGAGAAAGAAAGAAAGGAAAA
1 AAAGAGAGGAAGAAAGAAAGAAAGGAAAA
*
985591 AAAGAGGAGGAAGAAA-AAGGAAAGGAAA
1 AAAGA-GAGGAAGAAAGAAAGAAAGGAAA
985619 GATTGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (29 bp):
AAAGAGAGGAAGAAAGAAAGAAAGGAAAA
Found at i:988573 original size:12 final size:12
Alignment explanation
Indices: 988556--988608 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
988546 CCAGTCCACT
988556 TGGACAGATTTA
1 TGGACAGATTTA
988568 TGGACAGATTTA
1 TGGACAGATTTA
* *
988580 GGGATAGAGCCTTTA
1 TGGACAGA---TTTA
988595 TGGACAGATTTA
1 TGGACAGATTTA
988607 TG
1 TG
988609 CCTCATAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 24 0.71
15 10 0.29
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.32
Consensus pattern (12 bp):
TGGACAGATTTA
Found at i:999337 original size:21 final size:21
Alignment explanation
Indices: 999306--999394 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
999296 GGATATGTTC
*
999306 ATGCAGTTCATGACAAAGACTG
1 ATGCA-TTCATAACAAAGACTG
*
999328 ATGCATTCATTACAAAGACTG
1 ATGCATTCATAACAAAGACTG
*
999349 ATACATTCATAACAAAGACTG
1 ATGCATTCATAACAAAGACTG
* *
999370 ATGCATTTATAATAAAGACTG
1 ATGCATTCATAACAAAGACTG
999391 ATGC
1 ATGC
999395 CTCCATTCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
21 56 0.92
22 5 0.08
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (21 bp):
ATGCATTCATAACAAAGACTG
Done.