Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 2 of 210
Found at i:541290 original size:6 final size:6
Alignment explanation
Indices: 541279--541304 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
541269 TTATAAATGA
541279 TAAAAT TAAAAT TAAAAT TAAAAT TA
1 TAAAAT TAAAAT TAAAAT TAAAAT TA
541305 GAAAAATTAT
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):
TAAAAT
Found at i:551840 original size:16 final size:17
Alignment explanation
Indices: 551815--551848 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
551805 GAAAATTTTT
551815 AATAAATAA-TTAATTC
1 AATAAATAATTTAATTC
*
551831 AATAATTAATTTAATTC
1 AATAAATAATTTAATTC
551848 A
1 A
551849 TGTGACAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATAATTTAATTC
Found at i:556971 original size:22 final size:21
Alignment explanation
Indices: 556943--556983 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
556933 AATTTAATTT
556943 TTTTCTTTTATGTTTTTTTAAC
1 TTTTCTTTT-TGTTTTTTTAAC
*
556965 TTTTCTTTTTTTTTTTTTA
1 TTTTCTTTTTGTTTTTTTA
556984 TTTTCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTGTTTTTTTAAC
Found at i:573881 original size:30 final size:30
Alignment explanation
Indices: 573847--573932 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
573837 CTCCTTATAT
*
573847 CTATCTCTATGCCTACT-CCTATCTCTGCCC
1 CTATCTCTATCCCTA-TGCCTATCTCTGCCC
573877 CTATCTCTATCCCTATGCCTATCTCTGTCCC
1 CTATCTCTATCCCTATGCCTATCTCTG-CCC
* *
573908 TCTTATCCCTATCCCTATCCCTATC
1 -C-TATCTCTATCCCTATGCCTATC
573933 CCTATCCTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.02
30 24 0.49
31 3 0.06
32 1 0.02
33 20 0.41
ACGTcount: A:0.14, C:0.43, G:0.05, T:0.38
Consensus pattern (30 bp):
CTATCTCTATCCCTATGCCTATCTCTGCCC
Found at i:573890 original size:12 final size:12
Alignment explanation
Indices: 573864--573939 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
573854 TATGCCTACT
**
573864 CCTATCTCTGCC
1 CCTATCTCTATC
573876 CCTATCTCTATC
1 CCTATCTCTATC
573888 CCTATGC-CTATC
1 CCTAT-CTCTATC
* *
573900 TCTGTCCCTCTTATC
1 CCTAT--CTC-TATC
*
573915 CCTATCCCTATC
1 CCTATCTCTATC
*
573927 CCTATCCCTATC
1 CCTATCTCTATC
573939 C
1 C
573940 TTGTCCTTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 40 0.77
13 4 0.08
14 1 0.02
15 7 0.13
ACGTcount: A:0.13, C:0.46, G:0.04, T:0.37
Consensus pattern (12 bp):
CCTATCTCTATC
Found at i:573922 original size:6 final size:6
Alignment explanation
Indices: 573875--573939 Score: 67
Period size: 6 Copynumber: 10.3 Consensus size: 6
573865 CTATCTCTGC
* * * *
573875 CCCTAT CTCTAT CCCTAT GCCTAT CTCTGT CCCTCTTAT CCCTAT CCCTAT
1 CCCTAT CCCTAT CCCTAT CCCTAT CCCTAT -CC-C-TAT CCCTAT CCCTAT
573926 CCCTAT CCCTAT CC
1 CCCTAT CCCTAT CC
573940 TTGTCCTTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 41 0.85
7 2 0.04
8 3 0.06
9 2 0.04
ACGTcount: A:0.14, C:0.46, G:0.03, T:0.37
Consensus pattern (6 bp):
CCCTAT
Found at i:574514 original size:2 final size:2
Alignment explanation
Indices: 574509--574537 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
574499 AAGAAATCTA
574509 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
574538 TTTAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:582861 original size:22 final size:21
Alignment explanation
Indices: 582804--582849 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
582794 AGCCCGGCCC
582804 ATTTTTTAATAAATACCAAAA
1 ATTTTTTAATAAATACCAAAA
582825 ATTTTTTAATAAATACCAAAA
1 ATTTTTTAATAAATACCAAAA
582846 ATTT
1 ATTT
582850 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTTTTAATAAATACCAAAA
Found at i:582875 original size:17 final size:18
Alignment explanation
Indices: 582853--582887 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
582843 AAAATTTATT
582853 TTAAAAA-TATTTTAAAA
1 TTAAAAAGTATTTTAAAA
582870 TTAAAAAGTATTTTAAAA
1 TTAAAAAGTATTTTAAAA
582888 AGTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAAAAGTATTTTAAAA
Found at i:582881 original size:29 final size:30
Alignment explanation
Indices: 582849--582928 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 30
582839 ACCAAAAATT
*
582849 TATTTTAAAAA-TATTTTAAAATTAAAAAG
1 TATTTTAAAAAGTATTTTAAAATTAAAAAA
582878 TATTTTAAAAAGTA-TTTAAAATTAAAAAA
1 TATTTTAAAAAGTATTTTAAAATTAAAAAA
* *
582907 TA-ATAAAAAAGTATTTTAAAAT
1 TATTTTAAAAAGTATTTTAAAAT
582929 ATTTTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 9 0.20
29 35 0.76
30 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAAGTATTTTAAAATTAAAAAA
Found at i:588461 original size:23 final size:23
Alignment explanation
Indices: 588436--588480 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
588426 TATAAATTAA
* *
588436 AAAAAAT-TGAATATATAAAAAT
1 AAAAAATATGAAAATAAAAAAAT
588458 AAAAAATATGAAAATAAAAAAAT
1 AAAAAATATGAAAATAAAAAAAT
588481 TACATTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAAATATGAAAATAAAAAAAT
Found at i:588466 original size:15 final size:15
Alignment explanation
Indices: 588448--588478 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
588438 AAAATTGAAT
588448 ATATAAAAATAAAAA
1 ATATAAAAATAAAAA
*
588463 ATATGAAAATAAAAA
1 ATATAAAAATAAAAA
588478 A
1 A
588479 ATTACATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
ATATAAAAATAAAAA
Found at i:588549 original size:18 final size:18
Alignment explanation
Indices: 588527--588572 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
588517 TGTTTAAAAT
*
588527 ATTTTTAAATTTTTTGT-
1 ATTTTTAAATTTCTTGTA
588544 ATTTTTACAATTTCTTGTA
1 ATTTTTA-AATTTCTTGTA
588563 ATTTTGTAAA
1 ATTTT-TAAA
588573 AAAAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 7 0.28
20 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (18 bp):
ATTTTTAAATTTCTTGTA
Found at i:592925 original size:13 final size:14
Alignment explanation
Indices: 592901--592934 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
592891 AAACAGCATT
*
592901 AGAAGGTTTATGGA
1 AGAAGATTTATGGA
592915 A-AAGATTTATGGA
1 AGAAGATTTATGGA
592928 AGAAGAT
1 AGAAGAT
592935 ATTCCACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (14 bp):
AGAAGATTTATGGA
Found at i:594205 original size:48 final size:48
Alignment explanation
Indices: 594148--594243 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
594138 GATCTAACTG
594148 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
1 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
* *
594196 GTTTGATTTTTACATCATTGAAAAATATGAACTAAATCTCTTTCCTTT
1 GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
594244 CAATTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (48 bp):
GTTTGATTTTTACAGCATTGAAAAATACGAACTAAATCTCTTTCCTTT
Found at i:601033 original size:84 final size:83
Alignment explanation
Indices: 600922--601270 Score: 372
Period size: 84 Copynumber: 4.2 Consensus size: 83
600912 ACTTTGGCCC
600922 CTTCAACAGCCTTCTT-AT--TTTCTTCTGCAATCTTCCTTTGC-TCTTCTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTC-TCTGCTTTAGCCATCTC
** *
600983 AATATCAGCTTGTTTTCTTA
65 AA-ATCAGCACGTTTTCTTT
* *
601003 CTTCAACAGCCTTCTTCAT-GTTTTCTTCTGCAATCTTCCTTTGCTTCACTGCTTCAGCCATCTC
1 CTTCAACAGCCTTCTTCATAG-TTTCTTCTGCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCTC
601067 TAAATCAGCACGTTTTCTTT
65 -AAATCAGCACGTTTTCTTT
* * *
601087 CTTCAACAGCCTTTTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCT-GCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCT-
*
601151 CAAATCAGCACATTTTCTTT
64 CAAATCAGCACGTTTTCTTT
* * * * *** *
601171 CGTCAACAGCCTTTTTCTTAGTTTCTTCAGCAATCTTCCTCAAC-TCGCTTGCTTTAGCCATCTC
1 CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTCTC-TGCTTTAGCCATCT-
***
601235 CAAATC-GACAAACTTTCTTT
64 CAAATCAG-CACGTTTTCTTT
*
601255 CTTCAACTGCCTTCTT
1 CTTCAACAGCCTTCTT
601271 TTTCTCTTCT
Statistics
Matches: 236, Mismatches: 21, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
81 16 0.07
82 2 0.01
83 5 0.02
84 207 0.88
85 6 0.03
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.43
Consensus pattern (83 bp):
CTTCAACAGCCTTCTTCATAGTTTCTTCTGCAATCTTCCTTTGCTTCTCTGCTTTAGCCATCTCA
AATCAGCACGTTTTCTTT
Found at i:606572 original size:25 final size:25
Alignment explanation
Indices: 606520--606574 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
606510 TTACATTTTT
* * *
606520 TTTTTGTTAATTTGATCATTATTAC
1 TTTTAGTTAATTTGACCATTAATAC
606545 TTTTAGTTAAATTTGACCATTAAT-C
1 TTTTAGTT-AATTTGACCATTAATAC
606570 TTTTA
1 TTTTA
606575 AAAAGAGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.56
Consensus pattern (25 bp):
TTTTAGTTAATTTGACCATTAATAC
Found at i:606722 original size:21 final size:18
Alignment explanation
Indices: 606691--606732 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
606681 CGAGTGCTAA
606691 TTTTTTGAATTTTTATGATT
1 TTTTTTGAATTTTT-T-ATT
606711 TTTTTTGTAATTTTTTATT
1 TTTTTTG-AATTTTTTATT
606730 TTT
1 TTT
606733 GAATATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTTGAATTTTTTATT
Found at i:609534 original size:22 final size:22
Alignment explanation
Indices: 609506--609580 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
609496 AATCAAAGCA
609506 AGTACGTTAGCCATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
* *
609528 AGTACGTTAGCCATGAGGGTTT
1 AGTACGTTAGCCATGAGAGCTT
* **
609550 AGTTCGTTAAACATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
609572 AGTACGTTA
1 AGTACGTTA
609581 AACATTGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (22 bp):
AGTACGTTAGCCATGAGAGCTT
Found at i:611238 original size:7 final size:7
Alignment explanation
Indices: 611226--611252 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
611216 TACCTTTATT
611226 AATTTTA
1 AATTTTA
611233 AATTTTA
1 AATTTTA
611240 AATTTTA
1 AATTTTA
611247 AATTTT
1 AATTTT
611253 CCAAAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:632085 original size:33 final size:32
Alignment explanation
Indices: 632024--632086 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
632014 ATCATATAAT
*
632024 TAACTATGATTTTGTAATTTTTTTATAATTAAA
1 TAACTAT-ATTTTATAATTTTTTTATAATTAAA
632057 TAACTAT-TTTTATAATTTCTTTTCATAATT
1 TAACTATATTTTATAATTT-TTTT-ATAATT
632087 TGATGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 10 0.37
32 4 0.15
33 13 0.48
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (32 bp):
TAACTATATTTTATAATTTTTTTATAATTAAA
Found at i:636023 original size:31 final size:30
Alignment explanation
Indices: 635956--636028 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
635946 TAATTTACTG
* * * *
635956 TAATTATACATATGAAACTTTGATTTGGTT
1 TAATTGTACACATAAAACTTTGATTTGATT
* *
635986 CAATTGTACACATAAAATTTTGATCTTGATT
1 TAATTGTACACATAAAACTTTGAT-TTGATT
636017 TAATTGTACACA
1 TAATTGTACACA
636029 ATTTTTAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (30 bp):
TAATTGTACACATAAAACTTTGATTTGATT
Found at i:637910 original size:120 final size:122
Alignment explanation
Indices: 637694--637912 Score: 309
Period size: 120 Copynumber: 1.8 Consensus size: 122
637684 AGTGGAAACC
* * * *
637694 ATGCATGTTAAAAGGTATCATATTACCAACAATCCATGCTTAAAAGAACATGCTTTTTCTCTAAG
1 ATGCATGTTAAAAGCTAGCA-ATTACCAACAATCCATGCTTAAAAGAACATGCTATTTCTCAAAG
* *
637759 GAAAATCGATATCGGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
65 GAAAATCAATATCAGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
* *
637817 ATGCATGTTAAAAGCTAGC-ATTACCAACCATCCATGCTTAACA-AACA-GCCTATTTCTCAAAG
1 ATGCATGTTAAAAGCTAGCAATTACCAACAATCCATGCTTAAAAGAACATG-CTATTTCTCAAAG
* *
637879 GGAAATCAATATCAGTTTGTTTATATACCCATCA
65 GAAAATCAATATCAGTTTGTTTACATACCCATCA
637913 CTACAACAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
119 1 0.01
120 45 0.53
121 22 0.26
123 17 0.20
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (122 bp):
ATGCATGTTAAAAGCTAGCAATTACCAACAATCCATGCTTAAAAGAACATGCTATTTCTCAAAGG
AAAATCAATATCAGTTTGTTTACATACCCATCAATACGAAATTGAAATGGTGATCAT
Found at i:642537 original size:63 final size:63
Alignment explanation
Indices: 642404--642585 Score: 241
Period size: 63 Copynumber: 3.0 Consensus size: 63
642394 GTCGCCGGCG
* * * * * * *
642404 AAACCCAAGGAACCGGAGAAGAAACCCGACAAA-CC-AA-AAGAAGCTGAGAAGAAGCCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
642464 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
* *
642527 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAGCCCAAAG-A-C-GGTGAGAAGAAACCGGA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGA
642586 GAAGCCTAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
60 44 0.40
61 3 0.03
62 3 0.03
63 60 0.55
ACGTcount: A:0.51, C:0.21, G:0.25, T:0.03
Consensus pattern (63 bp):
AAACCCAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
Found at i:642597 original size:30 final size:30
Alignment explanation
Indices: 642404--642585 Score: 247
Period size: 30 Copynumber: 6.0 Consensus size: 30
642394 GTCGCCGGCG
* * * * *
642404 AAACCCAAGGAACCGGAGAAGAAACCCGAC
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
* *
642434 AAACCAAAAGAAGCTGAGAAGAAGCCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
642464 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
642494 AAACCCAAAGAAGCAGCTGAGAAGAAACCGGAA
1 AAACCCAAAG-A--AGCTGAGAAGAAACCGGAA
642527 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGAA
* * *
642557 AAGCCCAAAGACGGTGAGAAGAAACCGGA
1 AAACCCAAAGAAGCTGAGAAGAAACCGGA
642586 GAAGCCTAAA
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
30 106 0.77
31 1 0.01
32 1 0.01
33 29 0.21
ACGTcount: A:0.51, C:0.21, G:0.25, T:0.03
Consensus pattern (30 bp):
AAACCCAAAGAAGCTGAGAAGAAACCGGAA
Found at i:642613 original size:93 final size:93
Alignment explanation
Indices: 642417--642585 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
642407 CCCAAGGAAC
* *
642417 CGGAGAAGAAACCCGACAAACCAAAAGAAGCTGAGAAGAAGCCGGAAAAACCCAAAGAAGCTGAG
1 CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
642482 AAGAAACCGGAAAAACCCAAAGAAGCAG
66 AAGAAACCGGAAAAACCCAAAGAAGCAG
* * * * * *
642510 CTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAGAAGAAACCGGAAAAGCCCAAAGACGGTGAG
1 CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
642575 AAGAAACCGGA
66 AAGAAACCGGA
642586 GAAGCCTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.50, C:0.21, G:0.26, T:0.03
Consensus pattern (93 bp):
CGGAGAAGAAACCCGAAAAACCAAAAGAAGCTGAGAAGAAACCGGAAAAACCCAAAGAAGCTGAG
AAGAAACCGGAAAAACCCAAAGAAGCAG
Found at i:660364 original size:57 final size:58
Alignment explanation
Indices: 660266--660392 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 58
660256 AAACGTTTGG
* * *
660266 CAAGTACCAAATCGAACACAAAAAAATTAGGTACCAAATTAGGAAAAAGA-GTTAAATT
1 CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTA-GAAAAAAATGTAAAATT
* ** *
660324 CAAGTACCAAATCGAATA-AAAAAGTTTAAGTACCAGATTAGAAAAAAATGTAAAATT
1 CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTAGAAAAAAATGTAAAATT
* *
660381 TATGTACCAAAT
1 CAAGTACCAAAT
660393 ATTATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 7 0.12
57 35 0.59
58 17 0.29
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.22
Consensus pattern (58 bp):
CAAGTACCAAATCGAACACAAAAAAATTAAGTACCAAATTAGAAAAAAATGTAAAATT
Found at i:667647 original size:6 final size:6
Alignment explanation
Indices: 667638--667664 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
667628 CAGTCTCAAG
667638 CTCGGA CTCGGA CTCGGA CTCGGA CTC
1 CTCGGA CTCGGA CTCGGA CTCGGA CTC
667665 AGTCGTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.19
Consensus pattern (6 bp):
CTCGGA
Found at i:695403 original size:2 final size:2
Alignment explanation
Indices: 695396--695430 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
695386 CAATTAAAGG
*
695396 TA TA TA TA TA CA 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 TA TA TA T
695431 TCACACACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:695675 original size:137 final size:137
Alignment explanation
Indices: 695422--695691 Score: 339
Period size: 137 Copynumber: 2.0 Consensus size: 137
695412 TATATATATA
* * *
695422 TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTATAATGACTAATTTGAACATTTT
1 TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTACAAAGACTAATTTAAACATTTT
* * * *
695487 TTTGATAGATCGGCCACAATGCAATCCTACTCCTACTCTAAGGGCATCTATGGTACTTTTACCAA
66 TTTGATAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTACCAA
695552 TTAGAGG
131 TTAGAGG
* * * *
695559 TATATATATTCAGACACTTTTAATTGCTCTTTTG-TCTAA-GATACAAAGATTAATTTAAACATT
1 TATATATATTCACACACCTTTAATTACTC-TTTGATCTAATG-TACAAAGACTAATTTAAACATT
* * * * * *
695622 TTTTT-AGTAGATTGGCCAAAATGCAATCATGCTCTTAGTTTAAGGATAGCTATGGTACTTTTAC
64 TTTTTGA-TAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTAC
695686 CAATTA
128 CAATTA
695692 AACATGTGTG
Statistics
Matches: 113, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
136 2 0.02
137 107 0.95
138 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (137 bp):
TATATATATTCACACACCTTTAATTACTCTTTGATCTAATGTACAAAGACTAATTTAAACATTTT
TTTGATAGATCGGCCAAAATGCAATCATACTCCTACTCTAAGGACAGCTATGGTACTTTTACCAA
TTAGAGG
Found at i:695708 original size:2 final size:2
Alignment explanation
Indices: 695703--695771 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
695693 ACATGTGTGA
695703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
695745 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 A
695772 CACAAACATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:705347 original size:182 final size:181
Alignment explanation
Indices: 704717--705428 Score: 789
Period size: 182 Copynumber: 3.9 Consensus size: 181
704707 TACTTTTATG
* * * * * * * *
704717 CTTTACTGACACAAACAAATACATAAATAGATTACTTTCATCAACTTAACCTGATTTTTAACACT
1 CTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACT
* * *
704782 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTATTGATTAATTGCAGTTTGCTTCTAAAAAA
65 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAA
* * * *
704847 GAAACTTAACTGACTGAAGCCTGATTATAACATGTAATACTTCAACTTTCTC
130 GAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* *
704899 CTTTTCTGAGACAAATATATACATGAATGGACTATTTTCATCAATTTAACCTGACA-TTTAACCC
1 C-TTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGA-ATTTTAACAC
* ** * * *
704963 TCCATTAAGCTTAATA-CAGCTGCAATTCACAGCTTCTTGATTAATAACAA-TTGGTCACT-GGA
64 TCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCT-TCTAAG-
* * * * *
705025 AAAGAAACTAAACTGACCCAAGCCTGGTTACAACATTTGATACTTGAA--TCCT-
127 AAAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* * *
705077 C-TTCTGAGACAAATACGA-ACATAAATGGACTATTTTCATCAATTTAATCTGAGTTTTAACACT
1 CTTTCTGAGACAAATA-TATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACT
* * *
705140 CCATTAAGCTTAATATTAGCTGCAATTCGCAGCTTCTTGATTGATTGTAATTTGCTTCTAAGAAA
65 CCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAA
* *
705205 GAAACTAAACTGACTGAAGCCTGATTACAACATGTGATACATCAACTTTCTC
130 GAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
* * * ** * *
705257 CTTTCCTAAGACAAATATATACATAAACGGATTATTTTTGTCAATGTAA-CTCAATTTCTAACAC
1 CTTT-CTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTT-TAACAC
* * ** * * * *
705321 TCCGTCAAGCTTAATATTAGCTGCAATTTGCATCTTCTTGATGAATTTCAAATTGCTTCCTAA-A
64 TCCATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTT-CTAAGA
* *
705385 AAGAAACTAAACTAACCGAAGCCTGATTACAACACGTGATACTT
128 AAGAAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTT
705429 AATCCATAAT
Statistics
Matches: 442, Mismatches: 71, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
176 69 0.16
177 73 0.17
178 6 0.01
179 6 0.01
180 5 0.01
181 80 0.18
182 196 0.44
183 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (181 bp):
CTTTCTGAGACAAATATATACATAAATGGACTATTTTCATCAATTTAACCTGAATTTTAACACTC
CATTAAGCTTAATATTAGCTGCAATTCACAGCTTCTTGATTAATTGCAATTTGCTTCTAAGAAAG
AAACTAAACTGACCGAAGCCTGATTACAACATGTGATACTTCAACTTTCTC
Found at i:711323 original size:4 final size:4
Alignment explanation
Indices: 711289--711353 Score: 66
Period size: 4 Copynumber: 16.5 Consensus size: 4
711279 TGAACTGAAA
*
711289 AACT AACT CAAC- AACT AATT CAACT --CT AACT AACT ATACT AAC- AACT
1 AACT AACT -AACT AACT AACT -AACT AACT AACT AACT A-ACT AACT AACT
711336 AACT AACT AACT AACT AA
1 AACT AACT AACT AACT AA
711354 AACAAATATG
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 2 0.04
3 6 0.12
4 34 0.65
5 10 0.19
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
AACT
Found at i:714521 original size:23 final size:24
Alignment explanation
Indices: 714483--714546 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
714473 CAATCTAATT
*
714483 AATTTTTTATTAAAAATTTCATCA
1 AATTTTTTGTTAAAAATTTCATCA
714507 AATTTTTTGTTAAAAATTTCATCA
1 AATTTTTTGTTAAAAATTTCATCA
* *
714531 ATTTTTTTGATAAAAA
1 AATTTTTTGTTAAAAA
714547 AACAGACACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTTTTTGTTAAAAATTTCATCA
Found at i:728886 original size:15 final size:15
Alignment explanation
Indices: 728863--728892 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
728853 AGTTTTGTAT
728863 TAAAAAATAATTAAA
1 TAAAAAATAATTAAA
*
728878 TAAATAATAATTAAA
1 TAAAAAATAATTAAA
728893 CCATAAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAATAATTAAA
Found at i:731928 original size:10 final size:12
Alignment explanation
Indices: 731902--731930 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
731892 AATAGTGTTT
731902 TATTTATAAATA
1 TATTTATAAATA
731914 TATTTATAAATA
1 TATTTATAAATA
731926 T-TTTA
1 TATTTA
731931 ATATTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTATAAATA
Found at i:732760 original size:20 final size:20
Alignment explanation
Indices: 732724--732763 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
732714 TTAATATATA
*
732724 TAATGAATTTAATTTTAAAT
1 TAATGAATTTAAGTTTAAAT
732744 TAATCGAATTT-AGTTTAAAT
1 TAAT-GAATTTAAGTTTAAAT
732764 AGTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
TAATGAATTTAAGTTTAAAT
Found at i:732790 original size:19 final size:19
Alignment explanation
Indices: 732712--732791 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
732702 TCATTGTTTC
*
732712 TTTTAATATATATAATGAA
1 TTTTAATATAAATAATGAA
*
732731 -TTTAATTTTAAATTAATCGAA
1 TTTTAA-TATAAA-TAAT-GAA
* * * *
732752 -TTTAGTTTAAATAGTTAA
1 TTTTAATATAAATAATGAA
*
732770 TTTTAATATATATAATGAA
1 TTTTAATATAAATAATGAA
732789 TTT
1 TTT
732792 CGGAATTTGG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
18 7 0.15
19 23 0.49
20 10 0.21
21 7 0.15
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAATATAAATAATGAA
Found at i:734880 original size:126 final size:124
Alignment explanation
Indices: 734598--735038 Score: 512
Period size: 124 Copynumber: 3.5 Consensus size: 124
734588 GATCAAATCA
* * * * * * *
734598 AAGCAGGATGATTTATTAGAAGGATTTTTTAAGTCGCGCCCACGTGTACG-GCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
734662 AGGTCCAGGAAAAATAATTTTGAGTTGACATTTATGAGCAAATAGTTTAAAAAACACTTC
66 AGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAG-TAAAAAAACGCTTC
* *
734722 AAGCAAGATGCTTTATGAGAAGAATATT-TGAAATCGCG-CCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTTTATGAGAAGAAT-TTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * * *
734785 TTGATTCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAAAAGTACAAAACAACGCTGC
65 TAGGTCCTGGAA-AAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTA-AAAA-AACGCTTC
* * * *
734848 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGTGCTTTTGCTATAA
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * * * *
734912 TAGGTCCTGAAAAAATAATTTTGACTTGACATTTCTGAGCAAACAGTATAAAATCGCTTC
65 TAGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTAAAAAAACGCTTC
* * *
734972 TAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCTCACGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
735037 AG
66 AG
735039 CGTGTTTGGG
Statistics
Matches: 267, Mismatches: 41, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
123 11 0.04
124 114 0.43
125 41 0.15
126 69 0.26
127 32 0.12
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTTGAGTTGACATTTCTGAGCAAAAAGTAAAAAAACGCTTC
Found at i:735748 original size:21 final size:21
Alignment explanation
Indices: 735707--736340 Score: 282
Period size: 22 Copynumber: 26.9 Consensus size: 21
735697 CATCCAATTA
735707 AAGTTAAGGGTTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTT
* * *
735729 AATTTAAGGGTTACGGTTTTA
1 AAGTTAAGGGTTAGGGTTTTT
* * * *
735750 AAGTGAATGGTTTATGTTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
* * *
735772 AAGTTAAGGGTTACGGCTTTA
1 AAGTTAAGGGTTAGGGTTTTT
*
735793 AAGTTAACGGTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGTTTTT
* *
735814 AGGTTAAGGGGTTAGGATTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
735836 AAGTTAAGGGTTAGGGTTAGTGTTTTT
1 AAGTTAAGGGTTA--G---G-GTTTTT
* *
735863 AGGTTAAGGGGTTAAGGTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
735885 AAGTTAAGGGTTTAGGG-TTTT
1 AAGTTAAGGG-TTAGGGTTTTT
* *
735906 AGGTTAAGAGGCTAGGGTTTTT
1 AAGTTAAG-GGTTAGGGTTTTT
*
735928 AAGTTAACGGTTAGGGTTGGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
*
735955 AGGTTAATGTGTTAGGGTTAGGGTTTTT
1 AAGTT-A------AGGGTTAGGGTTTTT
*
735983 AAGTTAATGGTTAGTGTTAAGGTTTTT
1 AAGTTAA--G---G-GTTAGGGTTTTT
*
736010 AGGTTAAGGGGTTAGGGTTTTT
1 AAGTTAA-GGGTTAGGGTTTTT
736032 AAGTTAAGGGTTAGAGTTGGGGTTTTT
1 AAGTTAAGGGTT--A----GGGTTTTT
*
736059 ATGTTAATGGTTAGGGTTAGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
736086 AAGTTAAGAGGTTAGGGTTTTT
1 AAGTTAAG-GGTTAGGGTTTTT
*
736108 AAGTTAACGGTTAGGGTTGGGGTTTTT
1 AAGTT-A-----AGGGTTAGGGTTTTT
* *
736135 AGGTTAAAGAGTTAGGG-TTTT
1 AAGTT-AAGGGTTAGGGTTTTT
736156 AAGTTAAAGGTTAGGGTTAGGGTTTTT
1 AAGTT--A----AGGGTTAGGGTTTTT
* *
736183 AGGTTAAGGTGTTAAGGTTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
*
736205 AAGTTTAAGGTTTAAGGTTTAAGGTTTTT
1 AAG-TTAA-G-----GG-TTAGGGTTTTT
*
736234 AGGTTAAGGGGTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTT
*
736256 AAGTTAAGGGTTAGAGTTTTT
1 AAGTTAAGGGTTAGGGTTTTT
* *
736277 AGGTTAAGGTGTTAGGATTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
* * * *
736299 AGGTTAAGGATTTAAGATTTTT
1 AAGTTAAGG-GTTAGGGTTTTT
*
736321 AGGTTAAAGGGTTAGGGTTT
1 AAGTT-AAGGGTTAGGGTTT
736341 GTCAATTAAA
Statistics
Matches: 484, Mismatches: 67, Indels: 122
0.72 0.10 0.18
Matches are distributed among these distances:
21 108 0.22
22 190 0.39
23 15 0.03
24 1 0.00
25 1 0.00
26 14 0.03
27 97 0.20
28 37 0.08
29 14 0.03
31 1 0.00
33 6 0.01
ACGTcount: A:0.24, C:0.01, G:0.32, T:0.43
Consensus pattern (21 bp):
AAGTTAAGGGTTAGGGTTTTT
Found at i:735854 original size:49 final size:49
Alignment explanation
Indices: 735801--736104 Score: 341
Period size: 49 Copynumber: 6.1 Consensus size: 49
735791 TAAAGTTAAC
*
735801 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGATTTTTAAGTTAAGGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
735850 GGTTAGTGTTTTTAGGTTAAGGGGTTAAGGTTTTTAAGTTAAGGG-T--
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* * *
735896 --TTAGGG-TTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAACGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
735942 GGTTGGGGTTTTTAGGTTAATGTGTTAGGGTTAGGGTTTTTAAGTTAATGGTTAG
1 GGTTAGGGTTTTTAGGTTAA---G---GGGTTAGGGTTTTTAAGTTAAGGGTTAG
* *
735997 TGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
* * *
736046 AGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTTTTTAAGTTAAGAGGTTAG
1 GGTTAGGGTTTTTAGGTTAA--G---GGGTTAGGGTTTTTAAGTTAAG-GGTTAG
736101 GGTT
1 GGTT
736105 TTTAAGTTAA
Statistics
Matches: 216, Mismatches: 21, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
43 32 0.15
44 6 0.03
48 6 0.03
49 96 0.44
51 1 0.00
52 2 0.01
54 22 0.10
55 51 0.24
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (49 bp):
GGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAG
Found at i:735925 original size:43 final size:42
Alignment explanation
Indices: 735707--735945 Score: 196
Period size: 43 Copynumber: 5.5 Consensus size: 42
735697 CATCCAATTA
** *
735707 AAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTACGGTTTTA
1 AAGTTAAGGGTTTAGGG-TTTTAGGTTAAGGGTTACGGTTTTT
* * ** * * *
735750 AAGTGAATGGTTTATGTTTTTTAAGTTAAGGGTTACGGCTTTA
1 AAGTTAAGGGTTTA-GGGTTTTAGGTTAAGGGTTACGGTTTTT
*
735793 AAGTTAACGG-TTAGGGTTTTTAGGTTAAGGGGTTA-GGATTTTT
1 AAGTTAAGGGTTTAGGG-TTTTAGGTTAA-GGGTTACGG-TTTTT
* *
735836 AAGTTAAGGGTTAGGGTTAGTGTTTTTAGGTTAAGGGGTTAAGGTTTTT
1 AAGTTAAGGG-T----TTAG-GGTTTTAGGTTAA-GGGTTACGGTTTTT
* *
735885 AAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTT
1 AAGTTAAGGGTTTAGGGTTTTAGGTTAAG-GGTTACGGTTTTT
*
735928 AAGTTAACGG-TTAGGGTT
1 AAGTTAAGGGTTTAGGGTT
735946 GGGGTTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
41 1 0.01
42 24 0.15
43 93 0.57
44 5 0.03
48 1 0.01
49 37 0.23
50 3 0.02
ACGTcount: A:0.24, C:0.03, G:0.31, T:0.42
Consensus pattern (42 bp):
AAGTTAAGGGTTTAGGGTTTTAGGTTAAGGGTTACGGTTTTT
Found at i:736017 original size:14 final size:14
Alignment explanation
Indices: 735948--736018 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
735938 TTAGGGTTGG
735948 GGTTTTTAGGTTAA
1 GGTTTTTAGGTTAA
* * *
735962 TG-TGTTAGGGTTAG
1 GGTTTTTA-GGTTAA
*
735976 GGTTTTTAAGTTAA
1 GGTTTTTAGGTTAA
735990 TGG---TTAGTGTTAA
1 -GGTTTTTAG-GTTAA
736003 GGTTTTTAGGTTAA
1 GGTTTTTAGGTTAA
736017 GG
1 GG
736019 GGTTAGGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
12 5 0.12
13 9 0.21
14 18 0.43
15 10 0.24
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (14 bp):
GGTTTTTAGGTTAA
Found at i:736035 original size:104 final size:97
Alignment explanation
Indices: 735778--736205 Score: 369
Period size: 92 Copynumber: 4.4 Consensus size: 97
735768 TTTTAAGTTA
* * * * * * *
735778 AGGGTTACGGCTTTAAAGTTAACGG-TTAGGGTTTTTAGGTTAAGGGGTTAGGATTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-TTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTA
* * * *
735842 AGGGTTAGGGTTAGTGTTTTTAGGTTAA--G--
65 ACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
*
735871 -GGGTTAAGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
1 AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
*
735935 CGGTTAGGGTTGGGGTTTTTAGGTTAATGTGTT
66 CGGTTAGAGTTGGGGTTTTTAGGTTAATG-GTT
* * *
735968 AGGGTTAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAA-GG---GT-TT-AGGGTTTTAGGTTAAGAGGCTAGGGTTTTTA
* *
736033 AGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTT
60 AGTTAACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
* * *
736071 AGGGTTAGGGTTTTTAAGTTAAGAGG-TTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTT
1 AGGGTTAGGGTTTTTAAGTTAAG-GGTTTAGGG-TTTTAGGTTAA--G--A-GGCTAGGGTTTTT
* * * *
736135 AGGTTAA-----AGAGTTAGGG-TTTTAAGTTAAAGGTT
59 AAGTTAACGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
* * *
736168 AGGGTTAGGGTTTTTAGGTTAAGGTGTTAAGGTTTTTA
1 AGGGTTAGGGTTTTTAAGTTAAGG-GTTTAGGGTTTTA
736206 AGTTTAAGGT
Statistics
Matches: 285, Mismatches: 28, Indels: 40
0.81 0.08 0.11
Matches are distributed among these distances:
92 74 0.26
93 6 0.02
95 1 0.00
96 1 0.00
97 45 0.16
98 45 0.16
99 2 0.01
100 2 0.01
102 3 0.01
103 46 0.16
104 60 0.21
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.42
Consensus pattern (97 bp):
AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGTTAAGAGGCTAGGGTTTTTAAGTTAA
CGGTTAGAGTTGGGGTTTTTAGGTTAATGGTT
Found at i:736066 original size:76 final size:76
Alignment explanation
Indices: 735941--736273 Score: 339
Period size: 76 Copynumber: 4.4 Consensus size: 76
735931 TTAACGGTTA
* * * * *
735941 GGGTTGGGGTTTTTAGGTTAATGTGTTAGGGTTAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGT
1 GGGTTAGGGTTTTTAAGTTAA-GGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGT
736006 TTTTAGGTTAAG
65 TTTTAGGTTAAG
* * *
736018 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTT
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTT
*
736083 TTTAAGTTAAG
66 TTTAGGTTAAG
* * * * * *
736094 AGGTTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAAAGAGTTAGGGTTTTAA-
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATG-GTTA--GTGTTAAG
**
736158 G-TTAAAGGTT-A-
63 GTTTTTAGGTTAAG
*
736169 GGGTTAGGGTTTTTAGGTTAAGGTGTTA-A-----GGTTTTTAAGTTTAA-GGTTTAAG-GTTTA
1 GGGTTAGGGTTTTTAAGTTAAGG-GTTAGAGTTGGGGTTTTTAAG-TTAATGG-TT-AGTG-TTA
736226 AGGTTTTTAGGTTAAG
61 AGGTTTTTAGGTTAAG
736242 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTT
1 GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTT
736274 TTTAGGTTAA
Statistics
Matches: 211, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
69 6 0.03
70 13 0.06
71 12 0.06
72 5 0.02
73 23 0.11
75 20 0.09
76 98 0.46
77 29 0.14
78 1 0.00
79 4 0.02
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.43
Consensus pattern (76 bp):
GGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTT
TTTAGGTTAAG
Found at i:736105 original size:49 final size:49
Alignment explanation
Indices: 735918--736269 Score: 299
Period size: 49 Copynumber: 6.9 Consensus size: 49
735908 GTTAAGAGGC
* * *
735918 TAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAATGTGTTAGGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAA-G-GTTAGGGT
* * *
735973 TAGGGTTTTTAAGTTAATGGTTAGTGTTAAGGTTTTTAGGTTAA-G---GGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAAGGTTAGGGT
* *
736022 TAGGGTTTTTAAGTTAAGGGTTAGAGTTGGGGTTTTTATGTTAATGGTTAGGGT
1 TAGGGTTTTTAAGTTAA--G--AGAGTTAGGGTTTTTAAGTTAA-GGTTAGGGT
736076 TAGGGTTTTTAAGTTAAGAG-GTTAGGGTTTTTAAGTTAACGGTTAGGGT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAA-GGTTAGGGT
* *
736125 TGGGGTTTTTAGGTTAA-AGAGTTAGGG-TTTTAAGTTAAAGGTTAGGGT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTT-AAGGTTAGGGT
* * * *
736173 TAGGGTTTTTAGGTTAAG-GTGTTAAGGTTTTTAAGTTTAAGGTTTAAGGTT
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAG-TTAAGG-TT-AGGGT
* * *
736224 TAAGGTTTTTAGGTTAAG-GGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAA-GGTTAG
736270 AGTTTTTAGG
Statistics
Matches: 263, Mismatches: 21, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
48 43 0.16
49 106 0.40
50 12 0.05
51 39 0.15
52 2 0.01
54 21 0.08
55 40 0.15
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.43
Consensus pattern (49 bp):
TAGGGTTTTTAAGTTAAGAGAGTTAGGGTTTTTAAGTTAAGGTTAGGGT
Found at i:736134 original size:28 final size:28
Alignment explanation
Indices: 736095--736189 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 28
736085 TAAGTTAAGA
*
736095 GGTTAGGGTTTTTAAGTTAACG-GTTAG
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
* *
736122 GGTTGGGGTTTTTAGGTT-AA-AG--A-
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
736145 -GTTAGGG-TTTTAAGTTAAAG-GTTAG
1 GGTTAGGGTTTTTAAGTTAAAGAGTTAG
*
736170 GGTTAGGGTTTTTAGGTTAA
1 GGTTAGGGTTTTTAAGTTAA
736190 GGTGTTAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
21 8 0.15
22 9 0.17
24 2 0.04
26 9 0.17
27 26 0.48
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.41
Consensus pattern (28 bp):
GGTTAGGGTTTTTAAGTTAAAGAGTTAG
Found at i:736170 original size:97 final size:100
Alignment explanation
Indices: 736044--736269 Score: 300
Period size: 97 Copynumber: 2.3 Consensus size: 100
736034 GTTAAGGGTT
* * * *
736044 AGAGTTGGGGTTTTTATGTTAATGGTTAGGGTTAGGGTTTTTAAGTTAAGAG-GTTAGGGTTTTT
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAG-GTGTTAAGGTTTTT
**
736108 AAG-TTAACGG-TT-AGGGTTGGGGTTTTTAGGTTAA
65 AAGTTTAA-GGTTTAAGGGTTAAGGTTTTTAGGTTAA
*
736142 AGAGTTAGGG-TTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAGGTTAAGGTGTTAAGGTTTTTA
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAGGTGTTAAGGTTTTTA
*
736206 AGTTTAAGGTTTAAGGTTTAAGGTTTTTAGGTTAA
66 AGTTTAAGGTTTAAGGGTTAAGGTTTTTAGGTTAA
* * *
736241 GGGGTTAGGGTTTTTAAGTTAAGGGTTAG
1 AGAGTTAGGGTTTTTAAGTTAAAGGTTAG
736270 AGTTTTTAGG
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
96 1 0.01
97 52 0.46
98 15 0.13
99 27 0.24
100 17 0.15
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.42
Consensus pattern (100 bp):
AGAGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTAGGGTTTTTAAGTTAAGGTGTTAAGGTTTTTA
AGTTTAAGGTTTAAGGGTTAAGGTTTTTAGGTTAA
Found at i:736219 original size:7 final size:7
Alignment explanation
Indices: 736186--736231 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
736176 GGTTTTTAGG
736186 TTAAGGT
1 TTAAGGT
736193 GTTAAGGTTT
1 -TTAAGG--T
736203 TTAA-GT
1 TTAAGGT
736209 TTAAGGT
1 TTAAGGT
736216 TTAAGGT
1 TTAAGGT
736223 TTAAGGT
1 TTAAGGT
736230 TT
1 TT
736232 TTAGGTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 5 0.14
7 18 0.51
8 7 0.20
9 4 0.11
10 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (7 bp):
TTAAGGT
Found at i:736252 original size:29 final size:29
Alignment explanation
Indices: 736184--736253 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
736174 AGGGTTTTTA
*
736184 GGTTAAGGTGTTAAGGTTTTTAAGTTTAAG
1 GGTTAAGGT-TTAAGGTTTTTAAGGTTAAG
*
736214 GTTTAAGGTTTAAGGTTTTT-AGGTTAAGG
1 GGTTAAGGTTTAAGGTTTTTAAGGTTAA-G
*
736243 GGTTAGGGTTT
1 GGTTAAGGTTT
736254 TTAAGTTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.17
29 21 0.60
30 8 0.23
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (29 bp):
GGTTAAGGTTTAAGGTTTTTAAGGTTAAG
Found at i:736263 original size:43 final size:43
Alignment explanation
Indices: 736216--736340 Score: 171
Period size: 43 Copynumber: 2.9 Consensus size: 43
736206 AGTTTAAGGT
736216 TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
1 TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
* * * *
736259 TTAAGGGTT-AGAGTTTTTAGGTTAAGGTGTTAGGATTTTTAGG
1 TTAAGGTTTAAG-GTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
* *
736302 TTAAGGATTTAAGATTTTTAGGTTAAAGGGTTAGGGTTT
1 TTAAGG-TTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTT
736341 GTCAATTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 42 0.60
44 24 0.34
45 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (43 bp):
TTAAGGTTTAAGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAG
Found at i:736618 original size:21 final size:21
Alignment explanation
Indices: 736594--736640 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
736584 GCGACGGTTG
*
736594 TGGTTCCTCCGGT-GGGGATTC
1 TGGTTCCTCCGGTAGGGCA-TC
*
736615 TGGTTCTTCCGGTAGGGCATC
1 TGGTTCCTCCGGTAGGGCATC
736636 TGGTT
1 TGGTT
736641 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.36, T:0.36
Consensus pattern (21 bp):
TGGTTCCTCCGGTAGGGCATC
Found at i:736916 original size:18 final size:18
Alignment explanation
Indices: 736893--736939 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
736883 TGAAATATAT
736893 AAGGGTTAGGATACATAA
1 AAGGGTTAGGATACATAA
736911 AAGGGTTAGGATACATAA
1 AAGGGTTAGGATACATAA
*
736929 AAGGGCTAGGA
1 AAGGGTTAGGA
736940 AACGCACCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.32, T:0.19
Consensus pattern (18 bp):
AAGGGTTAGGATACATAA
Found at i:738075 original size:39 final size:39
Alignment explanation
Indices: 738028--738107 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
738018 ATACCAATCG
738028 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
1 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
738067 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
1 ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
738106 AC
1 AC
738108 ATGTGCTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (39 bp):
ACTAGCGAATGATGAAAATATTAATTTTATTTAATACTT
Found at i:738266 original size:20 final size:20
Alignment explanation
Indices: 738229--738266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
738219 TTTATTTTTA
*
738229 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
738249 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
738267 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:739216 original size:30 final size:30
Alignment explanation
Indices: 739160--739217 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
739150 ATTTTTACGG
*
739160 TTTAAAAAAATTTAAAAAAATTAAATTTTT
1 TTTAAAAAAATTTAAAAAAATGAAATTTTT
* *
739190 TTTAAAAATTATTTAAAAATA-GAAATTT
1 TTTAAAAA-AATTTAAAAAAATGAAATTT
739218 AAGAGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTTAAAAAAATTTAAAAAAATGAAATTTTT
Found at i:739239 original size:12 final size:11
Alignment explanation
Indices: 739210--739239 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
739200 ATTTAAAAAT
739210 AGAAATTTAAG
1 AGAAATTTAAG
739221 AGAAATTTAAG
1 AGAAATTTAAG
739232 AGGAAATT
1 A-GAAATT
739240 GAGAGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (11 bp):
AGAAATTTAAG
Found at i:739244 original size:11 final size:11
Alignment explanation
Indices: 739230--739331 Score: 90
Period size: 11 Copynumber: 9.6 Consensus size: 11
739220 GAGAAATTTA
739230 AGAGGAAATTG
1 AGAGGAAATTG
*
739241 AGAGCAAATTG
1 AGAGGAAATTG
**
739252 AGATTAAA-T-
1 AGAGGAAATTG
* *
739261 A-TGG-ATTTG
1 AGAGGAAATTG
739270 AGA-GAAATTTG
1 AGAGGAAA-TTG
739281 -GAAGGAAATTG
1 AG-AGGAAATTG
739292 AGAGGAAATTG
1 AGAGGAAATTG
739303 AGAGGAAATTG
1 AGAGGAAATTG
*
739314 AAAGGAAATTG
1 AGAGGAAATTG
739325 AGAGGAA
1 AGAGGAA
739332 GTTTGAAAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 59 0.82
12 5 0.07
ACGTcount: A:0.46, C:0.01, G:0.31, T:0.22
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:739304 original size:33 final size:33
Alignment explanation
Indices: 739267--739331 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
739257 AAATATGGAT
*
739267 TTGAGA-GAAATTTGGAAGGAAATTGAGAGGAAA
1 TTGAGAGGAAA-TTGAAAGGAAATTGAGAGGAAA
739300 TTGAGAGGAAATTGAAAGGAAATTGAGAGGAA
1 TTGAGAGGAAATTGAAAGGAAATTGAGAGGAA
739332 GTTTGAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (33 bp):
TTGAGAGGAAATTGAAAGGAAATTGAGAGGAAA
Found at i:739346 original size:23 final size:22
Alignment explanation
Indices: 739283--739340 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
739273 GAAATTTGGA
*
739283 AGGAAATTGAGAGGAAATTGAG
1 AGGAAATTGAAAGGAAATTGAG
739305 AGGAAATTGAAAGGAAATTGAG
1 AGGAAATTGAAAGGAAATTGAG
*
739327 AGGAAGTTTGAAAG
1 AGGAA-ATTGAAAG
739341 AGAATTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (22 bp):
AGGAAATTGAAAGGAAATTGAG
Found at i:744606 original size:25 final size:26
Alignment explanation
Indices: 744569--744623 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
744559 AGACTATAAA
*
744569 AAAATATATAAATGTATG-A-ATTAT
1 AAAATATAGAAATGTATGAATATTAT
744593 AAAATATAGGAAATGTATGAATATTAT
1 AAAATATA-GAAATGTATGAATATTAT
744620 AAAA
1 AAAA
744624 CATAAACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 9 0.33
26 1 0.04
27 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (26 bp):
AAAATATAGAAATGTATGAATATTAT
Found at i:745831 original size:77 final size:77
Alignment explanation
Indices: 745704--745859 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 77
745694 TTCAGTTTTT
745704 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
1 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
745769 TGAGTCCGGGCC
66 TGAGTCCGGGCC
745781 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
1 TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
**
745846 TGAGTTTGGGCC
66 TGAGTCCGGGCC
745858 TT
1 TT
745860 AGGCTTAGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (77 bp):
TTTTTTCTGCTGAAACTGTTCCATAGCTTGGGCTGTAATTTGGACTAACAGATGGGCTTGTAACT
TGAGTCCGGGCC
Found at i:757194 original size:3 final size:3
Alignment explanation
Indices: 757186--757213 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
757176 CATCTTTTGA
757186 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
757214 TGTAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:762552 original size:36 final size:36
Alignment explanation
Indices: 762505--762579 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
762495 TATGATTTAC
* *
762505 GATTATAGTACTTCTTGTCAATGCATCATACCTTGT
1 GATTATAGTACTTATTGTCAATGCATCATACCATGT
762541 GATTATAGTACTTATTGTCAATGCATCATACCATGT
1 GATTATAGTACTTATTGTCAATGCATCATACCATGT
762577 GAT
1 GAT
762580 CTCTCATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (36 bp):
GATTATAGTACTTATTGTCAATGCATCATACCATGT
Found at i:764693 original size:23 final size:22
Alignment explanation
Indices: 764666--764715 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
764656 TTTTTTAATT
764666 ATATTCACTATTTTAAAT-ATAAA
1 ATATTCAC--TTTTAAATCATAAA
* *
764689 ATATTTACTTTTATATCATAAA
1 ATATTCACTTTTAAATCATAAA
764711 ATATT
1 ATATT
764716 AAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTCACTTTTAAATCATAAA
Found at i:768593 original size:14 final size:14
Alignment explanation
Indices: 768574--768607 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
768564 AAATTTAAAC
768574 ATTAACCATTAGAG
1 ATTAACCATTAGAG
768588 ATTAACCATTAGAG
1 ATTAACCATTAGAG
768602 ATTAAC
1 ATTAAC
768608 AAAATTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (14 bp):
ATTAACCATTAGAG
Found at i:768936 original size:13 final size:14
Alignment explanation
Indices: 768918--768964 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
768908 TTACTACTGG
*
768918 AAAAAGAAAAT-AC
1 AAAAAGAAAATAAA
*
768931 AAAAAGAAGATAAA
1 AAAAAGAAAATAAA
768945 AAAAAGAAAA-AGAA
1 AAAAAGAAAATA-AA
768959 AAAAAG
1 AAAAAG
768965 GAAACCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAGAAAATAAA
Found at i:769341 original size:36 final size:36
Alignment explanation
Indices: 769299--769374 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
769289 CAGGTTCAAG
* *
769299 GTTACTACTGCTAAATTTTTTTTGTTAAATTTGTTA
1 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
769335 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
1 GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
769371 GTTA
1 GTTA
769375 GGAATTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.54
Consensus pattern (36 bp):
GTTACTACTGCTAAAATTTTTTTATTAAATTTGTTA
Found at i:782048 original size:2 final size:2
Alignment explanation
Indices: 782036--782074 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
782026 AGGCTGAAGA
*
782036 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
782075 AGAGATATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:790427 original size:5 final size:5
Alignment explanation
Indices: 790419--790443 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
790409 TTTTTTTTCT
790419 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
790444 AATCTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:797515 original size:7 final size:7
Alignment explanation
Indices: 797503--797528 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
797493 AAAATATTTT
797503 AAAAATA
1 AAAAATA
797510 AAAAATA
1 AAAAATA
797517 AAAAATA
1 AAAAATA
797524 AAAAA
1 AAAAA
797529 AATATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:798956 original size:142 final size:142
Alignment explanation
Indices: 798695--798984 Score: 499
Period size: 142 Copynumber: 2.0 Consensus size: 142
798685 CCAGATAAAT
* * *
798695 TAATTATAACTAATAGCTAATTATTGTGGTTTGCTTGTATATGGAACCTAATGAACTTGGTTACG
1 TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
* *
798760 CGGTTTAATGTTTGTTTGAATACTTAAGTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGCT
66 CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
798825 CTTTGAGTTCCC
131 CTTTGAGTTCCC
* * *
798837 TAATAATAACTAATAGGTAATTATTGTGGTTTGATTGTATGTGGAACCTAATGAACTTGGTGATG
1 TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
*
798902 TGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
66 CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
798967 CTTTGAGTTCCC
131 CTTTGAGTTCCC
798979 TAATAA
1 TAATAA
798985 GTGTAGTTGA
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (142 bp):
TAATAATAACTAATAGCTAATTATTGTGGTTTGATTGTATATGGAACCTAATGAACTTGGTGACG
CGGTTTAATGTTTGTTTGAATACTTAACTTTCATTAATGATTAATTGTTTGATCTCTAAGGAGAT
CTTTGAGTTCCC
Found at i:806210 original size:18 final size:18
Alignment explanation
Indices: 806177--806249 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
806167 GAATTGATTT
*
806177 TATAATTTT-CTATTTTA
1 TATAATTTTAATATTTTA
806194 TATAATTTTAATATTTTA
1 TATAATTTTAATATTTTA
* * *
806212 TTTAATTTGAAT-TGGAGTTA
1 TATAATTTTAATAT---TTTA
806232 -ATAATTTTAATATTTTA
1 TATAATTTTAATATTTTA
806249 T
1 T
806250 TTACCCCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
17 13 0.30
18 17 0.40
19 9 0.21
20 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (18 bp):
TATAATTTTAATATTTTA
Found at i:809748 original size:19 final size:18
Alignment explanation
Indices: 809745--809829 Score: 58
Period size: 19 Copynumber: 4.8 Consensus size: 18
809735 TTTAAAATAC
809745 TTTTAAAATACTTTTTTTAAA
1 TTTTAAAATA--TTTTTT-AA
* *
809766 TTTTTTAAAT-TTTTTAAA
1 -TTTTAAAATATTTTTTAA
809784 TTTT-AAA-A-TTTTT--
1 TTTTAAAATATTTTTTAA
809797 -TTTAAAATACTTTTTTAA
1 TTTTAAAATA-TTTTTTAA
809815 TTTTAAAATATTTTT
1 TTTTAAAATATTTTT
809830 AAAATATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 1 0.02
15 4 0.08
16 8 0.15
17 4 0.08
18 7 0.13
19 14 0.27
22 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:809750 original size:11 final size:11
Alignment explanation
Indices: 809734--809759 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
809724 ATTTTTTTAA
809734 TTTTAAAATAC
1 TTTTAAAATAC
809745 TTTTAAAATAC
1 TTTTAAAATAC
809756 TTTT
1 TTTT
809760 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:809778 original size:8 final size:9
Alignment explanation
Indices: 809757--809797 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
809747 TTAAAATACT
809757 TTTTTTAAA
1 TTTTTTAAA
809766 TTTTTTAAA
1 TTTTTTAAA
809775 TTTTTTAAA
1 TTTTTTAAA
*
809784 -TTTTAAAA
1 TTTTTTAAA
809792 TTTTTT
1 TTTTTT
809798 TTAAAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:809780 original size:18 final size:17
Alignment explanation
Indices: 809757--809797 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
809747 TTAAAATACT
*
809757 TTTTTTAAATTTTTTAAA
1 TTTTTTAAA-TTTTAAAA
809775 TTTTTTAAATTTTAAAA
1 TTTTTTAAATTTTAAAA
809792 TTTTTT
1 TTTTTT
809798 TTAAAATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTAAATTTTAAAA
Found at i:809811 original size:32 final size:32
Alignment explanation
Indices: 809774--809851 Score: 106
Period size: 31 Copynumber: 2.4 Consensus size: 32
809764 AATTTTTTAA
*
809774 ATTTTTTAAATTTTAAAATTTTTTTTAAAATA-
1 ATTTTTTAAATTTTAAAA-TATTTTTAAAATAT
*
809806 CTTTTTT-AATTTTAAAATATTTTTAAAATAT
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAT
809837 ATTTTTTAAAATTTT
1 ATTTTTT-AAATTTT
809852 TGTTTTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 12 0.30
31 16 0.40
32 6 0.15
33 6 0.15
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATAT
Found at i:809817 original size:49 final size:50
Alignment explanation
Indices: 809717--809832 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
809707 TATTTTTATT
*
809717 ATTTTTT--ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
**
809765 ATTTTTTAAATTTTTTAAATTTTAAAATTTTTTTTAAAATAC-TTTTTT-A
1 ATTTTTTAAATTTTTTAAATTTTAAAA-TACTTTTAAAATACTTTTTTTAA
*
809814 A-TTTTAAAATATTTTTAAA
1 ATTTTTTAAAT-TTTTTAAA
809833 ATATATTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
48 15 0.25
49 10 0.17
50 23 0.38
51 12 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (50 bp):
ATTTTTTAAATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
Found at i:809894 original size:26 final size:26
Alignment explanation
Indices: 809843--809894 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
809833 ATATATTTTT
* **
809843 TAAAATTTTTGTTTTAATTTTTAAAA
1 TAAAATTTTGGTTTTAATTTAAAAAA
809869 TAAAATTTTGGTATTT-ATTTAAAAAA
1 TAAAATTTTGGT-TTTAATTTAAAAAA
809895 CGGGCCGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
TAAAATTTTGGTTTTAATTTAAAAAA
Found at i:811356 original size:25 final size:25
Alignment explanation
Indices: 811317--811365 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
811307 ATTTTGGCTT
*
811317 TCAAAGACATAATTGGCTTACGTTG
1 TCAAAGACATAATTGGCTCACGTTG
811342 TCAAAGACA-AGATTGGCTCACGTT
1 TCAAAGACATA-ATTGGCTCACGTT
811366 TGCCTTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (25 bp):
TCAAAGACATAATTGGCTCACGTTG
Found at i:811495 original size:43 final size:42
Alignment explanation
Indices: 811439--811563 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 42
811429 CACTTGATTG
811439 TTTCATTTTAATTTAATCTCACTTTAAATATTCTCACTAATTC
1 TTTCATTTTAATTTAATCT-ACTTTAAATATTCTCACTAATTC
* *
811482 TTTCATTTTAATTTAATCAAACTTTAAATTTTCTCACTAATTC
1 TTTCATTTTAATTTAATC-TACTTTAAATATTCTCACTAATTC
*
811525 TTTCATTTTAATTTAATCTACTTTATAATATGCTCACTA
1 TTTCATTTTAATTTAATCTACTTTA-AATATTCTCACTA
811564 CTTTGTCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
42 6 0.08
43 69 0.92
ACGTcount: A:0.31, C:0.17, G:0.01, T:0.51
Consensus pattern (42 bp):
TTTCATTTTAATTTAATCTACTTTAAATATTCTCACTAATTC
Found at i:813117 original size:16 final size:16
Alignment explanation
Indices: 813096--813132 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
813086 TAAGTTTCTT
813096 ATTTGAATTA-ATTTAA
1 ATTTGAATTAGA-TTAA
813112 ATTTGAATTAGATTAA
1 ATTTGAATTAGATTAA
813128 ATTTG
1 ATTTG
813133 TTTACGGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
ATTTGAATTAGATTAA
Found at i:841719 original size:2 final size:2
Alignment explanation
Indices: 841712--841754 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
841702 TATTGTGTTA
841712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
841754 A
1 A
841755 ATCAAGGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:847993 original size:20 final size:20
Alignment explanation
Indices: 847955--847998 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
847945 GTCATTTCGC
**
847955 TATTA-TATTGTTATTATAT
1 TATTATTATTGTTAGAATAT
847974 TATTATTATTGTTAGAATAT
1 TATTATTATTGTTAGAATAT
847994 T-TTAT
1 TATTAT
847999 AACTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TATTATTATTGTTAGAATAT
Found at i:848968 original size:31 final size:31
Alignment explanation
Indices: 848930--848989 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
848920 TCATATTTTA
*
848930 ATTTGATCAAGTTTAGTCCTTGTACTTTTCT
1 ATTTGATCAAGTTTAGTCCATGTACTTTTCT
** *
848961 ATTTGATCATTTTTAGTTCATGTACTTTT
1 ATTTGATCAAGTTTAGTCCATGTACTTTT
848990 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.55
Consensus pattern (31 bp):
ATTTGATCAAGTTTAGTCCATGTACTTTTCT
Found at i:849450 original size:14 final size:14
Alignment explanation
Indices: 849431--849458 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
849421 ATATATTTAT
849431 TGTGAATTGTGAAA
1 TGTGAATTGTGAAA
849445 TGTGAATTGTGAAA
1 TGTGAATTGTGAAA
849459 CCAACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TGTGAATTGTGAAA
Found at i:858616 original size:19 final size:18
Alignment explanation
Indices: 858588--858626 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
858578 ATAATATTGT
*
858588 ATTAAATTAATATAAAAA
1 ATTAAATTAAAATAAAAA
*
858606 ATTAAATTTAAAATAATAA
1 ATTAAA-TTAAAATAAAAA
858625 AT
1 AT
858627 AATAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAATTAAAATAAAAA
Found at i:875673 original size:34 final size:34
Alignment explanation
Indices: 875596--875666 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
875586 ACTATCGATA
* * *
875596 TTATATCAATCAAGTTTTTCTATTATTGAAACTG
1 TTATATTAATTAAGTTTTTCTATTATTGAAACCG
875630 TTATATTAATTAAGTCTTTT-TATTATTGAAACCG
1 TTATATTAATTAAGT-TTTTCTATTATTGAAACCG
875664 TTA
1 TTA
875667 ATTTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.49
Consensus pattern (34 bp):
TTATATTAATTAAGTTTTTCTATTATTGAAACCG
Found at i:879512 original size:39 final size:39
Alignment explanation
Indices: 879465--879571 Score: 187
Period size: 39 Copynumber: 2.7 Consensus size: 39
879455 TGATATGAAT
879465 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
879504 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
* * *
879543 GAAAGAAACCCTCAGGAGACTAAAAAGGA
1 GAAAGAAGCCCTCGGGAGACTAAGAAGGA
879572 AAATTGCAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.42, C:0.18, G:0.29, T:0.11
Consensus pattern (39 bp):
GAAAGAAGCCCTCGGGAGACTAAGAAGGATGCAATGATC
Found at i:879527 original size:132 final size:130
Alignment explanation
Indices: 879147--879527 Score: 367
Period size: 132 Copynumber: 2.9 Consensus size: 130
879137 GGCTACTGTG
* * * * * *
879147 TTTATGAACATTAAAAAGCGGAGCAAACGTAGAAATTTGGACGGTGCGATGACTGAAAGAATCCC
1 TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
* *
879212 TCAGGAG-AATAAGGATGCAATGACTGAAAGAAGCCCT-GAAGAGACTAAGAAGGAAAACTGCGA
66 TCAGGAGTAAGAAGGATGCAATGACTGAAAGAAGCCCTCG-GGAGACT---AAGGAAAACTGCGA
879275 TCGT
127 TCGT
* * * **
879279 TTTATGAACGTTAAAGTGCAGAGCAAAG-GCAGAAACTTGGTTGGTGCGATGACA-GAAAGAAGC
1 TTTATGAACATTAAAGAGCAGAGC-AAGCGCAGAAATTTGGACGGTGCGATGA-ATGAAAGAAGC
* * * * * * * *
879342 CCTCAGGAGTGTGAGGAGAATGCGATGACTGAAAGTATCCCTCAGGAGACTAAGGAAAACTGTGA
64 CCTCAGGA--GTAAGAAGGATGCAATGACTGAAAGAAGCCCTCGGGAGACTAAGGAAAACTGCGA
*
879407 TCTT
127 TCGT
* * * * **
879411 TTTATGAACATTAAAGCGCAGAGCAAGCACAGGAATTTGGACAGTGATATGAATGAAAGAAGCCC
1 TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
*
879476 TCGGGAGACTAAGAAGGATGCAATGA-TCGAAAGAAGCCCTCGGGAGACTAAG
66 TCAGGAG--TAAGAAGGATGCAATGACT-GAAAGAAGCCCTCGGGAGACTAAG
879528 AAGGATGCAA
Statistics
Matches: 198, Mismatches: 40, Indels: 22
0.76 0.15 0.08
Matches are distributed among these distances:
130 1 0.01
131 5 0.03
132 160 0.81
133 2 0.01
134 1 0.01
135 29 0.15
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (130 bp):
TTTATGAACATTAAAGAGCAGAGCAAGCGCAGAAATTTGGACGGTGCGATGAATGAAAGAAGCCC
TCAGGAGTAAGAAGGATGCAATGACTGAAAGAAGCCCTCGGGAGACTAAGGAAAACTGCGATCGT
Found at i:879821 original size:96 final size:96
Alignment explanation
Indices: 879603--879824 Score: 252
Period size: 96 Copynumber: 2.3 Consensus size: 96
879593 TATTAAAGCG
* * *
879603 AATTTGGACAGTGCTATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCGATCTTTT
1 AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
*
879668 TATGAACACTAAAGCACGGAGCAAACATAGA
66 TATAAACACTAAAGCACGGAGCAAACATAGA
* * * ** * ** *
879699 AATCTGGACAGTGCGATAACCAAAAGAAGTCCTTGGGAGACTAAGAAGAAAAACTGTGATCTTTC
1 AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
* *
879764 TATAAACATTAAAGGGA-GGAGCAAAGGCA-A-A
66 TATAAACACTAAA-GCACGGAGCAAA--CATAGA
*
879795 AATTTGGACAGTGCAATGGCTGAAAGAAGC
1 AATTTGGACAGTGCAATGACTGAAAGAAGC
879825 GGCAATGATA
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
96 97 0.95
97 3 0.03
98 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (96 bp):
AATTTGGACAGTGCAATGACTGAAAGAAGCCCTCAGGAGACTAAGAAGAAAAACTGCGATCTTTC
TATAAACACTAAAGCACGGAGCAAACATAGA
Found at i:893208 original size:26 final size:26
Alignment explanation
Indices: 893159--893208 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
893149 ATTAATACGA
*
893159 TTTGTATTTGATATACCTTTAAAAGT
1 TTTGTATTTGATATACCTTCAAAAGT
893185 TTTGTATTTGATATA-CTTCCAAAA
1 TTTGTATTTGATATACCTT-CAAAA
893209 TCATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (26 bp):
TTTGTATTTGATATACCTTCAAAAGT
Found at i:894336 original size:33 final size:30
Alignment explanation
Indices: 894261--894336 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
894251 TTTGAGGTTC
*
894261 TAATTAAAATTTTTAAAAATGTTAGGAGAT
1 TAATTAAATTTTTTAAAAATGTTAGGAGAT
* * *
894291 TAATGATAATTTTTTTAAAATTTTAGGAGAACT
1 TAATTA-AATTTTTTAAAAATGTTAGGAG-A-T
894324 TAATTAACATTTT
1 TAATTAA-ATTTT
894337 CGAAAAACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 5 0.14
31 19 0.51
32 2 0.05
33 11 0.30
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (30 bp):
TAATTAAATTTTTTAAAAATGTTAGGAGAT
Found at i:899997 original size:16 final size:16
Alignment explanation
Indices: 899976--900006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
899966 TATATTTTTA
899976 TTTTTTAAATTTTAAT
1 TTTTTTAAATTTTAAT
*
899992 TTTTTTAGATTTTAA
1 TTTTTTAAATTTTAA
900007 ATTTCAAATC
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTAAATTTTAAT
Found at i:903521 original size:2 final size:2
Alignment explanation
Indices: 903480--903511 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
903470 CTAATTAAAT
903480 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
903512 AGTAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:911709 original size:2 final size:2
Alignment explanation
Indices: 911702--911747 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
911692 TAATAAAGTC
*
911702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
911744 AT AT
1 AT AT
911748 GAATATTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:913519 original size:19 final size:18
Alignment explanation
Indices: 913492--913527 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
913482 TGTGTGTTAT
*
913492 AAATTACATAATATAAAAA
1 AAATAACATAATA-AAAAA
913511 AAATAACATAATAAAAA
1 AAATAACATAATAAAAA
913528 GTATTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAACATAATAAAAAA
Found at i:915285 original size:45 final size:45
Alignment explanation
Indices: 915221--915308 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
915211 GAATCATTAG
* *
915221 CTTAAATATCGGGTTTGCTGAGTCGGACCGCACCGGGTCTAGGAA
1 CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGGAA
*
915266 CTTAAATATCGGGTTTGCTGAGTCGGACCCCATCGGATCTAGG
1 CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGG
915309 GATTTGACAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (45 bp):
CTTAAATATCGGGTTTGCTGAGTCGGACCCCACCGGATCTAGGAA
Found at i:929138 original size:51 final size:51
Alignment explanation
Indices: 929032--929143 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
929022 TACCCTTAAA
* * * *
929032 ATTTACACATTTTGTCAATTTTGTCCCGATTTAACAAATTTAGCTTGTAAC
1 ATTTACACATTTGGTCAATTTTGTCCCGATTTAACAAATTTAACCTGCAAC
* *
929083 ATTTACACATTTGGTCAATTTTAGT-CTGATTTAACAAATTTAACACT-CAAT
1 ATTTACACATTTGGTCAATTTT-GTCCCGATTTAACAAATTTAAC-CTGCAAC
*
929134 ATTTATACAT
1 ATTTACACAT
929144 ATCATGTCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 49 0.94
52 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (51 bp):
ATTTACACATTTGGTCAATTTTGTCCCGATTTAACAAATTTAACCTGCAAC
Found at i:929970 original size:2 final size:2
Alignment explanation
Indices: 929963--930014 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
929953 TCTTTTATTT
929963 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
930005 TA TA TA TA TA
1 TA TA TA TA TA
930015 AACTTTATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:931302 original size:19 final size:18
Alignment explanation
Indices: 931276--931318 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
931266 TTTAATAGAC
931276 AATAAAAACTTCACCGAAA
1 AATAAAAACTTCACC-AAA
* *
931295 ACTAAAAATTTCACCAAA
1 AATAAAAACTTCACCAAA
931313 AATAAA
1 AATAAA
931319 TTTTTGGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAAACTTCACCAAA
Found at i:934646 original size:17 final size:16
Alignment explanation
Indices: 934623--934666 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
934613 CTGTTTTATT
934623 TTTGAAATATTAATTA
1 TTTGAAATATTAATTA
934639 TATTGAAA-ATT-ATTA
1 T-TTGAAATATTAATTA
934654 TTT-AAATA-TAATT
1 TTTGAAATATTAATT
934667 TTATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.16
14 6 0.24
15 5 0.20
16 4 0.16
17 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTGAAATATTAATTA
Found at i:944584 original size:5 final size:5
Alignment explanation
Indices: 944576--944605 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
944566 AATTAAATTG
944576 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
944606 GAAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:947794 original size:38 final size:38
Alignment explanation
Indices: 947672--947804 Score: 110
Period size: 38 Copynumber: 3.4 Consensus size: 38
947662 GACCTCGAGT
* * *
947672 CGATGAGACATTGGGTGTCACTATTTTACTTCGAA-TAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGAACT--ATC
* * * *
947713 CGATGAGATACTGGGTATC-ACTTTACTTCG-GCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTA-TC
* *
947750 CAATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
*
947788 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
947805 CCAATTTGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.22
38 37 0.51
39 3 0.04
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
Found at i:951274 original size:24 final size:24
Alignment explanation
Indices: 951241--951293 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
951231 AAAGTTCATC
951241 ATTAA-ACAATTGGAAATTTGATA
1 ATTAAGACAATTGGAAATTTGATA
951264 ATTAAGACAATTGGAAATTTGATA
1 ATTAAGACAATTGGAAATTTGATA
951288 ATTAAG
1 ATTAAG
951294 TGCCTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (24 bp):
ATTAAGACAATTGGAAATTTGATA
Found at i:953252 original size:2 final size:2
Alignment explanation
Indices: 953245--953274 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
953235 TACATAATTA
953245 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
953275 GAAAATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:959684 original size:11 final size:11
Alignment explanation
Indices: 959668--959692 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
959658 GCGAGGATTC
959668 CATTCCTGTGT
1 CATTCCTGTGT
959679 CATTCCTGTGT
1 CATTCCTGTGT
959690 CAT
1 CAT
959693 CATCAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (11 bp):
CATTCCTGTGT
Found at i:963534 original size:51 final size:51
Alignment explanation
Indices: 963439--963706 Score: 347
Period size: 51 Copynumber: 5.3 Consensus size: 51
963429 ACTTCTAATC
*
963439 AGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
963489 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
963540 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG---A-T--C-AGTGACA
963598 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC---G---
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
963642 -GTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
963692 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
963707 ATGTGATCCG
Statistics
Matches: 193, Mismatches: 9, Indels: 31
0.83 0.04 0.13
Matches are distributed among these distances:
43 22 0.11
44 18 0.09
47 2 0.01
50 21 0.11
51 80 0.41
53 1 0.01
54 2 0.01
55 1 0.01
57 17 0.09
58 29 0.15
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:963596 original size:7 final size:7
Alignment explanation
Indices: 963584--963615 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
963574 TTATCTGATC
963584 AGTGACA
1 AGTGACA
963591 AGTGACA
1 AGTGACA
963598 AGTGACA
1 AGTGACA
*
963605 AGTGATA
1 AGTGACA
963612 AGTG
1 AGTG
963616 GTAGCTTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:963652 original size:57 final size:58
Alignment explanation
Indices: 963533--963658 Score: 218
Period size: 57 Copynumber: 2.2 Consensus size: 58
963523 TTATCTCATC
*
963533 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACA
1 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
963591 AGTGACAAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCGGTGACA
1 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
963648 AGTGATAAGTG
1 AGTGATAAGTG
963659 GTAGCTTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 35 0.55
58 29 0.45
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (58 bp):
AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:963658 original size:101 final size:104
Alignment explanation
Indices: 963439--963703 Score: 372
Period size: 101 Copynumber: 2.6 Consensus size: 104
963429 ACTTCTAATC
*
963439 AGTGACAAGTGATAAGTGGTAG-TTTAGCTACACTTATCTGATCAGTG---A-T---AAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTGACA
963496 AGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCAGTG
66 AGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCA--G
963537 ATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTG
1 ---AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTG
* *
963602 ACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC-G
63 ACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCAG
*
963642 -GTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATTAGTGACAAGTGACAAGTGA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTGA
963704 TAAATGTGAT
Statistics
Matches: 152, Mismatches: 4, Indels: 16
0.88 0.02 0.09
Matches are distributed among these distances:
101 83 0.55
102 24 0.16
105 2 0.01
106 1 0.01
108 19 0.12
109 23 0.15
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (104 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACAAGTGACA
AGTGATAAGTGATAGCTTTAGCTACACTTATCTCATCAG
Found at i:963660 original size:43 final size:44
Alignment explanation
Indices: 963598--963702 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
963588 ACAAGTGACA
963598 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* * *
963641 GGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATT
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
963685 AGTGACAAGTGACAAGTG
1 AGTGACAAGTGATAAGTG
963703 ATAAATGTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 22 0.39
44 34 0.61
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:964576 original size:31 final size:31
Alignment explanation
Indices: 964519--964580 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
964509 CAAAAAAAAG
964519 TTCAAACCCCAATATGAAAAAAAATTATCTAA
1 TTCAAACCCCAATATGAAAAAAAATTA-CTAA
* *
964551 TTCAATCCCCAATAT-AAAAACAATTACTAA
1 TTCAAACCCCAATATGAAAAAAAATTACTAA
964581 ATTTAGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 10 0.36
32 14 0.50
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.26
Consensus pattern (31 bp):
TTCAAACCCCAATATGAAAAAAAATTACTAA
Found at i:970586 original size:20 final size:19
Alignment explanation
Indices: 970561--970609 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
970551 ATCTCTTTCT
970561 ATCAAAAAATTACAAAAAAA
1 ATCAAAAAATT-CAAAAAAA
* * *
970581 ATCAAAATATTTATAAAAA
1 ATCAAAAAATTCAAAAAAA
*
970600 TTCAAAAAAT
1 ATCAAAAAAT
970610 CTAGAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (19 bp):
ATCAAAAAATTCAAAAAAA
Found at i:975431 original size:14 final size:14
Alignment explanation
Indices: 975412--975466 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
975402 TTGAAAGATA
975412 AAATATTAATATAT
1 AAATATTAATATAT
*
975426 AAATATTAATTTACT
1 AAATATTAATATA-T
* *
975441 TATTGATTTAATATAT
1 AAAT-A-TTAATATAT
975457 AAATATTAAT
1 AAATATTAAT
975467 TTATTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 17 0.53
15 4 0.12
16 4 0.12
17 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATATTAATATAT
Found at i:975455 original size:31 final size:31
Alignment explanation
Indices: 975417--975484 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
975407 AGATAAAATA
975417 TTAATATATAAATATTAATTTACTTATTGAT
1 TTAATATATAAATATTAATTTACTTATTGAT
* **
975448 TTAATATATAAATATTAATTTATTTATTTTT
1 TTAATATATAAATATTAATTTACTTATTGAT
975479 TTAATA
1 TTAATA
975485 AAAAGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (31 bp):
TTAATATATAAATATTAATTTACTTATTGAT
Found at i:981802 original size:48 final size:48
Alignment explanation
Indices: 981744--981837 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
981734 TCTCTTAATG
* *
981744 TACTCACAGTGCCATTTTCCGAGCCTATTTCTTTCTTCTCCAACCCAA
1 TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCCAA
* *
981792 TACTCGCAGTGCCATTTTCCGAACTTATCTCTTTCTTCTCCAACCC
1 TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCC
981838 GACAACATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.36, G:0.09, T:0.36
Consensus pattern (48 bp):
TACTCACAGTGCCATTTTCCGAACCTATCTCTTTCTTCTCCAACCCAA
Found at i:985328 original size:14 final size:16
Alignment explanation
Indices: 985297--985328 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
985287 GTGACCAAAT
985297 TTATAGAAAATGTAAA
1 TTATAGAAAATGTAAA
985313 TTAT-GAAAAT-TAAA
1 TTATAGAAAATGTAAA
985327 TT
1 TT
985329 TATTGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
TTATAGAAAATGTAAA
Found at i:985331 original size:15 final size:17
Alignment explanation
Indices: 985293--985331 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
985283 AATCGTGACC
985293 AAATTTATAGAAAATGT
1 AAATTTATAGAAAATGT
985310 AAA-TTAT-GAAAAT-T
1 AAATTTATAGAAAATGT
985324 AAATTTAT
1 AAATTTAT
985332 TGTTATACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 4 0.19
17 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAATTTATAGAAAATGT
Done.