Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 16
Found at i:565338 original size:29 final size:30
Alignment explanation
Indices: 565268--565327 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
565258 CAATTTAAGG
565268 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
565299 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
565328 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:565538 original size:20 final size:20
Alignment explanation
Indices: 565509--565582 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
565499 AATGCAATTA
*
565509 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
565529 GTGTATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
565550 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
565570 GTGCATCCATGCA
1 GTGCATCGATGCA
565583 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:565556 original size:41 final size:41
Alignment explanation
Indices: 565509--565591 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
565499 AATGCAATTA
* * *
565509 GTGCATCGATGCATCCTTCTGTGTATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCA-CGAAGGCT
565550 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
565591 G
1 G
565592 CAACGACTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
Found at i:568229 original size:34 final size:30
Alignment explanation
Indices: 568191--568259 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
568181 TTGATATAAC
568191 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
568225 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
568254 AATTTA
1 AATTTA
568260 TTCAAAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:568241 original size:30 final size:30
Alignment explanation
Indices: 568200--568259 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
568190 CAATTTAAGG
568200 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTA
568231 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATGGTTTTTGGACTTAATTGAATTTA
568260 TTCAAAGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTA
Found at i:568407 original size:20 final size:20
Alignment explanation
Indices: 568339--568530 Score: 105
Period size: 20 Copynumber: 9.7 Consensus size: 20
568329 AGGGTGTTAA
*
568339 AGTGCATCCATGCATCCCTGC
1 AGTGCATCGATGCAT-CCTGC
*
568360 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCGATGCATCCTG--C
*
568381 TAGTGCATCGATGCATCATGC
1 -AGTGCATCGATGCATCCTGC
*
568402 AGTGCATCCATGCA--CT-C
1 AGTGCATCGATGCATCCTGC
** *
568419 A-AACACCGAATGCAAT--T--
1 AGTGCATCG-ATGC-ATCCTGC
*
568436 AGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCATCCTGC
* *
568456 TGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCATCCTGC
* **
568476 TGTGCATCGATGCATCAAGGC
1 AGTGCATCGATGCATC-CTGC
* *
568497 TGTGCATCGATGCATCCTGT
1 AGTGCATCGATGCATCCTGC
* *
568517 TGTGCATCCATGCA
1 AGTGCATCGATGCA
568531 CGAAGGCTGC
Statistics
Matches: 139, Mismatches: 19, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
16 5 0.04
17 11 0.08
18 8 0.06
19 4 0.03
20 62 0.45
21 33 0.24
22 13 0.09
23 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTGC
Found at i:568510 original size:41 final size:41
Alignment explanation
Indices: 568437--568539 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 41
568427 AATGCAATTA
***
568437 GTGCATCGATGCATC-CTTCTGTGCATCGATGCATCCT-TCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTGT-T
568477 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTGTT
*
568518 GTGCATCCATGCA-CGAAGGCTG
1 GTGCATCGATGCATC-AAGGCTG
568540 CAACGGCTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
40 16 0.29
41 39 0.70
42 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTGTT
Found at i:568662 original size:21 final size:21
Alignment explanation
Indices: 568633--568672 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
568623 TTTGAGTAGA
568633 AAAATCATCCCTAAACGGCTCC
1 AAAATCATCCC-AAACGGCTCC
*
568655 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
568673 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:574719 original size:18 final size:18
Alignment explanation
Indices: 574696--574748 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
574686 AGGGATTATC
*
574696 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
574714 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
574732 AGTGGTCATTCAGGACA
1 AGTGGTCATTCGGGACA
574749 AATATTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:574954 original size:2 final size:2
Alignment explanation
Indices: 574947--574995 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
574937 ACATGCAAGT
*
574947 TA TA TA TA TA CA 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
574989 TA TA TA T
1 TA TA TA T
574996 GCCTCACTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:576137 original size:6 final size:6
Alignment explanation
Indices: 576126--576152 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
576116 GAATCGAGTT
576126 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
576153 TTTTCCATAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:581731 original size:17 final size:17
Alignment explanation
Indices: 581709--581745 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
581699 CCAAGTTAAC
581709 TTATTAAAGGATAATTG
1 TTATTAAAGGATAATTG
581726 TTATTAAAGGATAATTG
1 TTATTAAAGGATAATTG
581743 TTA
1 TTA
581746 ATGTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (17 bp):
TTATTAAAGGATAATTG
Found at i:584320 original size:35 final size:35
Alignment explanation
Indices: 584281--584487 Score: 297
Period size: 35 Copynumber: 5.9 Consensus size: 35
584271 TGAATAAGAA
584281 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
* *
584316 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAG-T
584352 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
** * * *
584387 GAACGGGATGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAG-T
584423 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
** **
584458 GAACGGGAGGAAGCATAAGCACTTTCGATT
1 GAACGAAAGGAAGCATCGGCACTTTCGATT
584488 TAATTGTTCA
Statistics
Matches: 152, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
35 89 0.59
36 63 0.41
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
Found at i:584368 original size:71 final size:71
Alignment explanation
Indices: 584276--584487 Score: 379
Period size: 71 Copynumber: 3.0 Consensus size: 71
584266 GAAGGTGAAT
*
584276 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCGGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATCGGCACTTT
584341 CGATTC
66 CGATTC
* *
584347 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGATGAAGCATCGACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATCGGCACTTT
584412 CGATTC
66 CGATTC
**
584418 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATAAGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATCGGCACTTT
584483 CGATT
66 CGATT
584488 TAATTGTTCA
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 134 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGGAGGAAGCATCGGCACTTT
CGATTC
Found at i:586116 original size:13 final size:13
Alignment explanation
Indices: 586098--586128 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
586088 AATAGAGAAG
*
586098 TAATATAATTAAA
1 TAATATAATCAAA
586111 TAATATAATCAAA
1 TAATATAATCAAA
586124 TAATA
1 TAATA
586129 GAGAAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATATAATCAAA
Found at i:588406 original size:42 final size:42
Alignment explanation
Indices: 588360--588444 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
588350 TTCTTTGAAA
* *
588360 TTTTGTGTTTGTTACATGTAATTCGTTTTTCGAAAAATATTT
1 TTTTGGGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTT
* *
588402 TTTTGGGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATTT
1 TTTTGGGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTT
588444 T
1 T
588445 CCAGTGTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.54
Consensus pattern (42 bp):
TTTTGGGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTT
Found at i:588454 original size:42 final size:42
Alignment explanation
Indices: 588364--588454 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
588354 TTGAAATTTT
* ***
588364 GTGTTTGTTACATGTAATTCGTTTTTCGAAAAATATTTTTTT
1 GTGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTTTCCA
* * *
588406 GGGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATTTTCCA
1 GTGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTTTCCA
588448 GTGTTTG
1 GTGTTTG
588455 GTTGGAGGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.51
Consensus pattern (42 bp):
GTGTTTGTTACACGTAATTCGTTTTTCGAAAAATATTTTCCA
Found at i:588695 original size:21 final size:20
Alignment explanation
Indices: 588669--588715 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
588659 TAATTATTAA
*
588669 AATATTTAAAATATATTTATT
1 AATATTTAAAATA-ATATATT
*
588690 AATATTTATAATAATATATT
1 AATATTTAAAATAATATATT
588710 -ATATTT
1 AATATTT
588716 TTAATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTAAAATAATATATT
Found at i:588715 original size:19 final size:20
Alignment explanation
Indices: 588669--588726 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
588659 TAATTATTAA
* *
588669 AATATTTAAAATATATTTATT
1 AATATTTATAATA-ATATATT
588690 AATATTTATAATAATATATT
1 AATATTTATAATAATATATT
* *
588710 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
588727 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
20 6 0.18
21 12 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTATAATAATATATT
Found at i:588871 original size:23 final size:23
Alignment explanation
Indices: 588845--588921 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
588835 ATAATATAAT
588845 AATATTTTAATAAATATATTTAA
1 AATATTTTAATAAATATATTTAA
** * *
588868 AATATACTAATTAATATTTTTAA
1 AATATTTTAATAAATATATTTAA
588891 AATATAATTATAA-AAATAATATTTAA
1 AATAT--TT-TAATAAAT-ATATTTAA
588917 TAATA
1 -AATA
588922 AATAAAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
23 24 0.59
25 3 0.07
26 10 0.24
27 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATTTTAATAAATATATTTAA
Found at i:588884 original size:35 final size:35
Alignment explanation
Indices: 588831--588918 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
588821 TTAATATTGA
*
588831 TATAATAAT-ATAA-TAATATTTTAATAAATAT-AT
1 TATAAAAATAATAATTAATATTTTAA-AAATATAAT
* *
588864 T-TAAAATATACTAATTAATATTTTTAAAATATAAT
1 TATAAAA-ATAATAATTAATATTTTAAAAATATAAT
*
588899 TATAAAAATAATATTTAATA
1 TATAAAAATAATAATTAATA
588919 ATAAATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
32 4 0.09
33 3 0.07
34 9 0.20
35 24 0.53
36 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (35 bp):
TATAAAAATAATAATTAATATTTTAAAAATATAAT
Found at i:588920 original size:22 final size:22
Alignment explanation
Indices: 588897--588978 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
588887 TTAAAATATA
588897 ATTAT-AAAAATAATATTTAAT
1 ATTATAAAAAATAATATTTAAT
*
588918 A--ATAAATAA-AATATTTTAAT
1 ATTATAAAAAATAATA-TTTAAT
* *
588938 ATTTTAAAATAATAATATTAAAT
1 ATTATAAAA-AATAATATTTAAT
* * *
588961 TTTATGATAAATAATATT
1 ATTATAAAAAATAATATT
588979 ATTTATTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.13
20 11 0.23
21 1 0.02
22 13 0.28
23 12 0.26
24 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
ATTATAAAAAATAATATTTAAT
Found at i:588922 original size:19 final size:20
Alignment explanation
Indices: 588895--588938 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
588885 TTTTAAAATA
*
588895 TAATTATAAA-AATAATA-TT
1 TAATAATAAATAA-AATATTT
588914 TAATAATAAATAAAATATTT
1 TAATAATAAATAAAATATTT
588934 TAATA
1 TAATA
588939 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAATAAATAAAATATTT
Found at i:589188 original size:30 final size:30
Alignment explanation
Indices: 589136--589217 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
589126 TTCAAAAAAT
*
589136 ATAATATATTTTTTCA--AATTCAAATT-TCA
1 ATAATTTA-TTTTTCAGTAATTCAAATTCT-A
589165 ATAATTTATTTTTCAGTAATTCAAATTCTA
1 ATAATTTATTTTTCAGTAATTCAAATTCTA
* *
589195 GTAATTTAAATTTT-AGTAATTCA
1 ATAATTT-ATTTTTCAGTAATTCA
589218 TTTTTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 7 0.15
29 7 0.15
30 26 0.57
31 6 0.13
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (30 bp):
ATAATTTATTTTTCAGTAATTCAAATTCTA
Found at i:589224 original size:15 final size:15
Alignment explanation
Indices: 589152--589217 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
589142 TATTTTTTCA
* *
589152 AATTCAAATTTCAAT
1 AATTCAAATTTTAGT
* *
589167 AATT-TATTTTTCAGT
1 AATTCAAATTTT-AGT
*
589182 AATTCAAATTCTAGT
1 AATTCAAATTTTAGT
*
589197 AATTTAAATTTTAGT
1 AATTCAAATTTTAGT
589212 AATTCA
1 AATTCA
589218 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 4 0.10
15 31 0.79
16 4 0.10
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (15 bp):
AATTCAAATTTTAGT
Found at i:591373 original size:39 final size:40
Alignment explanation
Indices: 591303--591381 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
591293 TTGATAATCA
591303 ATTATCACTTTAATATTTACCTGTCACATAATTATTATGT
1 ATTATCACTTTAATATTTACCTGTCACATAATTATTATGT
591343 ATTATCACTTTAATA-TTACCTGTCACATAATTATTATGT
1 ATTATCACTTTAATATTTACCTGTCACATAATTATTATGT
591382 TTTTTTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 24 0.62
40 15 0.38
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (40 bp):
ATTATCACTTTAATATTTACCTGTCACATAATTATTATGT
Found at i:595927 original size:7 final size:7
Alignment explanation
Indices: 595910--595947 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
595900 TCAGATCTTA
595910 TTTTCCTT
1 TTTTCC-T
595918 TTTTCCT
1 TTTTCCT
595925 TTTTCCT
1 TTTTCCT
595932 TTTTCCT
1 TTTTCCT
595939 TTTTCCT
1 TTTTCCT
595946 TT
1 TT
595948 AGTACAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCCT
Found at i:598253 original size:3 final size:3
Alignment explanation
Indices: 598245--598319 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
598235 CATTTTTTAT
* * * * *
598245 TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA TAA TAA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
598293 TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
598320 AAATAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:598265 original size:15 final size:15
Alignment explanation
Indices: 598247--598317 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
598237 TTTTTTATTT
598247 ATTATTATTATTATA
1 ATTATTATTATTATA
*
598262 ATTATTATAATTATA
1 ATTATTATTATTATA
*
598277 ATAATTATTATTATA
1 ATTATTATTATTATA
598292 ATTATTA-TA-TAT-
1 ATTATTATTATTATA
598304 ATTATTATTATTAT
1 ATTATTATTATTAT
598318 TAAAATAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
12 7 0.14
13 5 0.10
14 5 0.10
15 33 0.66
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:598803 original size:16 final size:16
Alignment explanation
Indices: 598766--598804 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
598756 GGAGCAACCA
598766 ACAGCAAACCCAAAGC
1 ACAGCAAACCCAAAGC
*
598782 AGAGCAAACCCACAA-C
1 ACAGCAAACCCA-AAGC
598798 ACAGCAA
1 ACAGCAA
598805 CCAGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.51, C:0.36, G:0.13, T:0.00
Consensus pattern (16 bp):
ACAGCAAACCCAAAGC
Found at i:599881 original size:22 final size:22
Alignment explanation
Indices: 599856--599899 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
599846 GGTATTTTAA
599856 AATTAAATATTATAAAAATTAT
1 AATTAAATATTATAAAAATTAT
* * **
599878 AATTTAATTTTATTTAAATTAT
1 AATTAAATATTATAAAAATTAT
599900 TATATTGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATATTATAAAAATTAT
Found at i:600000 original size:23 final size:24
Alignment explanation
Indices: 599968--600016 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
599958 TCTTTTCTGA
*
599968 TATTTCTAAA-TAAATAAATATTT
1 TATTTATAAACTAAATAAATATTT
*
599991 TATTTATAAACGTATATAAATATTT
1 TATTTATAAAC-TAAATAAATATTT
600016 T
1 T
600017 TTCATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
25 13 0.59
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTTATAAACTAAATAAATATTT
Found at i:611194 original size:10 final size:9
Alignment explanation
Indices: 611169--611234 Score: 57
Period size: 10 Copynumber: 7.2 Consensus size: 9
611159 ATTATGCTTG
611169 AAGAAAAAA
1 AAGAAAAAA
611178 AAG---AAA
1 AAGAAAAAA
611184 AAGAACAAAA
1 AAGAA-AAAA
611194 AAGAAAAAA
1 AAGAAAAAA
* *
611203 ATGAGGAAAA
1 AAGA-AAAAA
611213 AAGAAAGAAA
1 AAGAAA-AAA
611223 AAGAAAGAAA
1 AAGAAA-AAA
611233 AA
1 AA
611235 AGAGGGGGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
6 6 0.13
9 11 0.23
10 30 0.64
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:611195 original size:16 final size:15
Alignment explanation
Indices: 611169--611201 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
611159 ATTATGCTTG
611169 AAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
611184 AAGAACAAAAAAGAAA
1 AAGAA-AAAAAAGAAA
611200 AA
1 AA
611202 AATGAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:611632 original size:19 final size:17
Alignment explanation
Indices: 611590--611638 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
611580 TATTTTCTCT
611590 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
611606 ATATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
611624 AAAATTCAAATTATT
1 -AAATTCAATTTATT
611639 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:612329 original size:114 final size:115
Alignment explanation
Indices: 611933--612382 Score: 796
Period size: 115 Copynumber: 3.9 Consensus size: 115
611923 TACCATGTTA
611933 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
611998 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGC
612048 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
612113 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGC
612163 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
612228 TTTGGTATGAACCCC-AAAACCAATCATTGGATTTGAAAGATAAATTTGC
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGC
* * *
612277 TCATAATAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* * * * * *
612342 TTCGGTAGGAACCAC-AGAACCAATCATTAGAATTGAAAGAT
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGAT
612383 GAACTGCATG
Statistics
Matches: 325, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
114 131 0.40
115 194 0.60
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (115 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGC
Found at i:612335 original size:229 final size:229
Alignment explanation
Indices: 611933--612382 Score: 794
Period size: 229 Copynumber: 2.0 Consensus size: 229
611923 TACCATGTTA
611933 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
611998 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAA
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCATAATAGAAATAA
* * *
612063 GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC
131 GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC
* *
612128 AAAAACCAATCATTGGATTTGAAAGATAAATTTGC
196 -AAAACCAATCATTAGAATTGAAAGATAAATTTGC
612163 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
612228 TTTGGTATGAACCCC-AAAACCAATCATTGGATTTGAAAGATAAATTTGCTCATAATAGAAATAA
66 TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCATAATAGAAATAA
* *
612292 GGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC
131 GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC
*
612357 AGAACCAATCATTAGAATTGAAAGAT
196 AAAACCAATCATTAGAATTGAAAGAT
612383 GAACTGCATG
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 23 0.11
229 107 0.51
230 80 0.38
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (229 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCATAATAGAAATAA
GAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAACCAC
AAAACCAATCATTAGAATTGAAAGATAAATTTGC
Found at i:613439 original size:113 final size:113
Alignment explanation
Indices: 613312--613973 Score: 773
Period size: 113 Copynumber: 5.8 Consensus size: 113
613302 TCAGCATTAA
* *
613312 CATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGA
1 CATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * *
613377 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAATGGATCAC
66 GAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCAG
* *
613425 CATTTCCAGTTCGAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * *
613490 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGAACAG
66 GAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCAG
*
613538 CAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * *
613603 GAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATCAG
66 GAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCAG
* * * *
613651 TATTACCAGTTTGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * * * *
613716 GAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATCAA
66 GAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCAG
* *
613764 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAA
1 CATTGCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * *
613825 TGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCAC-AGAAAGAGAT-AG
63 TGAGAAGAACTTGTTCAACCTTTTGCTTAAATTC-ATCACTCG-ATG-GATCAG
* * *
613876 -ATTAGCATCAACCTTTCCGGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGA
1 CATT-GC--C-A--GTT-C---G--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
613940 AGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
54 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
613974 AATGACTCTA
Statistics
Matches: 484, Mismatches: 43, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
111 9 0.02
112 39 0.08
113 347 0.72
114 2 0.00
115 6 0.01
116 12 0.02
117 1 0.00
120 11 0.02
121 5 0.01
122 1 0.00
123 20 0.04
124 31 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTTAAATTCATCACTCGATGGATCAG
Found at i:613984 original size:124 final size:122
Alignment explanation
Indices: 613777--614061 Score: 348
Period size: 124 Copynumber: 2.3 Consensus size: 122
613767 TGCCAGGTAG
*
613777 AGTTCATAATGAGAAGAACTCGTCATCTG---AAG-AAGAAGAAATTCATAATGAGAAGAGCTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAAAAGAAAGAAGAAATTCATAATGAGAAGAGCTTA
* * * * *
613838 TTCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGCATCAACCTTTCC-G-GAGAA
63 TTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACC---CCAGCG-GAA
*
613900 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAATTCATAATGAGAAGAGCTTATTC
* * * *
613965 AACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCAGCGGAA
66 AACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACCCCAGCGGAA
614022 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
614062 TTTATTCAAC
Statistics
Matches: 143, Mismatches: 11, Indels: 15
0.85 0.07 0.09
Matches are distributed among these distances:
120 7 0.05
121 3 0.02
122 32 0.22
123 27 0.19
124 74 0.52
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAATTCATAATGAGAAGAGCTTATTC
AACCTTTTGAATAACTCTATCACAGAAAGAAATAGATCAACATCAACCCCAGCGGAA
Found at i:614212 original size:3 final size:3
Alignment explanation
Indices: 614204--614275 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
614194 CATTTTTTAT
* * * * * *
614204 TTA TTA TTA TTA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
614252 TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
614276 AAAAAATAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:614240 original size:30 final size:30
Alignment explanation
Indices: 614204--614293 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
614194 CATTTTTTAT
614204 TTATTATTATTATAATAATAATAATAATTA
1 TTATTATTATTATAATAATAATAATAATTA
* *
614234 TTATTATTATTATAATTATTAT-ATATATTA
1 TTATTATTATTATAATAATAATAATA-ATTA
* *
614264 TTATTATTATTAAAAAAATAATAATAATTA
1 TTATTATTATTATAATAATAATAATAATTA
614294 CAAGCCCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.06
30 46 0.88
31 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATTATTATTATAATAATAATAATAATTA
Found at i:614740 original size:16 final size:16
Alignment explanation
Indices: 614719--614755 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
614709 AGCAACCAAC
614719 AGCAAACCCA-AAGCAG
1 AGCAAACCCACAA-CAG
614735 AGCAAACCCACAACAG
1 AGCAAACCCACAACAG
614751 AGCAA
1 AGCAA
614756 CCAGAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.51, C:0.32, G:0.16, T:0.00
Consensus pattern (16 bp):
AGCAAACCCACAACAG
Found at i:615808 original size:22 final size:22
Alignment explanation
Indices: 615783--615826 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
615773 GGTATTTTAA
615783 AATTAAATATTATAAAAATTAT
1 AATTAAATATTATAAAAATTAT
* * **
615805 AATTTAATTTTATTTAAATTAT
1 AATTAAATATTATAAAAATTAT
615827 TATATTGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATATTATAAAAATTAT
Found at i:615927 original size:23 final size:24
Alignment explanation
Indices: 615895--615943 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
615885 TCTTTTCTGA
*
615895 TATTTCTAAA-TAAATAAATATTT
1 TATTTATAAACTAAATAAATATTT
*
615918 TATTTATAAACGTATATAAATATTT
1 TATTTATAAAC-TAAATAAATATTT
615943 T
1 T
615944 TTCATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
25 13 0.59
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTTATAAACTAAATAAATATTT
Found at i:616563 original size:15 final size:16
Alignment explanation
Indices: 616543--616582 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
616533 TCTTGTCATC
616543 TTTATATTTCCTTCT-
1 TTTATATTTCCTTCTA
616558 TTTATATTTCCTTCTA
1 TTTATATTTCCTTCTA
616574 TTT-TATTTC
1 TTTATATTTC
616583 ATCTAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTCCTTCTA
Found at i:618255 original size:63 final size:63
Alignment explanation
Indices: 618133--618257 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
618123 TGTCGAATCG
* **
618133 TCCTCCAACATGATGTTGGGGAGCTCGGCATTGTCTCCGATAACACCGTCAACTGTCGAATTA
1 TCCTCCAACATGATATTGGGGAGCTCGGCATTGTCTCCGATAACACCGTCAACCATCGAATTA
* ** * *
618196 TCCTCCAACATGATATTGGGTAGCTCGGCATTGTCTCTTATGACACCGTCGACCATCGAATT
1 TCCTCCAACATGATATTGGGGAGCTCGGCATTGTCTCCGATAACACCGTCAACCATCGAATT
618258 GTCTTCTGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (63 bp):
TCCTCCAACATGATATTGGGGAGCTCGGCATTGTCTCCGATAACACCGTCAACCATCGAATTA
Found at i:619185 original size:66 final size:66
Alignment explanation
Indices: 619107--619338 Score: 270
Period size: 66 Copynumber: 3.5 Consensus size: 66
619097 GTAACCGGAG
*
619107 ACAAGGCCGAGCTCCCCGATATCAAATTGGGAGAGGACAATTCGACAGTCGACGGTGTTGTCGGG
1 ACAAGGCCGAGCTCCCCGATATCAAGTTGGGAGAGGACAATTCGACAGTCGACGGTGTTGTCGGG
619172 A
66 A
* * * * * * * *
619173 ACAAGGCCGAGCTCCCTGATATCAAGTTGGAAGATGACAATTCAACAGTCGACGGGGTCGTCCGT
1 ACAAGGCCGAGCTCCCCGATATCAAGTTGGGAGAGGACAATTCGACAGTCGACGGTGTTGTCGGG
619238 A
66 A
* * * *
619239 ACAAGGCCGAGCTCCCCGATATCATGTTGGGGGAGGACAATTCGACAGTCGATGATGTTAGT-GT
1 ACAAGGCCGAGCTCCCCGATATCAAGTTGGGAGAGGACAATTCGACAGTCGACGGTGTT-GTCG-
619303 GGA
64 GGA
* *
619306 AGCCAAGGCCGAGCTCTCC-AGTATCATGTTGGG
1 A--CAAGGCCGAGCTCCCCGA-TATCAAGTTGGG
619339 TGGGACATCA
Statistics
Matches: 139, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
66 106 0.76
67 5 0.04
68 1 0.01
69 27 0.19
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (66 bp):
ACAAGGCCGAGCTCCCCGATATCAAGTTGGGAGAGGACAATTCGACAGTCGACGGTGTTGTCGGG
A
Found at i:622341 original size:2 final size:2
Alignment explanation
Indices: 622334--622411 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
622324 CATCCACCAC
622334 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
622376 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
622412 ATGAATGTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:623432 original size:16 final size:16
Alignment explanation
Indices: 623411--623442 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
623401 TGTCATCGTC
623411 TCTTTTGTTTTTATTT
1 TCTTTTGTTTTTATTT
623427 TCTTTTGTTTTTATTT
1 TCTTTTGTTTTTATTT
623443 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (16 bp):
TCTTTTGTTTTTATTT
Found at i:623448 original size:16 final size:16
Alignment explanation
Indices: 623413--623448 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
623403 TCATCGTCTC
**
623413 TTTTGTTTTTATTTTC
1 TTTTGTTTTTATTTAA
623429 TTTTGTTTTTATTTAA
1 TTTTGTTTTTATTTAA
623445 TTTT
1 TTTT
623449 TTTAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTGTTTTTATTTAA
Found at i:624084 original size:18 final size:16
Alignment explanation
Indices: 624052--624090 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
624042 CTAAAATAAT
624052 CTTTTTAATTATTAAA
1 CTTTTTAATTATTAAA
624068 CTTTTTAAATGTATTAAA
1 CTTTTT-AAT-TATTAAA
*
624086 ATTTT
1 CTTTT
624091 GATTTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (16 bp):
CTTTTTAATTATTAAA
Found at i:624687 original size:17 final size:18
Alignment explanation
Indices: 624667--624700 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
624657 ATGTATTTTT
624667 ATTT-TTTATAAAAATAA
1 ATTTATTTATAAAAATAA
*
624684 ATTTATTTCTAAAAATA
1 ATTTATTTATAAAAATA
624701 TTAATTACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTATTTATAAAAATAA
Found at i:625304 original size:36 final size:36
Alignment explanation
Indices: 625257--625366 Score: 204
Period size: 36 Copynumber: 3.1 Consensus size: 36
625247 TAATAATGGT
625257 TAGTTAAGGATGGATTAAAGAAGAAGAGACTTCTCA
1 TAGTTAAGGATGGATTAAAGAAGAAGAGACTTCTCA
625293 TAGTTAAGGATGGATTAAAGAAGAAGAGACTTCTCA
1 TAGTTAAGGATGGATTAAAGAAGAAGAGACTTCTCA
625329 TAGTTAAGGATGGATTAAAG-AGAAAGAGACTTCTCA
1 TAGTTAAGGATGGATTAAAGAAG-AAGAGACTTCTCA
625365 TA
1 TA
625367 TAGTTTAATA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 2 0.03
36 71 0.97
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (36 bp):
TAGTTAAGGATGGATTAAAGAAGAAGAGACTTCTCA
Found at i:626439 original size:137 final size:137
Alignment explanation
Indices: 626068--626458 Score: 386
Period size: 139 Copynumber: 2.8 Consensus size: 137
626058 AGATTGAACT
* * * * * *
626068 TAAAATGTAGGCTCTAATATTAATCCAAATTGATTTCAATCAATTATTGATTCAAATAATTAAAA
1 TAAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATTGATTCGAATAATTAAAA
* * *
626133 TGAAACCTCA-AGC-AAAA-GAGATGACCAAATTAAAAAATTACCTAAATT-AAAGGGCTAAATA
66 TGGAACCT-AGAACAAAAATGAGA--ACCAAATT-AAAAATT-CCTAAATTAAAAGGACTAAATA
626194 TGAAATTAAGCC
126 TGAAATTAAGCC
* * ** * * *
626206 TAAAATGGAGGCTCTAATTATTAA-CATGGTGAATTTTAATTAATTATGTGATTCGAATAACTAA
1 TAAAATGGAGACTCTAA-TATTAATCCTAATTAATTTTAATCAATTAT-TGATTCGAATAATTAA
* * * *
626270 AATGGAACCTTGAACAAAAACT-AGGACCAAATTTAAAATTCCTTAAATTAAAAGGACTAAATTT
64 AATGGAACCTAGAACAAAAA-TGAGAACCAAATTAAAAATTCC-TAAATTAAAAGGACTAAATAT
*
626334 GAAATTAGGCC
127 GAAATTAAGCC
* *
626345 TAAAGT-GATGACTCT-ATATTAATCCTAATTAATTTTAAACAATTATTGAATT-GAATAATTAA
1 TAAAATGGA-GACTCTAATATTAATCCTAATTAATTTTAATCAATTATTG-ATTCGAATAATTAA
* *
626407 AATGGAACCTAGAACAAAAATGAGAAACAAATTAAAAATTCCATAATTTAAA
64 AATGGAACCTAGAACAAAAATGAGAACCAAATTAAAAATTCC-TAAATTAAA
626459 GGGCTAATTA
Statistics
Matches: 207, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
136 1 0.00
137 63 0.30
138 66 0.32
139 71 0.34
140 4 0.02
141 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (137 bp):
TAAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATTGATTCGAATAATTAAAA
TGGAACCTAGAACAAAAATGAGAACCAAATTAAAAATTCCTAAATTAAAAGGACTAAATATGAAA
TTAAGCC
Found at i:630904 original size:33 final size:33
Alignment explanation
Indices: 630867--630942 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
630857 GCAAATAATG
630867 TTATGGGCCCTACTTTAGCATAGGCTTTAAACA
1 TTATGGGCCCTACTTTAGCATAGGCTTTAAACA
* *
630900 TTATGGGCCCTACTTTAGCATTGGCTTTAAATA
1 TTATGGGCCCTACTTTAGCATAGGCTTTAAACA
630933 TTATGGGCCC
1 TTATGGGCCC
630943 CTAACTGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (33 bp):
TTATGGGCCCTACTTTAGCATAGGCTTTAAACA
Found at i:631854 original size:30 final size:30
Alignment explanation
Indices: 631818--631878 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
631808 ACTTTATTAA
*
631818 ATAGATTTAATTATGAAGTAACATTCAACC
1 ATAGATTTAATTACGAAGTAACATTCAACC
631848 ATAGATTTAATTACGAAGTAACATTCAACC
1 ATAGATTTAATTACGAAGTAACATTCAACC
631878 A
1 A
631879 CTTGAATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (30 bp):
ATAGATTTAATTACGAAGTAACATTCAACC
Found at i:632135 original size:14 final size:15
Alignment explanation
Indices: 632109--632137 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
632099 ATTACTCCCA
632109 TACAACTAAACTCAT
1 TACAACTAAACTCAT
632124 TACAAC-AAACTCAT
1 TACAACTAAACTCAT
632138 CTTTCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (15 bp):
TACAACTAAACTCAT
Found at i:633612 original size:24 final size:24
Alignment explanation
Indices: 633571--633622 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
633561 ATAAGAGAGA
* * * *
633571 TTATAAACGATTCGATAAACGATC
1 TTATAAACCAGTCAATAAACGAAC
*
633595 TTATAAACCAGTCAATAAATGAAC
1 TTATAAACCAGTCAATAAACGAAC
633619 TTAT
1 TTAT
633623 CTGTAAACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (24 bp):
TTATAAACCAGTCAATAAACGAAC
Found at i:634210 original size:41 final size:41
Alignment explanation
Indices: 634149--634253 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
634139 TGTTTTCTGC
*
634149 CGAGAACGTGATCACCTGCTGCATCCTGCTGTAT-GGGGGGT
1 CGAGAACGTGATCA-CTGCTGCATCCTGCTGCATGGGGGGGT
634190 CGAGAACGTGATCACTTGCTGCATCCTGCTGCATGGGGGGGT
1 CGAGAACGTGATCAC-TGCTGCATCCTGCTGCATGGGGGGGT
*
634232 CGAGAATGTGATC-CTGCTGCAT
1 CGAGAACGTGATCACTGCTGCAT
634254 GTGGGGGGGC
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
40 9 0.15
41 32 0.53
42 19 0.32
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.25
Consensus pattern (41 bp):
CGAGAACGTGATCACTGCTGCATCCTGCTGCATGGGGGGGT
Found at i:634650 original size:40 final size:41
Alignment explanation
Indices: 634601--634677 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
634591 ATTAAATTGT
* *
634601 ATTTGAGTATAATATTATAATTGGAATATTT-TTTTTCTAG
1 ATTTAAGTATAATATTACAATTGGAATATTTATTTTTCTAG
634641 ATTTAAGTATAATATTACAATTGGAATATTTATTTTT
1 ATTTAAGTATAATATTACAATTGGAATATTTATTTTT
634678 TTCTATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 29 0.85
41 5 0.15
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (41 bp):
ATTTAAGTATAATATTACAATTGGAATATTTATTTTTCTAG
Found at i:638129 original size:14 final size:14
Alignment explanation
Indices: 638061--638141 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
638051 TTCATGAATT
*
638061 TAATTATTTAATAA
1 TAATGATTTAATAA
*
638075 TAATGATTAAATGCAA
1 TAATGATTTAAT--AA
638091 T--TGATTTAATAA
1 TAATGATTTAATAA
*
638103 T-A--A-TTACTAA
1 TAATGATTTAATAA
*
638113 TAATGATTTGATAA
1 TAATGATTTAATAA
638127 TAATGATTTAATAA
1 TAATGATTTAATAA
638141 T
1 T
638142 GATTACTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 3 0.06
13 1 0.02
14 37 0.70
16 3 0.06
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:638384 original size:11 final size:11
Alignment explanation
Indices: 638370--638512 Score: 76
Period size: 11 Copynumber: 11.7 Consensus size: 11
638360 ATATAATTTA
638370 TTAATAATGAT
1 TTAATAATGAT
638381 TTAATACTATGAT
1 TTAATA--ATGAT
638394 TTAATAAT-A-
1 TTAATAATGAT
*
638403 ATAATTTAATGAT
1 TTAA--TAATGAT
638416 TTGATACTAATGAT
1 TT-A-A-TAATGAT
638430 TTAATAATGATT
1 TTAATAATGA-T
*
638442 ATTAATAATAAT
1 -TTAATAATGAT
*
638454 TTAATAATTATT
1 TTAATAATGA-T
638466 ATTAATTTAATGAT
1 -TTAA--TAATGAT
638480 TTGATATTTAATGAT
1 TT-A-A--TAATGAT
*
638495 TTAGTAATGA-
1 TTAATAATGAT
638505 TTAATAAT
1 TTAATAAT
638513 AATTATTTAT
Statistics
Matches: 108, Mismatches: 8, Indels: 33
0.72 0.05 0.22
Matches are distributed among these distances:
9 3 0.03
10 8 0.07
11 33 0.31
12 5 0.05
13 28 0.26
14 13 0.12
15 18 0.17
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (11 bp):
TTAATAATGAT
Found at i:638420 original size:27 final size:27
Alignment explanation
Indices: 638355--638420 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
638345 AAATTAATAA
* * *
638355 TAATGATATAATTTATTAATAATGATT
1 TAATGATATGATTTAATAATAATAATT
638382 TAAT-ACTATGATTTAATAATAATAATT
1 TAATGA-TATGATTTAATAATAATAATT
*
638409 TAATGATTTGAT
1 TAATGATATGAT
638421 ACTAATGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.94
28 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (27 bp):
TAATGATATGATTTAATAATAATAATT
Found at i:638503 original size:65 final size:63
Alignment explanation
Indices: 638401--638574 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 63
638391 GATTTAATAA
* *
638401 TAATAATTTAATGATTTGATACTAATGATTTAATAATGATTATTAATAATAATTTAATAATTAT
1 TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAATAA-TTAATAATTAT
* * *
638465 TATTAATTTAATGATTTGATATTTAATGATTTAGTAATG---ATTAATAATAATTATTTATTAT
1 TAATAATTTAATGATTTGATA-TTAATGATTTAGTAATGATTATTAATAATAATTAATAATTAT
* *
638526 TAAT-ATTTAATGATTTGATATTAATGATTTAGTAATCATTACTAATAAT
1 TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAAT
638575 TAAATTATAA
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
59 16 0.16
60 16 0.16
61 12 0.12
62 19 0.19
64 20 0.20
65 15 0.15
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (63 bp):
TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAATAATTAATAATTAT
Found at i:638520 original size:24 final size:25
Alignment explanation
Indices: 638362--638521 Score: 93
Period size: 24 Copynumber: 6.4 Consensus size: 25
638352 TAATAATGAT
638362 ATAATT-TATTAATAATGATTTAATA
1 ATAATTAT-TTAATAATGATTTAATA
* * *
638387 CT-ATGATTTAATAAT-A-ATAAT-
1 ATAATTATTTAATAATGATTTAATA
* *
638408 TTAATGATTTGATACTAATGATTTAATA
1 ATAATTATTT-A-A-TAATGATTTAATA
* *
638436 ATGATTA-TTAATAATAATTTAATA
1 ATAATTATTTAATAATGATTTAATA
* *
638460 ATTATTA-TTAATTTAATGATTTGATA
1 ATAATTATTTAA--TAATGATTTAATA
* * *
638486 TTTAATGATTTAGTAATGA-TTAATA
1 -ATAATTATTTAATAATGATTTAATA
638511 ATAATTATTTA
1 ATAATTATTTA
638522 TTATTAATAT
Statistics
Matches: 104, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
21 1 0.01
22 11 0.11
23 2 0.02
24 42 0.40
25 12 0.12
26 19 0.18
27 10 0.10
28 7 0.07
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (25 bp):
ATAATTATTTAATAATGATTTAATA
Found at i:638536 original size:24 final size:24
Alignment explanation
Indices: 638423--638566 Score: 105
Period size: 24 Copynumber: 5.8 Consensus size: 24
638413 GATTTGATAC
* *
638423 TAATGATTTAATAATGATTATTAA
1 TAATGATTTAATAATTATTATTAT
*
638447 TAATAATTTAATAATTATTATTAATT
1 TAATGATTTAATAATTATTATT-A-T
* * * *
638473 TAATGATTTGATATTTAATGATTTAG
1 TAATGATTTAATAATT-ATTA-TTAT
638499 TAATGATTAATAATAATTATTTATTAT
1 TAATGATT--TAATAATTA-TTATTAT
* *
638526 TAAT-ATTTAATGATT-TGA-TAT
1 TAATGATTTAATAATTATTATTAT
* *
638547 TAATGATTTAGTAATCATTA
1 TAATGATTTAATAATTATTA
638567 CTAATAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 19
0.72 0.14 0.15
Matches are distributed among these distances:
21 7 0.08
22 10 0.11
23 2 0.02
24 27 0.29
25 1 0.01
26 24 0.26
27 12 0.13
28 10 0.11
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.50
Consensus pattern (24 bp):
TAATGATTTAATAATTATTATTAT
Found at i:638541 original size:21 final size:21
Alignment explanation
Indices: 638483--638556 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
638473 TAATGATTTG
638483 ATATTTAATGATTTAGTAATGATTA
1 ATATTTAATGATTTA-T--T-ATTA
* *
638508 ATA-ATAATTATTTATTATTA
1 ATATTTAATGATTTATTATTA
638528 ATATTTAATGATTTGA-TATTA
1 ATATTTAATGATTT-ATTATTA
638549 ATGATTTA
1 AT-ATTTA
638557 GTAATCATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 7 0.17
21 16 0.38
22 6 0.14
23 1 0.02
24 9 0.21
25 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
ATATTTAATGATTTATTATTA
Found at i:638622 original size:48 final size:48
Alignment explanation
Indices: 638483--638611 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 48
638473 TAATGATTTG
* * *
638483 ATATTTAATGA-TT--TAGTAATGATTAATAATAATTATTTATTATTA
1 ATATTTAATGATTTGATAATAATGATTAATAATAATTATTAATAATTA
* * * *
638528 ATATTTAATGATTTGATATTAATGATTTAGTAATCATTACTAATAATTA
1 ATATTTAATGATTTGATAATAATGA-TTAATAATAATTATTAATAATTA
*
638577 A-ATTATAA-GATTTGATAATAATGATTACTAATAAT
1 ATATT-TAATGATTTGATAATAATGATTAATAATAAT
638612 GATGTGATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
45 11 0.16
46 2 0.03
47 9 0.13
48 26 0.37
49 22 0.31
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (48 bp):
ATATTTAATGATTTGATAATAATGATTAATAATAATTATTAATAATTA
Found at i:641740 original size:14 final size:14
Alignment explanation
Indices: 641672--641752 Score: 73
Period size: 14 Copynumber: 6.1 Consensus size: 14
641662 TTCATGAATT
*
641672 TAATTATTTAATAA
1 TAATGATTTAATAA
* *
641686 TAATGATTAAAT-G
1 TAATGATTTAATAA
641699 TAATTGATTTAATAA
1 TAA-TGATTTAATAA
*
641714 T-A--A-TTACTAA
1 TAATGATTTAATAA
*
641724 TAATGATTTGATAA
1 TAATGATTTAATAA
641738 TAATGATTTAATAA
1 TAATGATTTAATAA
641752 T
1 T
641753 GATTACTACT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
13 4 0.08
14 38 0.73
15 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:641997 original size:11 final size:11
Alignment explanation
Indices: 641983--642125 Score: 76
Period size: 11 Copynumber: 11.7 Consensus size: 11
641973 ATATAATTTA
641983 TTAATAATGAT
1 TTAATAATGAT
641994 TTAATACTATGAT
1 TTAATA--ATGAT
642007 TTAATAAT-A-
1 TTAATAATGAT
*
642016 ATAATTTAATGAT
1 TTAA--TAATGAT
642029 TTGATACTAATGAT
1 TT-A-A-TAATGAT
642043 TTAATAATGATT
1 TTAATAATGA-T
*
642055 ATTAATAATAAT
1 -TTAATAATGAT
*
642067 TTAATAATTATT
1 TTAATAATGA-T
642079 ATTAATTTAATGAT
1 -TTAA--TAATGAT
642093 TTGATATTTAATGAT
1 TT-A-A--TAATGAT
*
642108 TTAGTAATGA-
1 TTAATAATGAT
642118 TTAATAAT
1 TTAATAAT
642126 AATTATTTAT
Statistics
Matches: 108, Mismatches: 8, Indels: 33
0.72 0.05 0.22
Matches are distributed among these distances:
9 3 0.03
10 8 0.07
11 33 0.31
12 5 0.05
13 28 0.26
14 13 0.12
15 18 0.17
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (11 bp):
TTAATAATGAT
Found at i:642033 original size:27 final size:27
Alignment explanation
Indices: 641968--642033 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
641958 AAATTAATAA
* * *
641968 TAATGATATAATTTATTAATAATGATT
1 TAATGATATGATTTAATAATAATAATT
641995 TAAT-ACTATGATTTAATAATAATAATT
1 TAATGA-TATGATTTAATAATAATAATT
*
642022 TAATGATTTGAT
1 TAATGATATGAT
642034 ACTAATGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.94
28 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (27 bp):
TAATGATATGATTTAATAATAATAATT
Found at i:642116 original size:65 final size:63
Alignment explanation
Indices: 642014--642187 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 63
642004 GATTTAATAA
* *
642014 TAATAATTTAATGATTTGATACTAATGATTTAATAATGATTATTAATAATAATTTAATAATTAT
1 TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAATAA-TTAATAATTAT
* * *
642078 TATTAATTTAATGATTTGATATTTAATGATTTAGTAATG---ATTAATAATAATTATTTATTAT
1 TAATAATTTAATGATTTGATA-TTAATGATTTAGTAATGATTATTAATAATAATTAATAATTAT
* *
642139 TAAT-ATTTAATGATTTGATATTAATGATTTAGTAATCATTACTAATAAT
1 TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAAT
642188 TAAATTATAA
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
59 16 0.16
60 16 0.16
61 12 0.12
62 19 0.19
64 20 0.20
65 15 0.15
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (63 bp):
TAATAATTTAATGATTTGATATTAATGATTTAGTAATGATTATTAATAATAATTAATAATTAT
Found at i:642133 original size:24 final size:25
Alignment explanation
Indices: 641975--642134 Score: 93
Period size: 24 Copynumber: 6.4 Consensus size: 25
641965 TAATAATGAT
641975 ATAATT-TATTAATAATGATTTAATA
1 ATAATTAT-TTAATAATGATTTAATA
* * *
642000 CT-ATGATTTAATAAT-A-ATAAT-
1 ATAATTATTTAATAATGATTTAATA
* *
642021 TTAATGATTTGATACTAATGATTTAATA
1 ATAATTATTT-A-A-TAATGATTTAATA
* *
642049 ATGATTA-TTAATAATAATTTAATA
1 ATAATTATTTAATAATGATTTAATA
* *
642073 ATTATTA-TTAATTTAATGATTTGATA
1 ATAATTATTTAA--TAATGATTTAATA
* * *
642099 TTTAATGATTTAGTAATGA-TTAATA
1 -ATAATTATTTAATAATGATTTAATA
642124 ATAATTATTTA
1 ATAATTATTTA
642135 TTATTAATAT
Statistics
Matches: 104, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
21 1 0.01
22 11 0.11
23 2 0.02
24 42 0.40
25 12 0.12
26 19 0.18
27 10 0.10
28 7 0.07
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (25 bp):
ATAATTATTTAATAATGATTTAATA
Found at i:642149 original size:24 final size:24
Alignment explanation
Indices: 642036--642179 Score: 105
Period size: 24 Copynumber: 5.8 Consensus size: 24
642026 GATTTGATAC
* *
642036 TAATGATTTAATAATGATTATTAA
1 TAATGATTTAATAATTATTATTAT
*
642060 TAATAATTTAATAATTATTATTAATT
1 TAATGATTTAATAATTATTATT-A-T
* * * *
642086 TAATGATTTGATATTTAATGATTTAG
1 TAATGATTTAATAATT-ATTA-TTAT
642112 TAATGATTAATAATAATTATTTATTAT
1 TAATGATT--TAATAATTA-TTATTAT
* *
642139 TAAT-ATTTAATGATT-TGA-TAT
1 TAATGATTTAATAATTATTATTAT
* *
642160 TAATGATTTAGTAATCATTA
1 TAATGATTTAATAATTATTA
642180 CTAATAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 19
0.72 0.14 0.15
Matches are distributed among these distances:
21 7 0.08
22 10 0.11
23 2 0.02
24 27 0.29
25 1 0.01
26 24 0.26
27 12 0.13
28 10 0.11
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.50
Consensus pattern (24 bp):
TAATGATTTAATAATTATTATTAT
Found at i:642154 original size:21 final size:21
Alignment explanation
Indices: 642096--642169 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
642086 TAATGATTTG
642096 ATATTTAATGATTTAGTAATGATTA
1 ATATTTAATGATTTA-T--T-ATTA
* *
642121 ATA-ATAATTATTTATTATTA
1 ATATTTAATGATTTATTATTA
642141 ATATTTAATGATTTGA-TATTA
1 ATATTTAATGATTT-ATTATTA
642162 ATGATTTA
1 AT-ATTTA
642170 GTAATCATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 7 0.17
21 16 0.38
22 6 0.14
23 1 0.02
24 9 0.21
25 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (21 bp):
ATATTTAATGATTTATTATTA
Found at i:642216 original size:27 final size:27
Alignment explanation
Indices: 642181--642235 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
642171 TAATCATTAC
*
642181 TAATAATTAAATTATAA-GATTTGATAA
1 TAATAATT-AATAATAATGATTTGATAA
* *
642208 TAATGATTACTAATAATGATTTGATAA
1 TAATAATTAATAATAATGATTTGATAA
642235 T
1 T
642236 GTTACTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (27 bp):
TAATAATTAATAATAATGATTTGATAA
Found at i:642221 original size:13 final size:13
Alignment explanation
Indices: 642205--642244 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
642195 TAAGATTTGA
642205 TAATAATGATTAC
1 TAATAATGATTAC
642218 TAATAATGATT--
1 TAATAATGATTAC
*
642229 TGATAATG-TTAC
1 TAATAATGATTAC
642241 TAAT
1 TAAT
642245 TTGATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
10 2 0.09
11 7 0.30
12 3 0.13
13 11 0.48
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (13 bp):
TAATAATGATTAC
Found at i:642235 original size:48 final size:47
Alignment explanation
Indices: 642096--642235 Score: 121
Period size: 48 Copynumber: 3.0 Consensus size: 47
642086 TAATGATTTG
* * *
642096 ATATTTAATGA-TT--TAGTAATGATTAATAATAATTATTTATTATTA
1 ATATTTAATGATTTGATAATAATGATT-ATAATAATCATTTATAATTA
* *
642141 ATATTTAATGATTTGATATTAATGATT-TAGTAATCATTACTAATAATTA
1 ATATTTAATGATTTGATAATAATGATTATAATAATCATT--T-ATAATTA
*
642190 A-ATTATAA-GATTTGATAATAATGATTACTAATAATGATTTGATAAT
1 ATATT-TAATGATTTGATAATAATGATTA-TAATAATCATTT-ATAAT
642236 GTTACTAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
45 11 0.14
46 11 0.14
48 37 0.47
49 10 0.13
50 9 0.12
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (47 bp):
ATATTTAATGATTTGATAATAATGATTATAATAATCATTTATAATTA
Found at i:642252 original size:22 final size:24
Alignment explanation
Indices: 642207--642256 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
642197 AGATTTGATA
642207 ATAATGATTACTAATAATGATTTG
1 ATAATGATTACTAATAATGATTTG
*
642231 ATAATG-TTACTAAT-TTGATTTG
1 ATAATGATTACTAATAATGATTTG
642253 ATAA
1 ATAA
642257 CATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (24 bp):
ATAATGATTACTAATAATGATTTG
Found at i:642830 original size:15 final size:16
Alignment explanation
Indices: 642810--642842 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
642800 TAAAAAATAA
642810 CAATAA-ACATTGCAC
1 CAATAATACATTGCAC
*
642825 CAATAATGCATTGCAC
1 CAATAATACATTGCAC
642841 CA
1 CA
642843 CTTACTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.21
Consensus pattern (16 bp):
CAATAATACATTGCAC
Found at i:642966 original size:22 final size:23
Alignment explanation
Indices: 642938--643016 Score: 106
Period size: 22 Copynumber: 3.3 Consensus size: 23
642928 ACGAGAATGC
642938 TTTAATATGATTATTAA-AATTA
1 TTTAATATGATTATTAATAATTA
642960 TTTAATATGATTATTAATAATTA
1 TTTAATATGATTATTAATAATTA
* *
642983 TTTAATAATTATTATTAATATAATGA
1 TTTAAT-ATGATTATT-A-ATAATTA
643009 TTTAATAT
1 TTTAATAT
643017 TTAATGATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.33
23 11 0.22
24 8 0.16
25 3 0.06
26 12 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAATATGATTATTAATAATTA
Found at i:642974 original size:13 final size:12
Alignment explanation
Indices: 642938--643016 Score: 62
Period size: 13 Copynumber: 6.7 Consensus size: 12
642928 ACGAGAATGC
642938 TTTAATATGATTA
1 TTTAATAT-ATTA
642951 -TTAA-A-ATTA
1 TTTAATATATTA
642960 TTTAATATGATTA
1 TTTAATAT-ATTA
642973 -TTAATA-ATTA
1 TTTAATATATTA
642983 TTTAATA-ATTA
1 TTTAATATATTA
*
642994 TTATTAATATAATGA
1 -T-TTAATAT-ATTA
643009 TTTAATAT
1 TTTAATAT
643017 TTAATGATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
9 4 0.07
10 8 0.14
11 12 0.21
12 11 0.20
13 17 0.30
14 1 0.02
15 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (12 bp):
TTTAATATATTA
Found at i:642982 original size:10 final size:10
Alignment explanation
Indices: 642947--643001 Score: 58
Period size: 10 Copynumber: 5.2 Consensus size: 10
642937 CTTTAATATG
642947 ATTATTAA-A
1 ATTATTAATA
642956 ATTATTTAATA
1 ATTA-TTAATA
642967 TGATTATTAATA
1 --ATTATTAATA
642979 ATTATTTAATA
1 ATTA-TTAATA
*
642990 ATTATTATTA
1 ATTATTAATA
643000 AT
1 AT
643002 ATAATGATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 4 0.10
10 15 0.38
11 11 0.28
12 6 0.15
13 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTATTAATA
Found at i:643011 original size:26 final size:24
Alignment explanation
Indices: 642933--643166 Score: 109
Period size: 24 Copynumber: 9.8 Consensus size: 24
642923 TAGTCACGAG
*
642933 AATGCTTTAAT-ATGATTATTAA-
1 AATGATTTAATAATGATTATTAAT
*
642955 AATTATTTAAT-ATGATTATTAAT
1 AATGATTTAATAATGATTATTAAT
* *
642978 AATTATTTAATAATTATTATTAATAT
1 AATGATTTAATAATGATTATT-A-AT
*
643004 AATGATTTAATATTTAATGATTTAGTAAT
1 AATGATTT-A-A--TAATGA-TTATTAAT
* *
643033 GATATGATTTAGTAATGATTATTATT
1 -A-ATGATTTAATAATGATTATTAAT
* * * *
643059 AATAATTT-ATTATAAATATT--T
1 AATGATTTAATAATGATTATTAAT
* *
643080 AATGATTTGAAT--T--TGA-TAGT
1 AATGATTT-AATAATGATTATTAAT
*
643100 AATGATTTAGTAATGATTATTAAT
1 AATGATTTAATAATGATTATTAAT
*
643124 AATAAATTT-ATAA-GATT-TGATAAT
1 AAT-GATTTAATAATGATTAT--TAAT
*
643148 AATAATTTAATAATGATTA
1 AATGATTTAATAATGATTA
643167 AATATTTGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 9 0.05
21 10 0.06
22 21 0.13
23 32 0.20
24 34 0.21
25 10 0.06
26 15 0.09
27 7 0.04
28 1 0.01
29 2 0.01
30 8 0.05
31 11 0.07
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
AATGATTTAATAATGATTATTAAT
Found at i:643041 original size:16 final size:16
Alignment explanation
Indices: 643020--643051 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
643010 TTAATATTTA
643020 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
643036 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
643052 TATTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:646332 original size:23 final size:23
Alignment explanation
Indices: 646285--646334 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
646275 AATAACATAT
* **
646285 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
646308 TAGGTAGCACTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
646331 TAGG
1 TAGG
646335 CATTTAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:646394 original size:87 final size:87
Alignment explanation
Indices: 646248--646410 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
646238 TATGTTATAT
* *
646248 CATTTAACCGGAAATATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAACACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGT
646313 AGCACTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* ** *
646335 CATTTAACTGGAAATATTATCAAGTACAATAACAAATTAGGTAACGCTTATATAATGTAATATGT
1 CATTTAACCGGAAATATTATCAAACACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGT
*
646400 AGCGCTTATAT
66 AGCACTTATAT
646411 TGACCTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAACACAATAACAAATTAGGTAACGCTTATATAATGTAATAGGT
AGCACTTATATAATAAAATAGG
Found at i:646762 original size:198 final size:195
Alignment explanation
Indices: 646429--646927 Score: 612
Period size: 198 Copynumber: 2.5 Consensus size: 195
646419 TTTCTCATAA
* * * * * *
646429 AACCGGTAAATTTAAACCGGTTACATTATAAATTGACATATTACATTATAAATATCGATTTTGAT
1 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTTG--
* * * * *
646494 ATTTTCGGGATCGATACAATTTT-AAATGTATCGACACTTTATGCGTGCAGCTCGTTTGTGCTTT
64 ATTTTCGGGATCGATAC-TTTTTAAAATGTATCGACACTTTATGCGTACACCTCGTTTGTCCTTC
* * *
646558 ATTTTGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCT
128 ATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CT
*
646622 AATT
192 AATG
* *
646626 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTTGAT
1 AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTTGAT
646691 GTTTCGAGGATCGATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATT
66 -TTTCG-GGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTACACCTCGTTTGTCC-TT
* * * *
646755 CATTTTGGAAAAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTCT
127 CATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCT
*
646820 CATG
192 AATG
* *
646824 AACCCGGTATATTTCT-ACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTCTCT
1 AA-CCGGTATATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC-G-AT-T
*
646888 TTGATTTT-GGGATCGATACTTGTTATAAATGTATCGACAC
61 TTGATTTTCGGGATCGATACTTTTTA-AAATGTATCGACAC
646928 AAAATCTAAC
Statistics
Matches: 263, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
195 2 0.01
196 9 0.03
197 66 0.25
198 94 0.36
199 79 0.30
200 3 0.01
201 4 0.02
202 6 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (195 bp):
AACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTTGAT
TTTCGGGATCGATACTTTTTAAAATGTATCGACACTTTATGCGTACACCTCGTTTGTCCTTCATT
TTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATG
Found at i:650694 original size:21 final size:23
Alignment explanation
Indices: 650645--650704 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
650635 TTCCCCTGTG
650645 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
** *
650668 AAGGGGAATTGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
650689 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
650705 TCTGCACCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 5 0.17
21 10 0.34
22 3 0.10
23 11 0.38
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:654404 original size:21 final size:20
Alignment explanation
Indices: 654362--654405 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
654352 TCAAAAGAAG
*
654362 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
654382 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
654403 TTT
1 TTT
654406 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:660161 original size:197 final size:198
Alignment explanation
Indices: 659772--660884 Score: 1479
Period size: 197 Copynumber: 5.6 Consensus size: 198
659762 ACTAATTTAA
* * * * * *
659772 AAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACCAGTAAATTTAAACCGGTTACAT
1 AAAGTATCGATACATTATGTATA-CTATTTT-T-TTAATAACCGGTATATTTAGACCGGTTACAT
* * * * * *
659836 TGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTAGGATCGACACTTTTTTCTA
63 TGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACAC-TTGTTATA
659901 AATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACA
127 AATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACA
659966 AATGTAT
192 AATGTAT
*
659973 AAAGTATCGATACATTATGTATA-TATTTTTTTAATAACCGATATATTTAGACCGGTTACATTGT
1 AAAGTATCGATACATTATGTATACTATTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGT
*
660037 TATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTCGGGATCGACACTTGTTATAAATG
66 TATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATG
*
660102 TATCGACACTTTTTCGTTAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
131 TATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
660167 TAT
196 TAT
*
660170 AAAGTATCGATACATTATGTATACT-TTTTTTTAATAACCGGTATATTTAGACCGTTTACATTGT
1 AAAGTATCGATACATTATGTATACTATTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGT
660234 TATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATG
66 TATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATG
660299 TATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
131 TATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
660364 TAT
196 TAT
* *
660367 AAAGTATCGATACATTATATATACCTTTCTTTTTTAATAACCGGTATATTTAGACCGGTTACATT
1 AAAGTATCGATACATTATGTATA-CTAT-TTTTTTAATAACCGGTATATTTAGACCGGTTACATT
* *
660432 GTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
64 GTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
* * ** * ** * *
660497 TGTATCGACACTTTTTTCTTGCACTTGGTTTGG-AAATACATTCTATACA-ACATGTATCGACAC
129 TGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATTTATTATGGACATA-AAGTGTCGACAC
*
660560 AAATGAAT
191 AAATGTAT
* * * * * *
660568 AAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA-AACCGGTAAATTTAAACCAGTTACA
1 AAAGTATCGATACATTA-TGTATA-CTATTTT-T-TTAATAACCGGTATATTTAGACCGGTTACA
* * * * * * *
660631 TTATAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGATACTTGATATA
62 TTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATA
** * *
660696 AATGTATCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAAATACATTATGGACACAAAGTATC
127 AATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAATTTATTATGGACATAAAGTGTC
660760 GACACAAATGTAT
186 GACACAAATGTAT
* * * * *
660773 AAAGTGTCGATACTTTATGTATACCT-CTTTTCTCATAAACCGGTATATTTAGACCGGTTACATT
1 AAAGTATCGATACATTATGTATA-CTATTTTTTTAAT-AACCGGTATATTTAGACCGGTTACATT
* * *
660837 GTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGA
64 GTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGA
660885 CGCTTATCAT
Statistics
Matches: 817, Mismatches: 73, Indels: 41
0.88 0.08 0.04
Matches are distributed among these distances:
197 293 0.36
198 77 0.09
199 8 0.01
200 123 0.15
201 177 0.22
202 12 0.01
203 1 0.00
204 71 0.09
205 52 0.06
206 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (198 bp):
AAAGTATCGATACATTATGTATACTATTTTTTTAATAACCGGTATATTTAGACCGGTTACATTGT
TATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATG
TATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
TAT
Found at i:662281 original size:3 final size:3
Alignment explanation
Indices: 662273--662322 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
662263 ACTTGTTTGG
* * * *
662273 ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
662321 AT
1 AT
662323 TGACCGCTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.26, C:0.32, G:0.02, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:663139 original size:2 final size:2
Alignment explanation
Indices: 663132--663167 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
663122 GTCTCCGGAG
663132 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
663168 CCTTTCCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663492 original size:15 final size:15
Alignment explanation
Indices: 663472--663524 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
663462 TGATTTCCTC
663472 AGAAGAGCTGGGTTG
1 AGAAGAGCTGGGTTG
*
663487 AGAAGAGGTGGGTTG
1 AGAAGAGCTGGGTTG
*
663502 AGAAGAGATGGGTTG
1 AGAAGAGCTGGGTTG
663517 AGAAGAGC
1 AGAAGAGC
663525 CCCGATTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.47, T:0.17
Consensus pattern (15 bp):
AGAAGAGCTGGGTTG
Found at i:664190 original size:82 final size:83
Alignment explanation
Indices: 664052--664214 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 83
664042 ACTTTATGTA
* *
664052 CACCTGTTTTCTCATAAACCGGTGTATTTAGACTGGTTAGATTCATAATTTACCTATTACATTGT
1 CACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTAT
664117 AATTATGAGTCTCGATAT
66 AATTATGAGTCTCGATAT
664135 CACCTGTTTTCTCATAAA-CGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTAT
1 CACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTAT
*
664199 AATTATGGGTCTCGAT
66 AATTATGAGTCTCGAT
664215 GTTTTTGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 59 0.77
83 18 0.23
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (83 bp):
CACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTAT
AATTATGAGTCTCGATAT
Found at i:664474 original size:197 final size:197
Alignment explanation
Indices: 664139--664649 Score: 896
Period size: 197 Copynumber: 2.6 Consensus size: 197
664129 CGATATCACC
664139 TGTTTTCTCATAAACGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTA
1 TGTTTTCTCATAAACGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTA
*
664204 TGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATATATCGACACATTTCCATGCACTTGG
66 TGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGG
* * *
664269 TAAGGAAATCAATCTGGACACAAAGTATCGACACAAATTCAACAATTGTTGATACTTTATGTACA
131 TAAGGAAATCAATCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACA
*
664334 CT
196 CA
* * *
664336 TGTTTTCTCATAAACGGTGTATTTAAACCGGTTAGATTCATAATTTACCTATTGCATTGTAATTA
1 TGTTTTCTCATAAACGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTA
* *
664401 TGGGTCTCGATTTTTTTGGGATCGATACTTTTTATAAATGTATTGACACATTTCCATGCACTTGG
66 TGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGG
* *
664466 TAAGGAAATCATTCTGGACACAAAGTATCGACACAAATTAAATAAGTGTCGATACTTTATGTACA
131 TAAGGAAATCAATCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACA
664531 CA
196 CA
*
664533 TGTTTTCTCATAAACCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATT
1 TGTTTTCTCATAAA-CGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATT
664598 ATGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAT
65 ATGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAT
664650 ATGTTTACCA
Statistics
Matches: 295, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
197 199 0.67
198 96 0.33
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (197 bp):
TGTTTTCTCATAAACGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTA
TGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTTCCATGCACTTGG
TAAGGAAATCAATCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACA
CA
Found at i:665006 original size:19 final size:19
Alignment explanation
Indices: 664982--665031 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
664972 TTACATTCAC
*
664982 ATACAAAATTATAAATCAT
1 ATACAAAATTAAAAATCAT
*
665001 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCAT
665020 ATACAAAATTAA
1 ATACAAAATTAA
665032 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCAT
Found at i:666177 original size:17 final size:17
Alignment explanation
Indices: 666155--666190 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
666145 GAATCATTAG
666155 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
666172 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
666189 GA
1 GA
666191 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:666515 original size:18 final size:18
Alignment explanation
Indices: 666492--666530 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
666482 TTCTCCTCAT
* *
666492 TTCCTCTATTTTTTCTTC
1 TTCCTCCATCTTTTCTTC
666510 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
666528 TTC
1 TTC
666531 AAATTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:666904 original size:15 final size:15
Alignment explanation
Indices: 666884--666913 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
666874 ACTATGTTTT
666884 CCCTGACCGTAATCC
1 CCCTGACCGTAATCC
*
666899 CCCTGACCGTCATCC
1 CCCTGACCGTAATCC
666914 ACCCCTCCAA
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:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGACCGTAATCC
Found at i:669172 original size:20 final size:20
Alignment explanation
Indices: 669126--669172 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
669116 ACCGATAGCG
669126 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
669146 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
669167 -TTTACC
1 CTTTACC
669173 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:669444 original size:184 final size:181
Alignment explanation
Indices: 669089--669750 Score: 805
Period size: 182 Copynumber: 3.6 Consensus size: 181
669079 TACGCGTACT
* * * * * * * * *
669089 TATTAAAGTACCGACACTTTCAACATAACCGATAGCGCTTTACCGGTTTTGTCATTTCGATACCG
1 TATTAACGTATCGACACTTTCAATATATCTGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCG
*
669154 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACGTTTTCATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACGTTTT-ATAAAGTATCGACACT
*
669219 TTTTAGGCGCTATAACTTCTTCTCTTTTAAA-TTACAAAAGTGTCGATACTTA
130 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTA-AAAAGTGTCGATACTTA
* * * * *
669271 TATT-ACTTTATCGACACTTTCAATATATTTGGTAGTTTTTTTTACCGATTTTATCATTTCGAGA
1 TATTAAC-GTATCGACACTTTCAATATATCTGGTAG--CTCTTTACCGGTTTTATCATTTCGAGA
* * * * * *
669335 CCTGTTTTGTCATATTTTTACATGTTATACTGCTATGGATCAATACATTTGTATAAAGTATCGAC
63 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACGTTT-TATAAAGTATCGAC
669400 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
127 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
* *
669455 TATTAACGTATCGACACTTTCAATATATCTGGTAGCTCTTTACCGGTTTTATCATTTTGTGACCG
1 TATTAACGTATCGACACTTTCAATATATCTGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCG
* * *
669520 GTTTTGTCATACTTATACCTGTTATATTGTTATGGATCGATACGTTTTTATAAAGTATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACG-TTTTATAAAGTATCGACACT
* **
669585 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
130 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
* * ** * *
669637 T-TTAAATC-TAATCGATACTTTCGATATATCCAGTAGCGGC-TTACCGGTTTTATCATAAT-GA
1 TATT-AA-CGT-ATCGACACTTTCAATATATCTGGTAGC-TCTTTACCGGTTTTATCAT-TTCGA
* * * * *
669698 AACCGGTTTTATCATATTTTTACCTGTTATATTGCTATGGAGCGATACATTTT
61 GACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACGTTTT
669751 TCATTTGTAT
Statistics
Matches: 413, Mismatches: 55, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
181 3 0.01
182 159 0.38
183 86 0.21
184 159 0.38
185 6 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
TATTAACGTATCGACACTTTCAATATATCTGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACGTTTTATAAAGTATCGACACTT
TATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
Found at i:669596 original size:182 final size:182
Alignment explanation
Indices: 669089--669751 Score: 816
Period size: 184 Copynumber: 3.6 Consensus size: 182
669079 TACGCGTACT
* * * * * * *
669089 TATTAAAGTACCGACACTTTCAACATAACCGATAGCGCTTTACCGGTTTTGTCATTTCGATACCG
1 TATTAACGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCG
* * * *
669154 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACGTTTTCATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACT
*
669219 TTTTAGGCGCTATAACTTCTTCTCTTTTAAA-TTACAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTA-AAAAGTGTCGATACTTA
* ** *** *
669271 TATT-ACTTTATCGACACTTTCAATATATTTGGTAGTTTTTTTTACCGATTTTATCATTTCGAGA
1 TATTAAC-GTATCGACACTTTCAATATATCCGGTAG--CGCTTTACCGGTTTTATCATTTCGAGA
* * * * *
669335 CCTGTTTTGTCATATTTTTACATGTTATACTGCTATGGATCAATACATTTGTATAAAGTATCGAC
63 CCGGTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGAC
669400 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
128 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
* * * *
669455 TATTAACGTATCGACACTTTCAATATATCTGGTAGCTCTTTACCGGTTTTATCATTTTGTGACCG
1 TATTAACGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCG
* * * * *
669520 GTTTTGTCATACTTATACCTGTTATATTGTTATGGATCGATACGTTTTTATAAAGTATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACT
* **
669585 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
* * * *
669637 T-TTAAATC-TAATCGATACTTTCGATATATCCAGTAGCGGC-TTACCGGTTTTATCATAAT-GA
1 TATT-AA-CGT-ATCGACACTTTCAATATATCCGGTAGC-GCTTTACCGGTTTTATCAT-TTCGA
* * *
669698 AACCGGTTTTATCATATTTTTACCTGTTATATTGCTATGGAGCGATACATTTTT
61 GACCGGTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCGATACATTTTT
669752 CATTTGTATC
Statistics
Matches: 413, Mismatches: 58, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
181 3 0.01
182 158 0.38
183 88 0.21
184 159 0.38
185 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAACGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTTAAAAAGTGTCGATACTTA
Found at i:670206 original size:15 final size:15
Alignment explanation
Indices: 670186--670216 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
670176 CAACAGATAG
670186 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
670201 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
670216 A
1 A
670217 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:670505 original size:24 final size:25
Alignment explanation
Indices: 670478--670545 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
670468 GATTTGATAC
*
670478 TAATGATTACTAATAATGA-AATTA
1 TAATGATTACTAATAATGATAATAA
* *
670502 TAATAATTACTAATAAAGATTAATAA
1 TAATGATTACTAATAATGA-TAATAA
670528 TAATGATT--TAATAATGAT
1 TAATGATTACTAATAATGAT
670546 TAAATATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 25 0.68
26 11 0.30
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.38
Consensus pattern (25 bp):
TAATGATTACTAATAATGATAATAA
Found at i:670546 original size:24 final size:24
Alignment explanation
Indices: 670430--670548 Score: 68
Period size: 24 Copynumber: 4.9 Consensus size: 24
670420 GCACCCTTAG
* *
670430 TAATGATTACTAATAATGATTTATTAT
1 TAATGATT--TAATAATGA-TTAATAA
* * *
670457 TAAT-ATTTAATGAT--TTGATAC
1 TAATGATTTAATAATGATTAATAA
670478 TAATGATTACTAATAATGAAATT-ATAA
1 TAATGATT--TAATAATG--ATTAATAA
* * *
670505 TAATTA-CTAATAAAGATTAATAA
1 TAATGATTTAATAATGATTAATAA
670528 TAATGATTTAATAATGATTAA
1 TAATGATTTAATAATGATTAA
670549 ATATTTAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
21 8 0.11
22 6 0.08
23 9 0.13
24 31 0.44
26 3 0.04
27 12 0.17
28 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (24 bp):
TAATGATTTAATAATGATTAATAA
Found at i:670589 original size:32 final size:32
Alignment explanation
Indices: 670551--670629 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
670541 ATGATTAAAT
670551 ATTTAAATTTT-ATCTTACTATTTGAATA-TTAA
1 ATTTAAATTTTAAT-TT-CTATTTGAATATTTAA
* *
670583 ATTTAAATCTTTAATTTTTATTTTAATATTTAA
1 ATTTAAAT-TTTAATTTCTATTTGAATATTTAA
*
670616 ATATAAA-TTTAATT
1 ATTTAAATTTTAATT
670630 GTACCATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 7 0.17
32 17 0.41
33 15 0.37
34 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (32 bp):
ATTTAAATTTTAATTTCTATTTGAATATTTAA
Found at i:670602 original size:40 final size:39
Alignment explanation
Indices: 670545--670627 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
670535 TTAATAATGA
* *
670545 TTAAATATTTAAATTTTATCTTACTATTTGAATATTAAAT
1 TTAAATATTTAAATTTTATCTTAATATTTAAATA-TAAAT
* * *
670585 TTAAATCTTTAATTTTTATTTTAATATTTAAATATAAAT
1 TTAAATATTTAAATTTTATCTTAATATTTAAATATAAAT
670624 TTAA
1 TTAA
670628 TTGTACCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 9 0.24
40 29 0.76
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (39 bp):
TTAAATATTTAAATTTTATCTTAATATTTAAATATAAAT
Found at i:670614 original size:19 final size:19
Alignment explanation
Indices: 670548--670615 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
670538 ATAATGATTA
* *
670548 AATATTTAAATTTTATCTT
1 AATATTTAATTTTTATTTT
* ** *
670567 ACTATTTGAATATTAAATTTA
1 AATATTT-AAT-TTTTATTTT
*
670588 AATCTTTAATTTTTATTTT
1 AATATTTAATTTTTATTTT
670607 AATATTTAA
1 AATATTTAA
670616 ATATAAATTT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
19 20 0.57
20 5 0.14
21 10 0.29
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (19 bp):
AATATTTAATTTTTATTTT
Found at i:677676 original size:21 final size:21
Alignment explanation
Indices: 677651--677698 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
677641 TAAACACGAC
677651 ATCCATAACAACAAACTTTAA
1 ATCCATAACAACAAACTTTAA
* *
677672 TTCCATAACAACCAACTTTAA
1 ATCCATAACAACAAACTTTAA
677693 ATCCAT
1 ATCCAT
677699 TATAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
ATCCATAACAACAAACTTTAA
Found at i:685008 original size:31 final size:32
Alignment explanation
Indices: 684962--685051 Score: 139
Period size: 31 Copynumber: 2.9 Consensus size: 32
684952 AGGACCACCA
*
684962 TCCATATATCTCGAAGGACATAGGTAACA-TG
1 TCCATATATCCCGAAGGACATAGGTAACACTG
*
684993 TCCATATGTCCCGAAGGACATAGGTAA-ACTG
1 TCCATATATCCCGAAGGACATAGGTAACACTG
*
685024 TCCATATCTCCCGAAGGACATAGGTAAC
1 TCCATATATCCCGAAGGACATAGGTAAC
685052 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (32 bp):
TCCATATATCCCGAAGGACATAGGTAACACTG
Found at i:686821 original size:18 final size:19
Alignment explanation
Indices: 686800--686843 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
686790 ATTGTTTTTA
*
686800 AAATAAAAG-ATAATAATT
1 AAATAAAAGAAAAATAATT
686818 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAATAATT
686837 AAATAAA
1 AAATAAA
686844 CAAATTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATAAAAGAAAAATAATT
Found at i:686843 original size:23 final size:23
Alignment explanation
Indices: 686798--686843 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
686788 AAATTGTTTT
* *
686798 TAAAATAAAAGATAATAATTAAA
1 TAAAAGAAAAGATAATAAATAAA
686821 TAAAAGAAAA-ATAATTAAATAAA
1 TAAAAGAAAAGATAA-TAAATAAA
686844 CAAATTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
TAAAAGAAAAGATAATAAATAAA
Found at i:687311 original size:12 final size:12
Alignment explanation
Indices: 687296--687325 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
687286 AAAAGTATGC
687296 GAAAAATAGAGA
1 GAAAAATAGAGA
*
687308 GAAAACTAGAGA
1 GAAAAATAGAGA
687320 GAAAAA
1 GAAAAA
687326 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:687531 original size:19 final size:19
Alignment explanation
Indices: 687491--687531 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
687481 AATATAAAAA
* *
687491 TAATATCCTAAAACTTAAT
1 TAATATACTAAAACCTAAT
*
687510 TAATATACTAAAACCTATT
1 TAATATACTAAAACCTAAT
687529 TAA
1 TAA
687532 ACTAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATATACTAAAACCTAAT
Found at i:694980 original size:15 final size:16
Alignment explanation
Indices: 694960--694990 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
694950 AAAAGATAAG
694960 AATTAAATAAA-AAAT
1 AATTAAATAAACAAAT
694975 AATTAAATAAACAAAT
1 AATTAAATAAACAAAT
694991 TAAAGAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAATAAACAAAT
Found at i:695790 original size:76 final size:74
Alignment explanation
Indices: 695577--695802 Score: 237
Period size: 76 Copynumber: 3.1 Consensus size: 74
695567 TAAAACATCT
* * * * *
695577 TAAATCCTAATTAAAACACTTTAAA-CTATTTAAACTAAAATAC---CTAAAAAATAATATTTAA
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAA
*
695638 AATAATATTC
65 AATAATATCC
* * * * *
695648 TAAATCCTAATTAAATTACTAAAACCTATTTAAACCAAAATACCTAAAATAAAGATAAAATA-TA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
695712 AAAATAATATCC
63 AAAATAATATCC
* * *
695724 TAAAACTTAATTAAAATACTAAAGCCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAA
*
695789 AATATTATCC
65 AATAATATCC
695799 TAAA
1 TAAA
695803 CTTGAGTTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
70 4 0.03
71 33 0.26
72 1 0.01
74 9 0.07
75 22 0.17
76 53 0.41
77 6 0.05
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (74 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
ATAATATCC
Found at i:700226 original size:15 final size:15
Alignment explanation
Indices: 700203--700232 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
700193 AAACATAATA
700203 AACAAAAAAAATAAC
1 AACAAAAAAAATAAC
*
700218 AACATAAAAAATAAC
1 AACAAAAAAAATAAC
700233 CATCCATTAA
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:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (15 bp):
AACAAAAAAAATAAC
Found at i:706017 original size:43 final size:43
Alignment explanation
Indices: 705943--706105 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
705933 GCTAAAGTTC
*
705943 GCGGCGTTTGGTAACAAAAAACGCCGCAATAGGTAACGATATATA
1 GCGGCGTTT-GT-CCAAAAAACGCCGCAATAGGTAACGATATATA
* * ** * *
705988 GCGGCGTTTGTCCAAGAAACGCCGTAATAGGTATTGATATTTG
1 GCGGCGTTTGTCCAAAAAACGCCGCAATAGGTAACGATATATA
* * * *** * *
706031 GCGGCATTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTA
1 GCGGCGTTTGTCCAAAAAACGCCGCAATAGGTAACGATATATA
* *
706074 GCGGCGTTT-TCCCCACAAACGCCGCAATAGGT
1 GCGGCGTTTGT-CCAAAAAACGCCGCAATAGGT
706106 GTTGAGATTT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 1 0.01
43 89 0.88
44 2 0.02
45 9 0.09
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (43 bp):
GCGGCGTTTGTCCAAAAAACGCCGCAATAGGTAACGATATATA
Found at i:706106 original size:43 final size:43
Alignment explanation
Indices: 705961--706179 Score: 267
Period size: 43 Copynumber: 5.1 Consensus size: 43
705951 TGGTAACAAA
** * * * * *
705961 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAG
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
* * * * *
706004 AAACGCCGTAATAGGTATTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
* *
706047 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
* * * *
706090 AAACGCCGCAATAGGTGTTGAGATTTATCGGCATTTTTTCCAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
*
706133 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
706176 AAAC
1 AAAC
706180 ACCGTAAAAG
Statistics
Matches: 153, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 153 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGAGATTTAGCGGCGTTTTTCCCAC
Done.