Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 1425817
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 5 of 8
Found at i:598321 original size:16 final size:16
Alignment explanation
Indices: 598291--598350 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 16
598281 ATAAATTTTA
598291 TATATAAAATT-AAAAT
1 TATA-AAAATTAAAAAT
598307 TATAAAAATTAAAAAT
1 TATAAAAATTAAAAAT
598323 TA-AATAAA-TAAAAAT
1 TATAA-AAATTAAAAAT
598338 T-T--AAATTAAAAAT
1 TATAAAAATTAAAAAT
598351 AATATATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.08
13 7 0.17
15 16 0.40
16 14 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAAATTAAAAAT
Found at i:598354 original size:22 final size:23
Alignment explanation
Indices: 598296--598354 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
598286 TTTTATATAT
*
598296 AAAATT-AAAATTATAAAAATTA
1 AAAATTAAAAATAATAAAAATTA
*
598318 AAAATTAAATA-AATAAAAATT-
1 AAAATTAAAAATAATAAAAATTA
*
598339 TAAATTAAAAATAATA
1 AAAATTAAAAATAATA
598355 TATTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.29
22 19 0.61
23 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTAAAAATAATAAAAATTA
Found at i:598623 original size:30 final size:31
Alignment explanation
Indices: 598584--598645 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
598574 ATTGTATTTG
*
598584 TATTATTTTATATATTTTATTA-TATAATAAT
1 TATTATTTTAAATATTTT-TTATTATAATAAT
*
598615 TATT-TTTTAAATATTTTTTATTATATTAAT
1 TATTATTTTAAATATTTTTTATTATAATAAT
598645 T
1 T
598646 TAATAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 21 0.75
31 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTATTTTAAATATTTTTTATTATAATAAT
Found at i:598672 original size:21 final size:21
Alignment explanation
Indices: 598648--598738 Score: 53
Period size: 23 Copynumber: 4.0 Consensus size: 21
598638 TATTAATTTA
598648 ATAATTAATAATTTATATTAT
1 ATAATTAATAATTTATATTAT
*
598669 ATAAAATTTAA-ATTTTATATTATT
1 AT--AA-TTAATAATTTATATTA-T
*
598693 ATTATATTATTATATATTATATTTAT
1 A-TA-ATTAATA-AT-TTATA-TTAT
598719 ATAATT-AT-ATTTAATATTAT
1 ATAATTAATAATTT-ATATTAT
598739 TAAATTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
20 6 0.11
21 7 0.13
23 17 0.31
24 11 0.20
25 4 0.07
26 7 0.13
27 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATTAATAATTTATATTAT
Found at i:598735 original size:15 final size:15
Alignment explanation
Indices: 598693--598746 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
598683 TTATATTATT
*
598693 ATTATA-TTATTATA
1 ATTATATTTAATATA
598707 TATTATATTT-ATATA
1 -ATTATATTTAATATA
*
598722 ATTATATTTAATATT
1 ATTATATTTAATATA
*
598737 ATTAAATTTA
1 ATTATATTTA
598747 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.26
15 23 0.68
16 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATTTAATATA
Found at i:598735 original size:26 final size:25
Alignment explanation
Indices: 598656--598738 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 25
598646 TAATAATTAA
598656 TAAT-TTATATTATATAA--A-ATT
1 TAATATTATATTATATAATTATATT
*
598677 TAAATTTTATATTAT-T-ATTATATTAT
1 T-AATATTATATTATATAATTATA-T-T
598703 TATATATTATATTTATATAATTATATT
1 TA-ATATTATA-TTATATAATTATATT
598730 TAATATTAT
1 TAATATTAT
598739 TAAATTTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
21 2 0.04
22 4 0.08
23 10 0.20
24 1 0.02
25 2 0.04
26 16 0.32
27 7 0.14
28 2 0.04
29 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATATTATATTATATAATTATATT
Found at i:601352 original size:17 final size:16
Alignment explanation
Indices: 601326--601364 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
601316 TATTTATAAA
*
601326 TATTTATTAATATTTTT
1 TATTTTTTAA-ATTTTT
601343 TATTTTTTAAATTTTT
1 TATTTTTTAAATTTTT
601359 T-TTTTT
1 TATTTTT
601365 ACATTAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 7 0.33
17 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTTTAAATTTTT
Found at i:604714 original size:2 final size:2
Alignment explanation
Indices: 604702--604739 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
604692 TATGATCTAA
* *
604702 AT AT TT AT AT AT AT AT AT AT AA 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
604740 GTATGGATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:605175 original size:22 final size:24
Alignment explanation
Indices: 605140--605188 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
605130 GATTAAGTTC
605140 TAATTAAATGTTA-TTTT-AAATT
1 TAATTAAATGTTATTTTTAAAATT
* *
605162 TAATTATATTTTATTTTTAAAATT
1 TAATTAAATGTTATTTTTAAAATT
605186 TAA
1 TAA
605189 ATTTGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 4 0.17
24 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATTAAATGTTATTTTTAAAATT
Found at i:605234 original size:14 final size:14
Alignment explanation
Indices: 605185--605243 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
605175 TTTTTAAAAT
605185 TTAAATTTGATTTAA
1 TTAAATTT-ATTTAA
* * *
605200 GTTAAAAATTGAATTAT
1 -TT--AAATTTATTTAA
605217 TTAAATTTATTTAA
1 TTAAATTTATTTAA
605231 TTAAATTTATTTA
1 TTAAATTTATTTA
605244 TTTAGTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 22 0.63
16 4 0.11
17 4 0.11
18 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TTAAATTTATTTAA
Found at i:605640 original size:27 final size:27
Alignment explanation
Indices: 605585--605640 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
605575 AAACTCAATT
* ** *
605585 ATTAATCTACATTGCAAATTTTTCGAC
1 ATTAATCTACAGTGCAAATTTCCCAAC
*
605612 ATTATTCTACAGTGCAAATTTCCCAAC
1 ATTAATCTACAGTGCAAATTTCCCAAC
605639 AT
1 AT
605641 CCCTTGCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (27 bp):
ATTAATCTACAGTGCAAATTTCCCAAC
Found at i:606518 original size:15 final size:16
Alignment explanation
Indices: 606493--606522 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
606483 TATAAATTTA
606493 TATATAAAATTAAAAT
1 TATATAAAATTAAAAT
606509 TATA-AAAATTAAAA
1 TATATAAAATTAAAA
606523 ATTAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATAAAATTAAAAT
Found at i:606523 original size:7 final size:7
Alignment explanation
Indices: 606498--606552 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
606488 ATTTATATAT
606498 AAAATTA
1 AAAATTA
*
606505 AAATTATA
1 AAAAT-TA
606513 AAAATTA
1 AAAATTA
606520 AAAATTA
1 AAAATTA
606527 AGTAAATTA
1 A--AAATTA
606536 AAAATT-
1 AAAATTA
606542 -AAATTA
1 AAAATTA
606548 AAAAT
1 AAAAT
606553 AATTTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 5 0.12
7 23 0.56
8 6 0.15
9 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
AAAATTA
Found at i:606523 original size:16 final size:17
Alignment explanation
Indices: 606493--606542 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
606483 TATAAATTTA
*
606493 TATATAAAATT-AAAAT
1 TATAGAAAATTAAAAAT
606509 TATA-AAAATTAAAAAT
1 TATAGAAAATTAAAAAT
*
606525 TA-AGTAAATTAAAAAT
1 TATAGAAAATTAAAAAT
606541 TA
1 TA
606543 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 24 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TATAGAAAATTAAAAAT
Found at i:606524 original size:22 final size:22
Alignment explanation
Indices: 606498--606544 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
606488 ATTTATATAT
*
606498 AAAATTAA-AATTATAAAAATTA
1 AAAATTAAGAAAT-TAAAAATTA
606520 AAAATTAAGTAAATTAAAAATTA
1 AAAATTAAG-AAATTAAAAATTA
606543 AA
1 AA
606545 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTAAGAAATTAAAAATTA
Found at i:606910 original size:23 final size:23
Alignment explanation
Indices: 606884--606945 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 23
606874 AATTCAAATT
*
606884 TTATATTATTATTATATTATATA
1 TTATATTATTATAATATTATATA
606907 TTATA-T-TTAT-ATAATTATAT-
1 TTATATTATTATAAT-ATTATATA
606927 TTAATATTATTA-AAT-TTAT
1 TT-ATATTATTATAATATTAT
606946 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 4 0.12
21 18 0.53
22 2 0.06
23 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATATTATTATAATATTATATA
Found at i:606927 original size:60 final size:61
Alignment explanation
Indices: 606765--606943 Score: 162
Period size: 60 Copynumber: 3.0 Consensus size: 61
606755 AGGAAATTCA
* * * **
606765 AATATTGATTATTGTATT-TGTATTAT-TTTATAT-ATTTTATTATATAATAATTATTTTTT
1 AATATT-ATTATTATATTATATATTATATTTATATAATTATATTATATAATAATTAAATTTT
*
606824 AAATATTATTTATTATATTA-AT-TTAATAATTA-ATAATTTATATTATATAA-AATTCAAATTT
1 -AATATTA-TTATTATATTATATATT-ATATTTATATAA-TTATATTATATAATAATT-AAATTT
606885 T
61 T
*
606886 -ATATTATTATTATATTATATATTATATTTATATAATTATATT-TA-ATATTATTAAATTT
1 AATATTATTATTATATTATATATTATATTTATATAATTATATTATATA-ATAATTAAATTT
606944 ATTTTTAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 25
0.75 0.06 0.19
Matches are distributed among these distances:
58 1 0.01
59 23 0.23
60 44 0.44
61 14 0.14
62 17 0.17
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (61 bp):
AATATTATTATTATATTATATATTATATTTATATAATTATATTATATAATAATTAAATTTT
Found at i:606937 original size:29 final size:29
Alignment explanation
Indices: 606833--606945 Score: 78
Period size: 29 Copynumber: 3.9 Consensus size: 29
606823 TAAATATTAT
*
606833 TTATTATATTA-AT-TTAATAATTA-ATAA
1 TTATTATATTATATATTAA-ATTTATATAA
*
606860 -T-TTATATTATATAAAATTCAAATTTTATATTA
1 TTATTATATTATAT---ATT-AAA-TTTATATAA
*
606892 TTATTATATTATATATTATATTTATATAA
1 TTATTATATTATATATTAAATTTATATAA
606921 TTA-TAT-TTAATATTATTAAATTTAT
1 TTATTATATT-ATA-TATTAAATTTAT
606946 TTTTAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
25 8 0.12
26 3 0.04
27 2 0.03
28 6 0.09
29 22 0.32
30 5 0.07
31 8 0.12
32 3 0.04
33 1 0.01
34 11 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
TTATTATATTATATATTAAATTTATATAA
Found at i:613092 original size:29 final size:29
Alignment explanation
Indices: 613039--613098 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
613029 TTTCATTTTT
**
613039 ATATATTTTATAATTAAATTTAAATTAAA
1 ATATATTTTATAATTAAATAAAAATTAAA
* * *
613068 ATATTTTTTATTATTAAATAAAAATTTAA
1 ATATATTTTATAATTAAATAAAAATTAAA
613097 AT
1 AT
613099 CAATTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATATATTTTATAATTAAATAAAAATTAAA
Found at i:615731 original size:16 final size:15
Alignment explanation
Indices: 615712--615742 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
615702 TTATTAAATC
615712 AATATATTAATATTAA
1 AATATATTAA-ATTAA
615728 AATATATTAAATTAA
1 AATATATTAAATTAA
615743 TTTAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAAATTAA
Found at i:619277 original size:23 final size:24
Alignment explanation
Indices: 619245--619291 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
619235 TTAATTAATT
** *
619245 TATTTAAATATTTTTAAAATATAA
1 TATTTAAATAAATTTAAAAAATAA
619269 TATTT-AATAAATTTAAAAAATAA
1 TATTTAAATAAATTTAAAAAATAA
619292 AAAATAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTTAAATAAATTTAAAAAATAA
Found at i:620041 original size:26 final size:25
Alignment explanation
Indices: 619998--620046 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
619988 TTTAATATAA
619998 ATTTATTTAAAAATTTAAAATTTTTT
1 ATTTATTTAAAAATTT-AAATTTTTT
*
620024 ATTTATTTAATGAA-TTAAATTTT
1 ATTTATTTAA-AAATTTAAATTTT
620047 AATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 12 0.57
27 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTATTTAAAAATTTAAATTTTTT
Found at i:620492 original size:29 final size:28
Alignment explanation
Indices: 620439--620493 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
620429 GTATTCAATA
*
620439 TTTATTTAACATAAAAATTATTTTAAAT
1 TTTATTTAACATAAAAATTAATTTAAAT
620467 TTTATTTAA-ATAAATCAATTAATTTAA
1 TTTATTTAACATAAA--AATTAATTTAA
620494 TCAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTATTTAACATAAAAATTAATTTAAAT
Found at i:620495 original size:13 final size:13
Alignment explanation
Indices: 620472--620507 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
620462 TAAATTTTAT
*
620472 TTAAATAAATCAA
1 TTAAATTAATCAA
*
620485 TTAATTTAATCAA
1 TTAAATTAATCAA
620498 TTAAATTAAT
1 TTAAATTAAT
620508 TAAATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAATTAATCAA
Found at i:628293 original size:19 final size:20
Alignment explanation
Indices: 628261--628307 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
628251 AAAATATAAA
* *
628261 AATATTATTTTTAATA-TTT
1 AATAATATTATTAATACTTT
*
628280 AATGATATTATTAATACTTT
1 AATAATATTATTAATACTTT
628300 AATAATAT
1 AATAATAT
628308 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AATAATATTATTAATACTTT
Found at i:628540 original size:7 final size:7
Alignment explanation
Indices: 628528--628553 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
628518 GTGCCTAAAC
628528 CAAAAGA
1 CAAAAGA
628535 CAAAAGA
1 CAAAAGA
628542 CAAAAGA
1 CAAAAGA
628549 CAAAA
1 CAAAA
628554 AACAGAAGGC
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:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (7 bp):
CAAAAGA
Found at i:628726 original size:21 final size:20
Alignment explanation
Indices: 628686--628726 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
628676 GTATTTGAAA
* *
628686 TTTAAATATAATATTTAATT
1 TTTAAAGATAATAATTAATT
628706 TTTAAAGATAATTAATTAATT
1 TTTAAAGATAA-TAATTAATT
628727 AATTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAAAGATAATAATTAATT
Found at i:629075 original size:20 final size:19
Alignment explanation
Indices: 629050--629090 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
629040 TTACTTATTC
629050 AACTTAAATAAAATAAATTA
1 AACTTAAATAAAAT-AATTA
*
629070 AACTTAAATATAATAATTA
1 AACTTAAATAAAATAATTA
629089 AA
1 AA
629091 AATTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AACTTAAATAAAATAATTA
Found at i:629657 original size:2 final size:2
Alignment explanation
Indices: 629650--629678 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
629640 CCAGCTTCCA
629650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
629679 AGCTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:633933 original size:2 final size:2
Alignment explanation
Indices: 633926--633969 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
633916 GGTTAAAATT
*
633926 GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GCA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA
633968 GA
1 GA
633970 AGCATGCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.45, T:0.00
Consensus pattern (2 bp):
GA
Found at i:638177 original size:36 final size:36
Alignment explanation
Indices: 638137--638208 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
638127 TTTCCAAAGC
638137 AATGCTGAAGAGAAGACAACCAATTCTTCAGTGGTT
1 AATGCTGAAGAGAAGACAACCAATTCTTCAGTGGTT
638173 AATGCTGAAGAGAAGACAACCAATTCTTCAGTGGTT
1 AATGCTGAAGAGAAGACAACCAATTCTTCAGTGGTT
638209 CTTGTCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (36 bp):
AATGCTGAAGAGAAGACAACCAATTCTTCAGTGGTT
Found at i:644845 original size:25 final size:26
Alignment explanation
Indices: 644794--644851 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
644784 TTTATTTTTT
*
644794 TAATAAAAAAATTTATAATTTAAAAA
1 TAATAAAAAAATTTATAAATTAAAAA
* *
644820 TAATAAAGAAA-TTATAAATTATAAA
1 TAATAAAAAAATTTATAAATTAAAAA
*
644845 TATTAAA
1 TAATAAA
644852 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
TAATAAAAAAATTTATAAATTAAAAA
Found at i:646579 original size:2 final size:2
Alignment explanation
Indices: 646572--646607 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
646562 TTTCACTATC
646572 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
646608 TTGTCTCAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:646934 original size:13 final size:13
Alignment explanation
Indices: 646858--646940 Score: 54
Period size: 13 Copynumber: 6.7 Consensus size: 13
646848 TTTACATAAA
646858 TATTATAATGTAA-
1 TATTATAAT-TAAT
646871 TATTATAA-TAAT
1 TATTATAATTAAT
*
646883 TATT-TGA-TAAT
1 TATTATAATTAAT
646894 T-TTAATATATT--T
1 TATT-ATA-ATTAAT
* *
646906 TATTATAAATATT
1 TATTATAATTAAT
646919 TATTATAATTAAT
1 TATTATAATTAAT
*
646932 TATAATAAT
1 TATTATAAT
646941 AAATATGATA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
10 2 0.04
11 12 0.21
12 10 0.18
13 31 0.55
14 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TATTATAATTAAT
Found at i:647153 original size:32 final size:31
Alignment explanation
Indices: 647093--647167 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
647083 GATAAAAATT
647093 AATATAAAATATAAATAATTAAAATTTATAA
1 AATATAAAATATAAATAATTAAAATTTATAA
* * * *
647124 AATATAAATTATTAATAAATTAAATTTTATAT
1 AATATAAAATATAAAT-AATTAAAATTTATAA
*
647156 AATATATAATAT
1 AATATAAAATAT
647168 TTTTTATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AATATAAAATATAAATAATTAAAATTTATAA
Found at i:647169 original size:19 final size:18
Alignment explanation
Indices: 647119--647177 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
647109 AATTAAAATT
*
647119 TATAAAATATAAATTATTA
1 TATAATATATAAATT-TTA
647138 -ATAA-AT-TAAATTTTA
1 TATAATATATAAATTTTA
*
647153 TATAATATATAATATTTTT
1 TATAATATATAA-ATTTTA
647172 TATAAT
1 TATAAT
647178 GCATGAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 4 0.11
18 7 0.20
19 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATATATAAATTTTA
Found at i:652547 original size:38 final size:38
Alignment explanation
Indices: 652505--652615 Score: 138
Period size: 38 Copynumber: 2.9 Consensus size: 38
652495 CGATTGATGA
652505 TTAGAAAATTCAATTT-GAGATTAGCTGGTAGCTGGCGG
1 TTAGAAAATTCAATTTGGA-ATTAGCTGGTAGCTGGCGG
* *
652543 TTAGAGAATTCAATTTGGAATTAGCTGGTGGCTGGCGG
1 TTAGAAAATTCAATTTGGAATTAGCTGGTAGCTGGCGG
* *
652581 TTA-AATAATTTAATTTGGAATT-GATTGGTAGCTGG
1 TTAGAA-AATTCAATTTGGAATTAG-CTGGTAGCTGG
652616 TTGCTAGGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.03
38 60 0.94
39 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.29, T:0.35
Consensus pattern (38 bp):
TTAGAAAATTCAATTTGGAATTAGCTGGTAGCTGGCGG
Found at i:655098 original size:145 final size:145
Alignment explanation
Indices: 654835--655124 Score: 553
Period size: 145 Copynumber: 2.0 Consensus size: 145
654825 TTATTCTCAC
654835 ATGCAAAGTTGTCAAAGATGTTTTGGGTTGAGGCTATACTTGTAGTTATTTATGTGTTAAACCTT
1 ATGCAAAGTTGTCAAAGATGTTTTGGGTTGAGGCTATACTTGTAGTTATTTATGTGTTAAACCTT
* *
654900 TCACCATGTGTCTCTTTACAATTTGATACTCCTGAAAAAGTATGGTCAGGCAATGATGTTTCTTA
66 TCACCATGTGTCCCTTTACAATTTGATACTCCTGAAAAAGTATGGTCAGGCAATAATGTTTCTTA
654965 TAATCATCTGCGAGT
131 TAATCATCTGCGAGT
654980 ATGCAAAGTTGTCAAAGATGTTTTGGGTTGAGGCTATACTTGTAGTTATTTATGTGTTAAACCTT
1 ATGCAAAGTTGTCAAAGATGTTTTGGGTTGAGGCTATACTTGTAGTTATTTATGTGTTAAACCTT
655045 TCACCATGTGTCCCTTTACAATTTGATACTCCTGAAAAAGTATGGTCAGGCAATAATGTTTCTTA
66 TCACCATGTGTCCCTTTACAATTTGATACTCCTGAAAAAGTATGGTCAGGCAATAATGTTTCTTA
*
655110 TAATTATCTGCGAGT
131 TAATCATCTGCGAGT
655125 GTTTGGTTGT
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 142 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (145 bp):
ATGCAAAGTTGTCAAAGATGTTTTGGGTTGAGGCTATACTTGTAGTTATTTATGTGTTAAACCTT
TCACCATGTGTCCCTTTACAATTTGATACTCCTGAAAAAGTATGGTCAGGCAATAATGTTTCTTA
TAATCATCTGCGAGT
Found at i:657335 original size:38 final size:38
Alignment explanation
Indices: 657229--657328 Score: 148
Period size: 38 Copynumber: 2.6 Consensus size: 38
657219 AAATTGAATT
*
657229 GCTGAC-GATTAGAGAATTAAATTTGAAATTGGTTGGCG
1 GCTGACAG-TTAGAGAATTCAATTTGAAATTGGTTGGCG
* *
657267 GCTGACGGTTAGAGAATTCAATTTGAAATTGGTTGGTG
1 GCTGACAGTTAGAGAATTCAATTTGAAATTGGTTGGCG
*
657305 GCTGGCAGTTAGAGAATTCAATTT
1 GCTGACAGTTAGAGAATTCAATTT
657329 AGAATTGACT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
38 56 0.98
39 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.33
Consensus pattern (38 bp):
GCTGACAGTTAGAGAATTCAATTTGAAATTGGTTGGCG
Found at i:657888 original size:16 final size:16
Alignment explanation
Indices: 657869--657900 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
657859 TCTTTGCTAA
657869 AGGTTTGAGTTTTGAC
1 AGGTTTGAGTTTTGAC
657885 AGGTTTGAGTTTTGAC
1 AGGTTTGAGTTTTGAC
657901 GTTAAAATTT
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:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
AGGTTTGAGTTTTGAC
Found at i:671600 original size:2 final size:2
Alignment explanation
Indices: 671593--671625 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
671583 GCCCGTTATG
671593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
671626 AACTAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:676479 original size:21 final size:21
Alignment explanation
Indices: 676437--676475 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
676427 ATAACTTTAC
* *
676437 AAAAAATTTTTAAATACATAA
1 AAAAAACTTTTAAATAAATAA
676458 AAAAAACTTTTAAA-AAAT
1 AAAAAACTTTTAAATAAAT
676476 TAAACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.19
21 13 0.81
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAACTTTTAAATAAATAA
Found at i:677625 original size:2 final size:2
Alignment explanation
Indices: 677620--677656 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
677610 CCACACACAA
677620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
677657 ACACTTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:681135 original size:19 final size:19
Alignment explanation
Indices: 681111--681165 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
681101 ATTAAAAAAT
681111 TATTTTAT-ATTAATATTTA
1 TATTTTATAATTAA-ATTTA
681130 TATTTTATAATTAAATTTAA
1 TATTTTATAATTAAATTT-A
681150 CTATTTT-TAATTAAAT
1 -TATTTTATAATTAAAT
681166 AAATAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.36
20 15 0.45
21 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTATAATTAAATTTA
Found at i:681532 original size:16 final size:17
Alignment explanation
Indices: 681500--681553 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
681490 ATTTAATTTG
*
681500 AAATATTATTTAATAATA
1 AAAT-TTATATAATAATA
681518 AAATTTATA-AATAAT-
1 AAATTTATATAATAATA
*
681533 AAATTTATATAATTATA
1 AAATTTATATAATAATA
681550 AAAT
1 AAAT
681554 AATTAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 9 0.28
16 11 0.34
17 8 0.25
18 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAATAATA
Found at i:681555 original size:28 final size:29
Alignment explanation
Indices: 681524--681591 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
681514 AATAAAATTT
*
681524 ATAAATAATAAATTTATATAATTA-TAAA
1 ATAAATAATAAATTTATATAAATATTAAA
* ** * *
681552 ATAATTAATTTATTTATTTAAATATTTAA
1 ATAAATAATAAATTTATATAAATATTAAA
681581 ATAAAT-ATAAA
1 ATAAATAATAAA
681592 ATAATAGATA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAAATAATAAATTTATATAAATATTAAA
Found at i:681653 original size:41 final size:41
Alignment explanation
Indices: 681568--681656 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
681558 AATTTATTTA
*
681568 TTTAAATATTTAAATAAATATAAAATAATAGATATTACAAT
1 TTTAAATATTTAAATAAATATAAAATAATAGATAATACAAT
*** *
681609 TTTAAATATTATTAAA-AAATAT-AAATAATTTTTAATACATT
1 TTTAAATA-T-TTAAATAAATATAAAATAATAGATAATACAAT
681650 TTTAAAT
1 TTTAAAT
681657 TAAATATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 29 0.71
42 7 0.17
43 5 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (41 bp):
TTTAAATATTTAAATAAATATAAAATAATAGATAATACAAT
Found at i:681671 original size:26 final size:30
Alignment explanation
Indices: 681625--681681 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
681615 TATTATTAAA
681625 AAATATAAATAATTTTTAAT-A-CATTTTT
1 AAATATAAATAATTTTTAATAATCATTTTT
681653 AAAT-TAAAT-ATTTTTAATAATCATTTTT
1 AAATATAAATAATTTTTAATAATCATTTTT
681681 A
1 A
681682 TTTTCATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 9 0.33
27 6 0.22
28 12 0.44
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATAAATAATTTTTAATAATCATTTTT
Found at i:682511 original size:15 final size:15
Alignment explanation
Indices: 682491--682543 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
682481 AATTAAAAGA
682491 TTATTTAAATTTAAT
1 TTATTTAAATTTAAT
*
682506 TTATTT-ATTTTAAT
1 TTATTTAAATTTAAT
**
682520 GAAGTTTAAATTTAAT
1 TTA-TTTAAATTTAAT
682536 TTATTTAA
1 TTATTTAA
682544 TTTGTACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 8 0.27
15 14 0.47
16 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTATTTAAATTTAAT
Found at i:683021 original size:19 final size:20
Alignment explanation
Indices: 682994--683050 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 20
682984 AAATTAACTA
*
682994 TTAATTAAATTTAATA-ATT
1 TTAAATAAATTTAATATATT
683013 TTAAATAAATATTATTATATATT
1 TTAAATAAAT-TTA--ATATATT
*
683036 ATAAATATAATTTAA
1 TTAAATA-AATTTAA
683051 AAATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 9 0.29
20 3 0.10
21 1 0.03
22 3 0.10
23 12 0.39
24 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATAAATTTAATATATT
Found at i:686645 original size:22 final size:22
Alignment explanation
Indices: 686620--686679 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
686610 TTAAATTTTT
686620 AATTATATAATAATATAATATA
1 AATTATATAATAATATAATATA
686642 AATTATATAATGAATA-AATATA
1 AATTATATAAT-AATATAATATA
* *
686664 TATCAT-T-ATAATATAA
1 AATTATATAATAATATAA
686680 ATATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 1 0.03
22 21 0.62
23 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTATATAATAATATAATATA
Found at i:687375 original size:32 final size:29
Alignment explanation
Indices: 687313--687416 Score: 70
Period size: 32 Copynumber: 3.5 Consensus size: 29
687303 AAATATGAAC
* * * *
687313 TTAAATTTATTTAT-ATTTATAT-TTATA
1 TTAAATTTATTTTTAATGTATATAATAAA
687340 TTAAATTTATTTTTAATCGATAATATAATAAA
1 TTAAATTTATTTTTAAT-G-T-ATATAATAAA
*
687372 TTAATATTATTAATTTTAATGTATATAATAAA
1 TTAA-A-T-TTATTTTTAATGTATATAATAAA
* *
687404 AT-ATTTTATTTTT
1 TTAAATTTATTTTT
687417 TTGAGATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
27 13 0.21
28 9 0.15
29 1 0.02
30 1 0.02
31 5 0.08
32 18 0.30
33 2 0.03
34 2 0.03
35 10 0.16
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (29 bp):
TTAAATTTATTTTTAATGTATATAATAAA
Found at i:687417 original size:29 final size:33
Alignment explanation
Indices: 687345--687417 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 33
687335 TTATATTAAA
*
687345 TTTA-TTTTTAATCGATAATATAATAAATTAAT
1 TTTATTTTTTAATCGATAATATAATAAAATAAT
*
687377 ATTATTAATTTTAAT-G-T-ATATAATAAAAT-AT
1 TTTATT--TTTTAATCGATAATATAATAAAATAAT
687408 TTTATTTTTT
1 TTTATTTTTT
687418 TGAGATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
29 4 0.11
31 7 0.20
32 14 0.40
33 2 0.06
34 1 0.03
35 7 0.20
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (33 bp):
TTTATTTTTTAATCGATAATATAATAAAATAAT
Found at i:687434 original size:17 final size:16
Alignment explanation
Indices: 687408--687449 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
687398 AATAAAATAT
*
687408 TTTATTTTTTTGAGATA
1 TTTATATTTTT-AGATA
687425 TTTATA-TTTTAGATA
1 TTTATATTTTTAGATA
*
687440 TTTTTATTTT
1 TTTATATTTT
687450 AATACAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
16 7 0.32
17 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (16 bp):
TTTATATTTTTAGATA
Found at i:687440 original size:15 final size:15
Alignment explanation
Indices: 687415--687450 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
687405 TATTTTATTT
687415 TTTTGAGATATTTATA
1 TTTT-AGATATTTATA
*
687431 TTTTAGATATTTTTA
1 TTTTAGATATTTATA
687446 TTTTA
1 TTTTA
687451 ATACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTAGATATTTATA
Found at i:687494 original size:21 final size:21
Alignment explanation
Indices: 687455--687494 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
687445 ATTTTAATAC
*
687455 AAAATTATTATAAATATTATT
1 AAAATTATTATAAAGATTATT
687476 AAAATTA-TATAAAAGATTA
1 AAAATTATTAT-AAAGATTA
687495 AAAAATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAATTATTATAAAGATTATT
Found at i:692319 original size:2 final size:2
Alignment explanation
Indices: 692314--692341 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
692304 GGGGGGGGGG
692314 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
692342 TAAGTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:693962 original size:21 final size:21
Alignment explanation
Indices: 693916--693963 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
693906 TTATTTTTAA
*
693916 AATTTTTAAAATAATATTTTT
1 AATTTTTAAAATAATATTATT
* *
693937 TATTTTTAAAA-ATTAATTATT
1 AATTTTTAAAATAAT-ATTATT
693958 AATTTT
1 AATTTT
693964 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTTAAAATAATATTATT
Found at i:695323 original size:22 final size:22
Alignment explanation
Indices: 695298--695357 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
695288 TATCAAATAA
*
695298 AAAATTAATTTAAATATAAATT
1 AAAATTTATTTAAATATAAATT
695320 AAAATTTATTTAAATATAAATT
1 AAAATTTATTTAAATATAAATT
695342 AAAATTTATTTAAATA
1 AAAATTTATTTAAATA
695358 CGATAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTTATTTAAATATAAATT
Found at i:698221 original size:3 final size:3
Alignment explanation
Indices: 698213--698237 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
698203 TTGATGTATA
698213 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
698238 TTGTATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:698671 original size:13 final size:12
Alignment explanation
Indices: 698650--698680 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
698640 ATTTTTTATT
698650 TAAATTTAATTA
1 TAAATTTAATTA
698662 TAAATATTAATTA
1 TAAAT-TTAATTA
698675 TAAATT
1 TAAATT
698681 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATTTAATTA
Found at i:699493 original size:3 final size:3
Alignment explanation
Indices: 699485--699516 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
699475 CCATGTAACT
699485 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
699517 TTTACCGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:701201 original size:3 final size:3
Alignment explanation
Indices: 701193--701237 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
701183 AAGAGCAACG
701193 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
701238 ATGTCATCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:706572 original size:24 final size:24
Alignment explanation
Indices: 706545--706595 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
706535 TTATGTTATC
* *
706545 ATATTTACTATATTTATTATAATA
1 ATATTTACTAAATTTATAATAATA
* *
706569 ATATTTATTAAATTTATAATTATA
1 ATATTTACTAAATTTATAATAATA
706593 ATA
1 ATA
706596 AACATGATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTTACTAAATTTATAATAATA
Found at i:707578 original size:2 final size:2
Alignment explanation
Indices: 707571--707602 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
707561 TATCTTAAAC
707571 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
707603 GTGTGGATAT
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):
AT
Found at i:713870 original size:16 final size:17
Alignment explanation
Indices: 713851--713967 Score: 71
Period size: 16 Copynumber: 6.5 Consensus size: 17
713841 ATAAAAAAAT
713851 AATATA-AATATTTTAA
1 AATATATAATATTTTAA
713867 AATATATTAATATTTTAA
1 AATATA-TAATATTTTAA
713885 ATATTTATATAATTAAATTATTAA
1 A-A--TATATAA-T--ATT-TTAA
*
713909 TATAT-TAA-ATTTT-A
1 AATATATAATATTTTAA
* *
713923 TATATAAAATATTTTAA
1 AATATATAATATTTTAA
**
713940 ATATTATATAATATAATAA
1 A-A-TATATAATATTTTAA
713959 AATATATAA
1 AATATATAA
713968 ATATAATCGA
Statistics
Matches: 81, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.07
15 4 0.05
16 14 0.17
17 8 0.10
18 13 0.16
19 14 0.17
20 6 0.07
21 8 0.10
23 4 0.05
24 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATAATATTTTAA
Found at i:713870 original size:19 final size:18
Alignment explanation
Indices: 713846--713971 Score: 80
Period size: 18 Copynumber: 6.8 Consensus size: 18
713836 AAATAATAAA
713846 AAAATAATATAAATATTTT
1 AAAAT-ATATAAATATTTT
*
713865 AAAATATATTAATATTTT
1 AAAATATATAAATATTTT
* **
713883 AAATATTTATATAATTAAATT
1 AAA-A--TATATAAATATTTT
* *
713904 ATTAATATATTAA-ATTTT
1 A-AAATATATAAATATTTT
*
713922 -ATATATA-AAATATTTT
1 AAAATATATAAATATTTT
**
713938 -AAATATTATATAATATAAT
1 AAAATA-TATA-AATATTTT
713957 AAAATATATAAATAT
1 AAAATATATAAATAT
713972 AATCGAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
15 2 0.02
16 14 0.17
17 2 0.02
18 24 0.29
19 22 0.27
20 5 0.06
21 12 0.15
22 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATATATAAATATTTT
Found at i:713888 original size:17 final size:17
Alignment explanation
Indices: 713847--713945 Score: 77
Period size: 16 Copynumber: 6.1 Consensus size: 17
713837 AATAATAAAA
* *
713847 AAATAATATAAATATTTT
1 AAAT-ATATTAATATATT
*
713865 AAAATATATTAATATTTT
1 -AAATATATTAATATATT
713883 AAATAT-TT-ATATAATT
1 AAATATATTAATAT-ATT
713899 AAAT-TATTAATATATT
1 AAATATATTAATATATT
*
713915 AAAT-T-TT-ATATATA
1 AAATATATTAATATATT
*
713929 AAATATTTTAA-ATATT
1 AAATATATTAATATATT
713945 A
1 A
713946 TATAATATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.14
15 8 0.11
16 25 0.36
17 11 0.16
18 12 0.17
19 4 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATATATTAATATATT
Found at i:713910 original size:23 final size:23
Alignment explanation
Indices: 713868--713914 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
713858 ATATTTTAAA
713868 ATATATTAATATTTTAAATATTT
1 ATATATTAATATTTTAAATATTT
713891 ATATAATTAA-ATTATTAATATATT
1 ATAT-ATTAATATT-TTAA-ATATT
713915 AAATTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATTAATATTTTAAATATTT
Found at i:713943 original size:32 final size:33
Alignment explanation
Indices: 713864--713972 Score: 124
Period size: 32 Copynumber: 3.5 Consensus size: 33
713854 ATAAATATTT
*
713864 TAAAATATATTAATATTTTAAATATTTATATAA
1 TAAAATATATTAATATATTAAATATTTATATAA
*
713897 TTAAAT-TATTAATATATTAAAT-TTTATAT-A
1 TAAAATATATTAATATATTAAATATTTATATAA
* *
713927 TAAAATATTTTAA-ATATT--ATA-TAATATAA
1 TAAAATATATTAATATATTAAATATTTATATAA
*
713956 TAAAATATATAAATATA
1 TAAAATATATTAATATA
713973 ATCGAATATG
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
28 7 0.11
29 12 0.18
30 14 0.22
31 12 0.18
32 15 0.23
33 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TAAAATATATTAATATATTAAATATTTATATAA
Found at i:713980 original size:28 final size:30
Alignment explanation
Indices: 713921--713981 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
713911 TATTAAATTT
* * *
713921 TATATATAAAATATTTTAAATATTATATAA
1 TATATATAAAATATTATAAATATAATAGAA
*
713951 TATA-ATAAAATA-TATAAATATAATCGAA
1 TATATATAAAATATTATAAATATAATAGAA
713979 TAT
1 TAT
713982 GCATCTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.56
29 8 0.30
30 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
TATATATAAAATATTATAAATATAATAGAA
Found at i:714092 original size:3 final size:3
Alignment explanation
Indices: 714084--714113 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
714074 CCCATTTTGT
714084 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
714114 GATTTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:714939 original size:10 final size:10
Alignment explanation
Indices: 714926--714958 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
714916 ATATTAATTC
714926 ATATTCATAT
1 ATATTCATAT
714936 ATATAT-ATAT
1 ATAT-TCATAT
714946 ATATTCATAT
1 ATATTCATAT
714956 ATA
1 ATA
714959 AATAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATTCATAT
Found at i:715120 original size:9 final size:9
Alignment explanation
Indices: 715108--715164 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 9
715098 CTTATATTTA
715108 TTATTATAT
1 TTATTATAT
715117 TTA-TATTAT
1 TTATTA-TAT
*
715126 TTTTTAT-T
1 TTATTATAT
715134 TTATTATATT
1 TTATTATA-T
715144 TTAATTAT-T
1 TT-ATTATAT
715153 TTA-TATAT
1 TTATTATAT
715161 TTAT
1 TTAT
715165 ACCTATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
7 3 0.08
8 14 0.36
9 12 0.31
10 5 0.13
11 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTATAT
Found at i:715122 original size:18 final size:17
Alignment explanation
Indices: 715099--715146 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
715089 AATCCAACAC
715099 TTATATTTATTATTATAT
1 TTATATTTATT-TTATAT
*
715117 TTATA-TTATTTTTTAT
1 TTATATTTATTTTATAT
715133 TT-TATTATATTTTA
1 TTATATT-TATTTTA
715147 ATTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 8 0.31
17 11 0.42
18 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTTATTTTATAT
Found at i:715140 original size:15 final size:16
Alignment explanation
Indices: 715099--715164 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
715089 AATCCAACAC
*
715099 TTATATTTATTATTATAT
1 TTATA-TTA-TATTTTAT
*
715117 TTATATTATTTTTTAT
1 TTATATTATATTTTAT
*
715133 TT-TATTATATTTTAA
1 TTATATTATATTTTAT
*
715148 TTATTTTATATATTTAT
1 TTATATTATAT-TTTAT
715165 ACCTATTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
15 13 0.32
16 15 0.38
17 7 0.17
18 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATATTATATTTTAT
Found at i:715141 original size:26 final size:27
Alignment explanation
Indices: 715099--715182 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 27
715089 AATCCAACAC
*
715099 TTATATTTATTATTATATTTATATTATT
1 TTATATAT-TTATTATATTTATATTATT
*
715127 TTTTAT-TTTATTATATTT-TAATTATT
1 TTATATATTTATTATATTTAT-ATTATT
715153 TTATATATTTA-TACCTATTTAATATTATT
1 TTATATATTTATTA--TATTT-ATATTATT
715182 T
1 T
715183 GGATTTGTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
25 1 0.02
26 24 0.50
27 5 0.10
28 10 0.21
29 7 0.15
30 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTATATATTTATTATATTTATATTATT
Found at i:715161 original size:18 final size:17
Alignment explanation
Indices: 715099--715162 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 17
715089 AATCCAACAC
715099 TTATAT-TTATTATTATAT
1 TTATATATT-TTATTAT-T
715117 TTATATTATTTT-TTATT
1 TTATA-TATTTTATTATT
715134 TTATTATATTTTAATTATT
1 TTA-TATATTTT-ATTATT
715153 TTATATATTT
1 TTATATATTT
715163 ATACCTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.24
18 18 0.44
19 11 0.27
20 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATATTTTATTATT
Found at i:715171 original size:19 final size:18
Alignment explanation
Indices: 715130--715182 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
715120 TATTATTTTT
*
715130 TATTTTATTATATTTTAAT
1 TATTTTA-TATATTTTAAC
*
715149 TATTTTATATATTTATACC
1 TATTTTATATATTT-TAAC
*
715168 TATTTAATATTATTT
1 TATTTTATA-TATTT
715183 GGATTTGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.24
19 17 0.59
20 5 0.17
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATATATTTTAAC
Found at i:715181 original size:10 final size:10
Alignment explanation
Indices: 715099--715182 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 10
715089 AATCCAACAC
715099 TTATATTTATTA
1 TTAT-TTTA-TA
715111 TTATATTTATA
1 TTAT-TTTATA
715122 TTA-TTT-T-
1 TTATTTTATA
715129 TTATTTTAT-
1 TTATTTTATA
715138 TATATTTTA-A
1 T-TATTTTATA
715148 TTATTTTATA
1 TTATTTTATA
715158 -TA-TTTATA
1 TTATTTTATA
* *
715166 CCTATTTAATA
1 -TTATTTTATA
715177 TTATTT
1 TTATTT
715183 GGATTTGTCG
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
7 3 0.05
8 10 0.16
9 14 0.23
10 16 0.26
11 10 0.16
12 9 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATTTTATA
Found at i:716183 original size:2 final size:2
Alignment explanation
Indices: 716176--716202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
716166 GTCAATTTCA
716176 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
716203 ATGCAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:718749 original size:2 final size:2
Alignment explanation
Indices: 718742--718766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
718732 CTAACCACTT
718742 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
718767 TTTAATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:722860 original size:16 final size:16
Alignment explanation
Indices: 722822--722888 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
722812 CGTAGAAATT
* *
722822 TTAAATTTAACTAAAA
1 TTAAATTTAATTTAAA
* *
722838 TTTAATTTAATTTATA
1 TTAAATTTAATTTAAA
*
722854 TTAAATTTTATTTTAAAAA
1 TTAAA-TTTAATTT--AAA
722873 CTTAAATTTAATTTAA
1 -TTAAATTTAATTTAA
722889 TATAAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 16 0.41
17 9 0.23
19 9 0.23
20 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATTTAATTTAAA
Found at i:722947 original size:25 final size:25
Alignment explanation
Indices: 722869--722947 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 25
722859 TTTTATTTTA
* *
722869 AAAACTTAAATTTAATTTAA-T-AT
1 AAAACTAAAAATTAATTTAATTAAT
* * *
722892 AAAAATATAAATT-ATTTAAATTCACT
1 AAAACTAAAAATTAATTT-AATT-AAT
*
722918 -CAACTAAAAATTAATTTAATTAAT
1 AAAACTAAAAATTAATTTAATTAAT
722942 AAAACT
1 AAAACT
722948 TATATATATA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 4 0.10
23 11 0.28
24 3 0.08
25 17 0.43
26 5 0.12
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAACTAAAAATTAATTTAATTAAT
Found at i:722986 original size:10 final size:10
Alignment explanation
Indices: 722966--723008 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
722956 TATATATAAA
722966 TTAAA-TTAT
1 TTAAATTTAT
722975 TTAAATTTAT
1 TTAAATTTAT
722985 TT-AATTATAT
1 TTAAATT-TAT
722995 CTTAAATTTAT
1 -TTAAATTTAT
723006 TTA
1 TTA
723009 TTTAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 5 0.17
12 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:723041 original size:6 final size:6
Alignment explanation
Indices: 723020--723098 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
723010 TTAATAAAAA
* * * *
723020 TTAATT TTTATAT TTAATT TTAAAT TT-A-T TTATTT TTAAGTT TAAATT
1 TTAATT TTAAT-T TTAATT TTAATT TTAATT TTAATT TTAA-TT TTAATT
** * *
723068 TTAATT TTAATT AAAATT TTTATC TTAATT T
1 TTAATT TTAATT TTAATT TTAATT TTAATT T
723099 AAAAATAAAA
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
4 3 0.06
5 1 0.02
6 40 0.74
7 10 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (6 bp):
TTAATT
Found at i:723084 original size:18 final size:19
Alignment explanation
Indices: 723048--723102 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
723038 TTTAAATTTA
* *
723048 TTTATTTTTAAGTTTAAAT
1 TTTAATTTTAAGTTAAAAT
723067 TTTAATTTTAA-TTAAAAT
1 TTTAATTTTAAGTTAAAAT
* * *
723085 TTTTATCTTAATTTAAAA
1 TTTAATTTTAAGTTAAAA
723103 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATTTTAAGTTAAAAT
Found at i:723205 original size:22 final size:21
Alignment explanation
Indices: 723165--723222 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
723155 TTAAAATTTA
*
723165 TAAAATTAATTTATTTAATAATT
1 TAAAATTAATTTA-ATAATAA-T
*
723188 TAAATTTAATTTAATAATAAT
1 TAAAATTAATTTAATAATAAT
* *
723209 TAAACTAAATTTAA
1 TAAAATTAATTTAA
723223 AAATTCGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.42
22 6 0.19
23 12 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTAATTTAATAATAAT
Found at i:724384 original size:19 final size:19
Alignment explanation
Indices: 724357--724410 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
724347 CGATAATTTT
*
724357 TTTTTTAATTTTAAAATAA
1 TTTTATAATTTTAAAATAA
* *
724376 TTTTATAATTTGATTAATAA
1 TTTTATAATTTTA-AAATAA
724396 -TTTATAA-TTTAAAAT
1 TTTTATAATTTTAAAAT
724411 TTTTTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 18 0.62
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTATAATTTTAAAATAA
Found at i:724442 original size:16 final size:15
Alignment explanation
Indices: 724407--724435 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
724397 TTATAATTTA
724407 AAAT-TTTTTAAAAT
1 AAATATTTTTAAAAT
724421 AAATATTTTTAAAAT
1 AAATATTTTTAAAAT
724436 TATATATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATTTTTAAAAT
Found at i:726606 original size:38 final size:33
Alignment explanation
Indices: 726563--726631 Score: 84
Period size: 38 Copynumber: 1.9 Consensus size: 33
726553 AACACAACCA
726563 ACCTTTTAGGCTTCGCTTTATTTTTATTTTTTGGGTGT
1 ACCTTTTAGGCTT---TTT-TTTTT-TTTTTTGGGTGT
*
726601 ACCTTTTCGGCTTTTTTTTTTTTTTTTGGGT
1 ACCTTTTAGGCTTTTTTTTTTTTTTTTGGGT
726632 ATCTAGATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 10 0.33
34 5 0.17
35 3 0.10
38 12 0.40
ACGTcount: A:0.07, C:0.13, G:0.17, T:0.62
Consensus pattern (33 bp):
ACCTTTTAGGCTTTTTTTTTTTTTTTTGGGTGT
Found at i:727551 original size:34 final size:34
Alignment explanation
Indices: 727505--727689 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
727495 GTAAAAACCA
*
727505 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
727539 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
727573 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
727607 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
727641 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
727674 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
727690 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:732146 original size:34 final size:34
Alignment explanation
Indices: 732100--732284 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
732090 GTAAAAACCA
*
732100 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
732134 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
732168 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
732202 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
732236 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
732269 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
732285 CATTAATTAA
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:733704 original size:2 final size:2
Alignment explanation
Indices: 733697--733729 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
733687 TATGTTTGTT
733697 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
733730 TAGTGGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:736525 original size:28 final size:27
Alignment explanation
Indices: 736487--736539 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
736477 TTAAGATTTT
*
736487 AAAAATATATAA-ATATATGAATTAATA
1 AAAAATATATAATATAAAT-AATTAATA
736514 AAAAATTATATAATATAAATAATTAA
1 AAAAA-TATATAATATAAATAATTAA
736540 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAAATATATAATATAAATAATTAATA
Found at i:737805 original size:21 final size:21
Alignment explanation
Indices: 737764--737806 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
737754 CTTGCTGCAG
* *
737764 CCTTTGCTTGCTCTGCTTCTT
1 CCTTTGCTTGCGCAGCTTCTT
737785 CCTTTGCTTTGCGCAGC-TCTT
1 CCTTTGC-TTGCGCAGCTTCTT
737806 C
1 C
737807 ATGAGCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.02, C:0.35, G:0.16, T:0.47
Consensus pattern (21 bp):
CCTTTGCTTGCGCAGCTTCTT
Found at i:741049 original size:2 final size:2
Alignment explanation
Indices: 741042--741077 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
741032 AATTTCATTT
741042 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
741078 GAAAGGAGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:742085 original size:25 final size:25
Alignment explanation
Indices: 742044--742107 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
742034 TTTGAAAATA
* *
742044 TATATTT-TATTATATTTTTATTAT
1 TATATTTATATTATATTTATATAAT
*
742068 TTTATTTATATTATATTTATATAAT
1 TATATTTATATTATATTTATATAAT
742093 TATATTTAATATTAT
1 TATATTT-ATATTAT
742108 TAAATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 6 0.18
25 21 0.62
26 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATATTTATATTATATTTATATAAT
Found at i:742098 original size:14 final size:14
Alignment explanation
Indices: 742052--742114 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
742042 TATATATTTT
742052 ATTATATTT-T-T-
1 ATTATATTTATATA
*
742063 ATTAT-TTTATTTA
1 ATTATATTTATATA
742076 TATTATATTTATATA
1 -ATTATATTTATATA
*
742091 ATTATATTTAATATT
1 ATTATATTT-ATATA
*
742106 ATTAAATTT
1 ATTATATTT
742115 TTTAAATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 1 0.02
14 14 0.33
15 19 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:742109 original size:15 final size:14
Alignment explanation
Indices: 742050--742114 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
742040 AATATATATT
*
742050 TTATTATATTTTTA
1 TTATTATATTTATA
*
742064 TTATTTTA-TT-TA
1 TTATTATATTTATA
742076 -TATTATATTTATA
1 TTATTATATTTATA
*
742089 TAATTATATTTAATA
1 TTATTATATTT-ATA
*
742104 TTATTAAATTT
1 TTATTATATTT
742115 TTTAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
11 6 0.14
12 4 0.10
13 4 0.10
14 16 0.38
15 12 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATATTTATA
Found at i:742902 original size:1 final size:1
Alignment explanation
Indices: 742896--742920 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
742886 GCTATTACAG
742896 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
742921 GCTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:745854 original size:2 final size:2
Alignment explanation
Indices: 745849--745874 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
745839 ATATTAAATC
745849 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
745875 AATGAACTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:746093 original size:20 final size:20
Alignment explanation
Indices: 746068--746110 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
746058 TTATATAATA
746068 TTTATAAATATTTTTTATAT
1 TTTATAAATATTTTTTATAT
** *
746088 TTTATATTTATTTTTTGTAT
1 TTTATAAATATTTTTTATAT
746108 TTT
1 TTT
746111 GTTTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATAAATATTTTTTATAT
Found at i:746573 original size:18 final size:19
Alignment explanation
Indices: 746533--746575 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
746523 ATATTTTGAC
*
746533 ATATTTATGTATTTATATT
1 ATATTTATGTATTTATATA
* *
746552 ATATTTAT-TTTTTATGTA
1 ATATTTATGTATTTATATA
746570 ATATTT
1 ATATTT
746576 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATATTTATGTATTTATATA
Found at i:746573 original size:23 final size:22
Alignment explanation
Indices: 746547--746589 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
746537 TTATGTATTT
*
746547 ATATTATATTTATTTTTTATGTA
1 ATATTATAATT-TTTTTTATGTA
*
746570 ATATTTTAATTTTTTTTATG
1 ATATTATAATTTTTTTTATG
746590 CTTTATTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
ATATTATAATTTTTTTTATGTA
Found at i:746867 original size:11 final size:12
Alignment explanation
Indices: 746848--746911 Score: 64
Period size: 11 Copynumber: 5.7 Consensus size: 12
746838 ACGTTCTGTA
746848 TTTATATTATAT
1 TTTATATTATAT
*
746860 TTTA-ATTATTT
1 TTTATATTATAT
*
746871 TTTATATTGTA-
1 TTTATATTATAT
746882 TTTATATTATAT
1 TTTATATTATAT
* *
746894 CTTA-ATT-CAT
1 TTTATATTATAT
746904 TTTATATT
1 TTTATATT
746912 TTCATAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 5 0.12
11 26 0.62
12 11 0.26
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:746975 original size:17 final size:18
Alignment explanation
Indices: 746953--746990 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
746943 CTTTAAATTC
*
746953 AATTATATAAAAT-TTTA
1 AATTATAAAAAATATTTA
746970 AATTATAAAAAATATTTA
1 AATTATAAAAAATATTTA
746988 AAT
1 AAT
746991 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATAAAAAATATTTA
Found at i:747048 original size:16 final size:17
Alignment explanation
Indices: 746982--747056 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 17
746972 TTATAAAAAA
746982 TATTTAAATAAATAATTAT
1 TATTTAAATAAATAA-T-T
*
747001 TATTTAATATAATTCAATT
1 TATTTAA-ATAAAT-AATT
*
747020 TAAATTTATATAAAT-ATT
1 T--ATTTAAATAAATAATT
747038 TATTTAAATAAAT-ATT
1 TATTTAAATAAATAATT
747054 TAT
1 TAT
747057 AGATATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
16 17 0.35
18 4 0.08
19 9 0.19
20 11 0.23
21 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTAAATAAATAATT
Found at i:747212 original size:36 final size:36
Alignment explanation
Indices: 747165--747238 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
747155 TTTACTGATG
* * * *
747165 TATGCTTATTATTACGTATACTTATTACGTGTTTAC
1 TATGCGTATTATGACGTATACTTATTACGCGTCTAC
747201 TATGCGTATTATGACGTATACTTATTACGCGTCTAC
1 TATGCGTATTATGACGTATACTTATTACGCGTCTAC
747237 TA
1 TA
747239 AACGGATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (36 bp):
TATGCGTATTATGACGTATACTTATTACGCGTCTAC
Found at i:747670 original size:16 final size:16
Alignment explanation
Indices: 747605--747672 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
747595 ATATTAAATA
*
747605 TAAATATATTTATTTT
1 TAAATATATTTATATT
* *
747621 TAAAT-TTTTTATTATA
1 TAAATATATTTA-TATT
747637 TAAA-A-A-TTATATT
1 TAAATATATTTATATT
747650 T---TATATTTATATT
1 TAAATATATTTATATT
747663 TAAATATATT
1 TAAATATATT
747673 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 16
0.65 0.08 0.27
Matches are distributed among these distances:
11 1 0.03
12 1 0.03
13 12 0.31
14 3 0.08
15 5 0.13
16 17 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATATATTTATATT
Found at i:747672 original size:10 final size:11
Alignment explanation
Indices: 747657--747721 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 11
747647 ATTTTATATT
747657 TATATT-TAAA
1 TATATTATAAA
747667 TATATTATAAA
1 TATATTATAAA
*
747678 TAAATATTTTAAA
1 T--ATATTATAAA
*
747691 -AAATTA-AAA
1 TATATTATAAA
*
747700 TATATAATAAAA
1 TATATTAT-AAA
747712 TATATTATAA
1 TATATTATAA
747722 TTTCTTAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
9 3 0.07
10 14 0.33
11 7 0.16
12 10 0.23
13 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATATTATAAA
Found at i:747690 original size:13 final size:15
Alignment explanation
Indices: 747663--747721 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
747653 TATTTATATT
747663 TAAATATATTATAAA
1 TAAATATATTATAAA
747678 TAAATAT-TT-TAAA
1 TAAATATATTATAAA
* *
747691 -AAATTAAAATATATAA
1 TAAA-TATATTATA-AA
747707 TAAAATATATTATAA
1 T-AAATATATTATAA
747722 TTTCTTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 3 0.09
15 9 0.26
16 3 0.09
17 7 0.21
18 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATATATTATAAA
Found at i:747811 original size:24 final size:24
Alignment explanation
Indices: 747780--747825 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
747770 TTATTTTTTT
*
747780 AAAAAATTAT-AATTTTAAAATAA
1 AAAAAATTATAAATATTAAAATAA
747803 AAAATAATTATAAATATTAAAAT
1 AAAA-AATTATAAATATTAAAAT
747826 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAAATTATAAATATTAAAATAA
Found at i:749475 original size:6 final size:6
Alignment explanation
Indices: 749464--749524 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
749454 TTTTATTAAT
* *
749464 AATATA AATATA AATAT- AATATA AAT-TA TATATA TATATTA AATATGA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA AATAT-A
*
749512 AATATG AATATA A
1 AATATA AATATA A
749525 TATGTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
5 9 0.19
6 27 0.57
7 11 0.23
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (6 bp):
AATATA
Found at i:749515 original size:42 final size:42
Alignment explanation
Indices: 749464--749545 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 42
749454 TTTTATTAAT
*
749464 AATATAAATATAAATATAATA-TAAATTATATATATATATTA
1 AATATAAATATAAATATAATAGTAAATTAAATATATATATTA
* *
749505 AATATGAAATATGAATATAATATGTATATTAAATATATATA
1 AATAT-AAATATAAATATAATA-GTAAATTAAATATATATA
749546 GTGTTAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 5 0.14
42 15 0.43
44 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (42 bp):
AATATAAATATAAATATAATAGTAAATTAAATATATATATTA
Found at i:749521 original size:13 final size:12
Alignment explanation
Indices: 749464--749540 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 12
749454 TTTTATTAAT
*
749464 AATATAAATATA
1 AATATGAATATA
749476 AATAT-AATATA
1 AATATGAATATA
749487 AAT-T-ATATATA
1 AATATGA-ATATA
* *
749498 TATATTAAATATGA
1 AATA-TGAATAT-A
749512 AATATGAATAT-
1 AATATGAATATA
*
749523 AATATGTATATTA
1 AATATGAATA-TA
749536 AATAT
1 AATAT
749541 ATATAGTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.04
11 25 0.46
12 6 0.11
13 16 0.30
14 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (12 bp):
AATATGAATATA
Found at i:749528 original size:11 final size:11
Alignment explanation
Indices: 749464--749527 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
749454 TTTTATTAAT
749464 AATATAAATATA
1 AATAT-AATATA
749476 AATATAATATA
1 AATATAATATA
749487 AAT-T-ATATA
1 AATATAATATA
*
749496 TATAT-AT-TA
1 AATATAATATA
*
749505 AATATGAAATATG
1 AATAT--AATATA
749518 AATATAATAT
1 AATATAATAT
749528 GTATATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
9 13 0.30
10 4 0.09
11 14 0.32
12 7 0.16
13 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AATATAATATA
Found at i:750371 original size:13 final size:14
Alignment explanation
Indices: 750345--750379 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
750335 TTTTAAAATT
750345 TTTTAAAAATATAA
1 TTTTAAAAATATAA
750359 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
750372 TTATTAAA
1 TT-TTAAA
750380 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:752068 original size:24 final size:24
Alignment explanation
Indices: 752022--752118 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 24
752012 TAACCACCAA
* **
752022 TTTTGACAAACAACAAGTTACAAT
1 TTTTGACAAACAAAAAGGAACAAT
752046 TTTTGACAAACAAAAAGGAACAACCAT
1 TTTTGACAAACAAAAAGGAAC-A--AT
* * *
752073 TTTTGACAAATACAAAGTAACCACAAT
1 TTTTGACAAACAAAAAG-GA--ACAAT
752100 TTTTGACAAACACAAAAGG
1 TTTTGACAAACA-AAAAGG
752119 TGGTTTTTGT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
24 18 0.32
25 1 0.02
27 30 0.53
28 5 0.09
29 1 0.02
30 2 0.04
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (24 bp):
TTTTGACAAACAAAAAGGAACAAT
Found at i:752082 original size:27 final size:27
Alignment explanation
Indices: 752041--752118 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
752031 ACAACAAGTT
752041 ACAATTTTTGACAAACAAAAAGGAACA
1 ACAATTTTTGACAAACAAAAAGGAACA
* * * * *
752068 ACCATTTTTGACAAATACAAAGTAACC
1 ACAATTTTTGACAAACAAAAAGGAACA
752095 ACAATTTTTGACAAACACAAAAGG
1 ACAATTTTTGACAAACA-AAAAGG
752119 TGGTTTTTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 37 0.90
28 4 0.10
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (27 bp):
ACAATTTTTGACAAACAAAAAGGAACA
Done.