Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:1702228 original size:2 final size:2
Alignment explanation
Indices: 1702221--1702251 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1702211 AATTTTGGTG
1702221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1702252 TACTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1702355 original size:15 final size:14
Alignment explanation
Indices: 1702310--1702346 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1702300 TGGTATTTAT
1702310 ATTTTTATAATTAA
1 ATTTTTATAATTAA
*
1702324 ATTTTTAAAAATTAA
1 ATTTTT-ATAATTAA
1702339 ATTTTTAT
1 ATTTTTAT
1702347 TATTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTATAATTAA
Found at i:1703247 original size:20 final size:22
Alignment explanation
Indices: 1703202--1703247 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1703192 TTTTTATATT
*
1703202 TAAATATATTTAATATAATTAT
1 TAAATATATTTAATATAATTAA
*
1703224 TAAATATCTTT-A-ATAATTAA
1 TAAATATATTTAATATAATTAA
1703244 TAAA
1 TAAA
1703248 AAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATATTTAATATAATTAA
Found at i:1704518 original size:2 final size:2
Alignment explanation
Indices: 1704513--1704542 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1704503 AAACTCACCA
1704513 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
1704543 GAAGAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1705573 original size:23 final size:26
Alignment explanation
Indices: 1705525--1705580 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1705515 TTAGAATTTC
*
1705525 TTATTTTTCTTAAGAATTTTTAAAAT
1 TTATTTATCTTAAGAATTTTTAAAAT
1705551 TTATTTAT-TTAA-AATTTTT-AAAT
1 TTATTTATCTTAAGAATTTTTAAAAT
*
1705574 TTTTTTA
1 TTATTTA
1705581 AAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.36
24 7 0.25
25 4 0.14
26 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTATTTATCTTAAGAATTTTTAAAAT
Found at i:1707326 original size:23 final size:23
Alignment explanation
Indices: 1707300--1707344 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1707290 TAAGTTCTCG
1707300 TCACATATTTATATATATATATA
1 TCACATATTTATATATATATATA
*
1707323 TCACATATTTATATGTATATAT
1 TCACATATTTATATATATATAT
1707345 TATATTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (23 bp):
TCACATATTTATATATATATATA
Found at i:1707446 original size:19 final size:18
Alignment explanation
Indices: 1707408--1707460 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1707398 TATATTTAGA
1707408 TATAAATATAAAATAAAATTT
1 TATAAATAT-AAA-AAAA-TT
*
1707429 TTTAAATATAAAAAAATT
1 TATAAATATAAAAAAATT
*
1707447 TATAAAAATAAAAA
1 TATAAATATAAAAA
1707461 TTTTCACATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 14 0.48
19 4 0.14
20 3 0.10
21 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAATATAAAAAAATT
Found at i:1713498 original size:17 final size:17
Alignment explanation
Indices: 1713476--1713508 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1713466 TTCAAATTAA
1713476 TATTTAATAA-TTAATTT
1 TATTTAA-AATTTAATTT
1713493 TATTTAAAATTTAATT
1 TATTTAAAATTTAATT
1713509 ATAAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAAAATTTAATTT
Found at i:1714081 original size:22 final size:19
Alignment explanation
Indices: 1714056--1714148 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 19
1714046 TAGATTTCAT
1714056 AATATTAAATATGATAAGTAAA
1 AATATT-AATAT-ATAA-TAAA
1714078 AATAATTAATATATAATAAA
1 AAT-ATTAATATATAATAAA
1714098 AATA--AATATATTAATATATCA
1 AATATTAATATA-TAATA-A--A
* *
1714119 AA-ATTTATATAAAAT-AA
1 AATATTAATATATAATAAA
*
1714136 ATTATTAATATAT
1 AATATTAATATAT
1714149 TAAAATTACT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
17 8 0.14
18 13 0.22
19 3 0.05
20 8 0.14
21 10 0.17
22 13 0.22
23 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATTAATATATAATAAA
Found at i:1714099 original size:20 final size:22
Alignment explanation
Indices: 1714063--1714102 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1714053 CATAATATTA
1714063 AATATGATAAGTAAAAATAATT
1 AATATGATAAGTAAAAATAATT
1714085 AATAT-ATAA-TAAAAATAA
1 AATATGATAAGTAAAAATAA
1714103 ATATATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AATATGATAAGTAAAAATAATT
Found at i:1714107 original size:17 final size:17
Alignment explanation
Indices: 1714061--1714113 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 17
1714051 TTCATAATAT
1714061 TAAATATGATAAGTAAAAA
1 TAAATAT-ATAA-TAAAAA
1714080 TAATTAATATATAATAAAAA
1 T-A--AATATATAATAAAAA
1714100 TAAATATATTAATA
1 TAAATATA-TAATA
1714114 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.20
18 5 0.17
19 2 0.07
20 8 0.27
21 4 0.13
22 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (17 bp):
TAAATATATAATAAAAA
Found at i:1714367 original size:20 final size:19
Alignment explanation
Indices: 1714337--1714376 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1714327 TATTTTTATT
1714337 TAAATTTAATA-AAAATATA
1 TAAATTTAATATAAAA-ATA
1714356 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
1714376 T
1 T
1714377 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:1715079 original size:15 final size:15
Alignment explanation
Indices: 1715040--1715087 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1715030 TCTTTTTTTT
1715040 TTTTA-CATTAAATA
1 TTTTACCATTAAATA
1715054 TTTTACCATTAATATA
1 TTTTACCATTAA-ATA
*
1715070 TTTT-CTATTAAAT-
1 TTTTACCATTAAATA
1715083 TTTTA
1 TTTTA
1715088 TCGTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 12 0.40
16 7 0.23
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTACCATTAAATA
Found at i:1715103 original size:16 final size:15
Alignment explanation
Indices: 1715046--1715104 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
1715036 TTTTTTTTAC
*
1715046 ATTAAATATTT-TACC
1 ATTAAATATTTAT-CT
1715061 ATTAATATATTT-TCT
1 ATTAA-ATATTTATCT
*
1715076 ATTAAATTTTTATCGT
1 ATTAAATATTTATC-T
*
1715092 ATTTAATATTTAT
1 ATTAAATATTTAT
1715105 TTAATATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 19 0.51
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTAAATATTTATCT
Found at i:1726198 original size:16 final size:18
Alignment explanation
Indices: 1726167--1726201 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1726157 ATTAAAGATA
1726167 ATTTTGTAGTTAAAAAAT
1 ATTTTGTAGTTAAAAAAT
1726185 ATTTTG-AG-TAAAAAAT
1 ATTTTGTAGTTAAAAAAT
1726201 A
1 A
1726202 AAAGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTTTGTAGTTAAAAAAT
Found at i:1726337 original size:31 final size:28
Alignment explanation
Indices: 1726268--1726337 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
1726258 TAAGTATATT
1726268 TTATA-TCAAACTTTAAGAAGGAAAAAA
1 TTATATTCAAACTTTAAGAAGGAAAAAA
*
1726295 ATATTATTCAAACTTTAA-AGAGGTAAATGAAA
1 TTA-TATTCAAACTTTAAGA-AGG-AAA--AAA
1726327 TTATATTCAAA
1 TTATATTCAAA
1726338 TTCAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 14 0.40
30 3 0.09
31 8 0.23
32 5 0.14
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (28 bp):
TTATATTCAAACTTTAAGAAGGAAAAAA
Found at i:1727783 original size:2 final size:2
Alignment explanation
Indices: 1727776--1727806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1727766 TCAAAGAAGG
1727776 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 A
1727807 GTTAATATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1728015 original size:12 final size:13
Alignment explanation
Indices: 1727996--1728031 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1727986 AATACGTGAA
1727996 ATATTTAATTATT
1 ATATTTAATTATT
1728009 A-ATTTAATTATT
1 ATATTTAATTATT
*
1728021 ATAATTAATTA
1 ATATTTAATTA
1728032 CATTGATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTAATTATT
Found at i:1729073 original size:2 final size:2
Alignment explanation
Indices: 1729066--1729091 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1729056 GGAATCAGAG
1729066 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
1729092 TCTATTCATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1729373 original size:15 final size:17
Alignment explanation
Indices: 1729343--1729376 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1729333 TATTTAACAT
1729343 TTTTTATCATATTTATA
1 TTTTTATCATATTTATA
1729360 TTTTTAT-A-ATTTATA
1 TTTTTATCATATTTATA
1729375 TT
1 TT
1729377 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATCATATTTATA
Found at i:1729534 original size:26 final size:31
Alignment explanation
Indices: 1729470--1729535 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1729460 ACATATTATG
1729470 TTTATATTATGATTTTAATATATTTAACAAT
1 TTTATATTATGATTTTAATATATTTAACAAT
* *
1729501 TTTTTATTAT-A-TTT-ATAT-TTTTACAA-
1 TTTATATTATGATTTTAATATATTTAACAAT
1729527 TTTATATTA
1 TTTATATTA
1729536 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 8 0.25
27 7 0.22
28 4 0.12
29 3 0.09
30 1 0.03
31 9 0.28
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTATATTATGATTTTAATATATTTAACAAT
Found at i:1729602 original size:159 final size:159
Alignment explanation
Indices: 1729262--1729720 Score: 685
Period size: 159 Copynumber: 2.9 Consensus size: 159
1729252 ATATATTATA
* * * *
1729262 TTTAAAGATGATTAAAATAATTAATTTAATGTATTTAATAAATATATTTTGTTTGTATTATGATT
1 TTTAAAGATGATTAAAATAATTAATTTAACGTATTTAATATATATATTATGTTTATATTATGATT
* * *
1729327 TTAATATATTTAAC-ATTTTTTATCATATTTATATTTTTATAATTTATATTAATAAAAAAATGT-
66 TTAATATATTTAACAATTTTTTATTATATTTATATTTTTACAATTTATATTAATAAAAAAATCTA
1729390 AAAAAATTAAAAAATAATTAATTCATATG
131 AAAAAATTAAAAAATAATTAATTCATATG
* * * *
1729419 TTTAAAGATAATTAAAATAATTAATTCAACATATTTAATATACATATTATGTTTATATTATGATT
1 TTTAAAGATGATTAAAATAATTAATTTAACGTATTTAATATATATATTATGTTTATATTATGATT
1729484 TTAATATATTTAACAATTTTTTATTATATTTATATTTTTACAATTTATATTAATAAAAAAATCTA
66 TTAATATATTTAACAATTTTTTATTATATTTATATTTTTACAATTTATATTAATAAAAAAATCTA
*
1729549 AAAAAATTTAAAAATAATTAATTCATACT-
131 AAAAAATTAAAAAATAATTAATTCATA-TG
* * * *
1729578 TTTAAAGATGATTAAAGTAATTAATTTAACGTATTTAATATATATATTATTTTTATATTATAATA
1 TTTAAAGATGATTAAAATAATTAATTTAACGTATTTAATATATATATTATGTTTATATTATGATT
* * * *
1729643 TTAATATATTTAATAATTTTTTATTATATTTATATTTCTACAATATATATTGATAAAAAAAT-T-
66 TTAATATATTTAACAATTTTTTATTATATTTATATTTTTACAATTTATATTAATAAAAAAATCTA
*
1729706 TAAAAATTAAAAAAT
131 AAAAAATTAAAAAAT
1729721 TAAAAAAATA
Statistics
Matches: 273, Mismatches: 26, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
157 84 0.31
158 47 0.17
159 141 0.52
160 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (159 bp):
TTTAAAGATGATTAAAATAATTAATTTAACGTATTTAATATATATATTATGTTTATATTATGATT
TTAATATATTTAACAATTTTTTATTATATTTATATTTTTACAATTTATATTAATAAAAAAATCTA
AAAAAATTAAAAAATAATTAATTCATATG
Found at i:1729647 original size:31 final size:31
Alignment explanation
Indices: 1729612--1729670 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1729602 TTTAACGTAT
*
1729612 TTAATATATAT-ATTATTTTTATATTATAATA
1 TTAATATATATAATAATTTTT-TATTATAATA
*
1729643 TTAATATATTTAATAATTTTTTATTATA
1 TTAATATATATAATAATTTTTTATTATA
1729671 TTTATATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTAATATATATAATAATTTTTTATTATAATA
Found at i:1729727 original size:8 final size:8
Alignment explanation
Indices: 1729698--1729727 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1729688 TATATTGATA
1729698 AAAAAATT
1 AAAAAATT
*
1729706 TAAAAATT
1 AAAAAATT
1729714 AAAAAATT
1 AAAAAATT
1729722 AAAAAA
1 AAAAAA
1729728 ATATACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:1730596 original size:5 final size:5
Alignment explanation
Indices: 1730586--1730613 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1730576 TCTGTTTACA
1730586 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1730614 TTGCATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1731577 original size:21 final size:23
Alignment explanation
Indices: 1731521--1731578 Score: 57
Period size: 26 Copynumber: 2.5 Consensus size: 23
1731511 ACAATTTAAA
* *
1731521 TTTTAAATTTTAATATAATAATTT
1 TTTTATATTTAAATATAATAA-TT
1731545 TTTTATAAATTTAAATA-AATAA-T
1 TTTTAT--ATTTAAATATAATAATT
1731568 TTTTATATTTA
1 TTTTATATTTA
1731579 TATTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.17
23 7 0.23
24 5 0.17
25 5 0.17
26 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATATTTAAATATAATAATT
Found at i:1731586 original size:26 final size:26
Alignment explanation
Indices: 1731524--1731575 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1731514 ATTTAAATTT
* *
1731524 TAAATTTTAATATAATAATTTTTTTA
1 TAAATTTAAATATAATAATTTTTATA
1731550 TAAATTTAAATA-AATAATTTTTATA
1 TAAATTTAAATATAATAATTTTTATA
1731575 T
1 T
1731576 TTATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAAATTTAAATATAATAATTTTTATA
Found at i:1731937 original size:16 final size:18
Alignment explanation
Indices: 1731897--1731954 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
1731887 TAATTAATTT
1731897 ATTTAAATATAAATTTGATATA
1 ATTTAAATA-AAA-TT-A-ATA
1731919 A-TTAAA-AAAATTAATA
1 ATTTAAATAAAATTAATA
1731935 ATTTAAATTAAAATTAATA
1 ATTTAAA-TAAAATTAATA
1731954 A
1 A
1731955 AATATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 2 0.06
19 14 0.42
20 1 0.03
21 5 0.15
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTTAAATAAAATTAATA
Found at i:1733462 original size:15 final size:15
Alignment explanation
Indices: 1733415--1733464 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
1733405 TACATATCTC
1733415 AAAATTTATATAATAT
1 AAAATTTATATAAT-T
*
1733431 AAATTATTA-ATATATT
1 AAAAT-TTATATA-ATT
1733447 AAAATTTATATAATT
1 AAAATTTATATAATT
1733462 AAA
1 AAA
1733465 TGTAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 9 0.31
16 15 0.52
17 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTTATATAATT
Found at i:1733750 original size:13 final size:14
Alignment explanation
Indices: 1733726--1733754 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1733716 TTTAATATTT
1733726 TAATATATTTTAAA
1 TAATATATTTTAAA
1733740 TAATA-ATTTTAAA
1 TAATATATTTTAAA
1733753 TA
1 TA
1733755 TCAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATATTTTAAA
Found at i:1734241 original size:31 final size:31
Alignment explanation
Indices: 1734206--1734266 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1734196 TTTAATTTAA
1734206 TTTTAATTATT-ATTA-AATAATAAAAATATTT
1 TTTTAATT-TTAATTATAA-AATAAAAATATTT
*
1734237 TTTTAATTTTAATTATAAAATATAAATATT
1 TTTTAATTTTAATTATAAAATAAAAATATT
1734267 AATATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 23 0.85
32 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTTAATTTTAATTATAAAATAAAAATATTT
Found at i:1734286 original size:12 final size:11
Alignment explanation
Indices: 1734255--1734293 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1734245 TTAATTATAA
*
1734255 AATATAAATATT
1 AATATAAA-AAT
1734267 AATATAAAAAT
1 AATATAAAAAT
1734278 AATATTAAAAAT
1 AATA-TAAAAAT
1734290 AATA
1 AATA
1734294 AAATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1734877 original size:17 final size:18
Alignment explanation
Indices: 1734857--1734901 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1734847 AAATGAGATC
1734857 ATAAAATAAAATAA-AAT
1 ATAAAATAAAATAATAAT
*
1734874 ATAAAAT-AATTAATAAT
1 ATAAAATAAAATAATAAT
*
1734891 TTAAAATAAAA
1 ATAAAATAAAA
1734902 AATTTTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.22
17 16 0.70
18 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAATAAAATAATAAT
Found at i:1735751 original size:20 final size:21
Alignment explanation
Indices: 1735728--1735775 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
1735718 TCATTATCAA
*
1735728 ATAAATTAAAAATTTTTA-AT
1 ATAAATTAAAAATTTATATAT
1735748 AT-AATT-AAAATTTATATAT
1 ATAAATTAAAAATTTATATAT
1735767 ATAAATTAA
1 ATAAATTAA
1735776 TTAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 6 0.25
21 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAATTAAAAATTTATATAT
Found at i:1735800 original size:19 final size:19
Alignment explanation
Indices: 1735778--1735819 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1735768 TAAATTAATT
1735778 AAATATTATC-AATAATAAC
1 AAATATT-TCAAATAATAAC
*
1735797 AAATATTTCAAATAATAAT
1 AAATATTTCAAATAATAAC
1735816 AAAT
1 AAAT
1735820 TAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATTTCAAATAATAAC
Found at i:1736002 original size:15 final size:13
Alignment explanation
Indices: 1735980--1736018 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1735970 AGATTATAAA
1735980 TAATTTAAATTGAT
1 TAATTTAAATT-AT
*
1735994 TCGATTTAAATTAT
1 T-AATTTAAATTAT
1736008 TAATTTAAATT
1 TAATTTAAATT
1736019 TTATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (13 bp):
TAATTTAAATTAT
Found at i:1737085 original size:66 final size:66
Alignment explanation
Indices: 1736979--1737127 Score: 244
Period size: 66 Copynumber: 2.3 Consensus size: 66
1736969 ATGATTTAGC
* * *
1736979 TTGCTAAACTTATTAGCTGCTTGATAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
1 TTGCTAAACTTTTTAGCTGCCTGAGAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
1737044 T
66 T
* *
1737045 TTGCTAATCTTTTTAGCTGCCTGAGAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAATAGAACAT
1 TTGCTAAACTTTTTAGCTGCCTGAGAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
1737110 T
66 T
*
1737111 TTGCTAAACTGTTTAGC
1 TTGCTAAACTTTTTAGC
1737128 AATTAGAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (66 bp):
TTGCTAAACTTTTTAGCTGCCTGAGAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
T
Found at i:1737140 original size:66 final size:66
Alignment explanation
Indices: 1736979--1737169 Score: 208
Period size: 66 Copynumber: 2.9 Consensus size: 66
1736969 ATGATTTAGC
* *
1736979 TTGCTAAACT-TATTAGCT-GCTTGATAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAAC
1 TTGCTAAACTGT-TTAGCTAAC-TGAAAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAAC
1737042 ATT
64 ATT
* * ** * *
1737045 TTGCTAATCTTTTTAGCTGCCTGAGAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAATAGAACAT
1 TTGCTAAACTGTTTAGCTAACTGAAAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
1737110 T
66 T
* ** * * *
1737111 TTGCTAAACTGTTTAGC-AATTAGAAAAATGGTTCTTTTGATCAAAACAAAAGCAGAACA
1 TTGCTAAACTGTTTAGCTAACT-GAAAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACA
1737170 CTGAACACTG
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 1 0.01
66 103 0.97
67 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (66 bp):
TTGCTAAACTGTTTAGCTAACTGAAAAATGGTTCTAGTGGTCCAAGCAAAAGCAGAACAGAACAT
T
Found at i:1737533 original size:124 final size:124
Alignment explanation
Indices: 1737313--1737555 Score: 414
Period size: 124 Copynumber: 2.0 Consensus size: 124
1737303 ATTCATAGAA
* * * *
1737313 TTGTAAAGCCATTGTTTTGAGAATTGCAATGGGCAACAGAGAAATTCGTGAATGATCCTTGTGTT
1 TTGTAAAGCCATTGTTTTGAGAATCGCAATGGACAACAGAGAAATTCATGAATGATCCTTGTGCT
* *
1737378 GTAATCTAGATCAGATGGATGTAGTTTCTTTTTAGGGTTTGTTTTAGTACTACTGACAT
66 GTAATCTAGATCAGATGAATGTAGTTTCTTTTTAGAGTTTGTTTTAGTACTACTGACAT
*
1737437 TTGTAAAGCCATTGTTTTGAGAATCGCAATGGACAACGGAGAAATTCATGAATGATCCTTGTGCT
1 TTGTAAAGCCATTGTTTTGAGAATCGCAATGGACAACAGAGAAATTCATGAATGATCCTTGTGCT
*
1737502 GTAATCTAGATCAGATGAATGTTGTTTCTTTTTAGAGTTTGTTTTAGTACTACT
66 GTAATCTAGATCAGATGAATGTAGTTTCTTTTTAGAGTTTGTTTTAGTACTACT
1737556 AACAATCCTT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (124 bp):
TTGTAAAGCCATTGTTTTGAGAATCGCAATGGACAACAGAGAAATTCATGAATGATCCTTGTGCT
GTAATCTAGATCAGATGAATGTAGTTTCTTTTTAGAGTTTGTTTTAGTACTACTGACAT
Found at i:1739813 original size:3 final size:3
Alignment explanation
Indices: 1739761--1739800 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1739751 TTCCTTCTGT
*
1739761 TCC TCT TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1739801 ACCGTTCCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:1740271 original size:12 final size:12
Alignment explanation
Indices: 1740256--1740280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1740246 CTACTGGATA
1740256 TATCCCGCAATC
1 TATCCCGCAATC
1740268 TATCCCGCAATC
1 TATCCCGCAATC
1740280 T
1 T
1740281 GGAGCAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.08, T:0.28
Consensus pattern (12 bp):
TATCCCGCAATC
Found at i:1740967 original size:22 final size:21
Alignment explanation
Indices: 1740927--1740972 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
1740917 GTCCGTGATG
1740927 ATTTTTTATTTAAAAATTTTA
1 ATTTTTTATTTAAAAATTTTA
*
1740948 ATTTTATTAATTTAAAATTTTTA
1 ATTTT-TT-ATTTAAAAATTTTA
1740971 AT
1 AT
1740973 AATTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 2 0.09
23 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTTATTTAAAAATTTTA
Found at i:1743422 original size:143 final size:143
Alignment explanation
Indices: 1743009--1743614 Score: 703
Period size: 143 Copynumber: 4.3 Consensus size: 143
1742999 CTTCTATGAG
** ** ** *
1743009 TTTAAGGAGCATGAAAAACCATGTCAATCTTTGAATAGCCTTTTTGTTAAAGGCATTTGGTTTAA
1 TTTAAGGAGCATG-AAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCATTTGGTTTAA
* ** * * * *
1743074 TCAATATGTAATTTGGTATTTGTGTTAGC-ATGAGTTTTAGGCGTTTGACTGACGT-GGTTTTG-
65 TCAGTATGTTCTTTGGTATTTATGTTA-CAACGAGTTTTAGGCATTTGAATGAC-TCGGTTTTGT
1743136 TCGAGCATAAGGTCTTC
128 TC-AGCATAAGGTCTTC
* * *
1743153 TTTAAGGAGCACGAAAACCACATCAATCTTCAAATAGAGTTTCTGTTAAA-G----T--TTAAAT
1 TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCATTTGGTTTAAT
* * * * ** *
1743211 CAGTATGTTCTTTGGTATTTATGTTAGAACGATTTTTAGGCTTTTGAGTGACTCAATTTTGTTGA
66 CAGTATGTTCTTTGGTATTTATGTTACAACGAGTTTTAGGCATTTGAATGACTCGGTTTTGTTCA
1743276 GCATAAGGTCTTC
131 GCATAAGGTCTTC
*
1743289 TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCCTTTGGTTTAAT
1 TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCATTTGGTTTAAT
*
1743354 CAGTATGTTCTTTGGTATTTATGTTACAACGAGTTTTAGGCATTTGAAAGACTCGGTTTTGTTCA
66 CAGTATGTTCTTTGGTATTTATGTTACAACGAGTTTTAGGCATTTGAATGACTCGGTTTTGTTCA
1743419 GCATAAGGTCTTC
131 GCATAAGGTCTTC
*** * ** * * *
1743432 TTTAAGGAATGTGAAAAACACATCAATCTTCTGACAGGGTTTCTGTTAAAGGCATTTTGTTTAAT
1 TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCATTTGGTTTAAT
* *** * *
1743497 CAGAAT-TTCTTTGGTATTTATGTTTGTACGAGTTTTAGGCATTTGAATGACTTGGTTTTGTTGA
66 CAGTATGTTCTTTGGTATTTATGTTACAACGAGTTTTAGGCATTTGAATGACTCGGTTTTGTTCA
*
1743561 GCATAAGATCTTC
131 GCATAAGGTCTTC
* *
1743574 TTTAAGTAGCATGAAAACCACATCAATCTTCCAATAGTGTT
1 TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTT
1743615 AAAAGTATAT
Statistics
Matches: 393, Mismatches: 59, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
135 1 0.00
136 114 0.29
137 2 0.01
138 1 0.00
141 1 0.00
142 97 0.25
143 165 0.42
144 12 0.03
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (143 bp):
TTTAAGGAGCATGAAAACCACATCAATCTTCAAATAGTGTTTCTGTTAAAGGCATTTGGTTTAAT
CAGTATGTTCTTTGGTATTTATGTTACAACGAGTTTTAGGCATTTGAATGACTCGGTTTTGTTCA
GCATAAGGTCTTC
Found at i:1743617 original size:279 final size:275
Alignment explanation
Indices: 1743052--1743617 Score: 685
Period size: 279 Copynumber: 2.0 Consensus size: 275
1743042 AATAGCCTTT
* * *
1743052 TTGTTAAAGGCATTTGGTTTAATCAATATGTAATTTGGTATTTGTGTTAGCATGAGTTTTAGGCG
1 TTGTTAAAGGCATTTGGTTTAATCAATATGTAATTTGGTATTTATGTTAGCACGAGTTTTAGGCA
** * *
1743117 TTTGACTGACGTGGTTTTGTCGAGCATAAGGTCTTCTTTAAGGAGCACGAAAACCACATCAATCT
66 TTTGAAAGACGTGGTTTTGTCGAGCATAAGGTCTTCTTTAAGGAACACGAAAAACACATCAATCT
* * *
1743182 TCAAATAGAGTTTCTGTTAAAGTTTAAATCAGTATGTTCTTTGGTATTTATGTTAGAACGATTTT
131 TCAAACAGAGTTTCTGTTAAAGTTTAAATCAGAATGTTCTTTGGTATTTATGTTAGAACGAGTTT
* * *
1743247 TAGGCTTTTGAGTGACTCAATTTTGTTGAGCATAAGGTCTTCTTTAAGGAGCATGAAAACCACAT
196 TAGGCATTTGAATGACTCAATTTTGTTGAGCATAAGATCTTCTTTAAGGAGCATGAAAACCACAT
1743312 CAATCTTCAAATAGTG
261 CAATCTTCAAATAG-G
* * **
1743328 TTTCTGTTAAAGGCCTTTGGTTTAATCAGTATGTTCTTTGGTATTTATGTTA-CAACGAGTTTTA
1 --T-TGTTAAAGGCATTTGGTTTAATCAATATGTAATTTGGTATTTATGTTAGC-ACGAGTTTTA
***
1743392 GGCATTTGAAAGAC-TCGGTTTTGTTC-AGCATAAGGTCTTCTTTAAGGAATGTGAAAAACACAT
62 GGCATTTGAAAGACGT-GGTTTTG-TCGAGCATAAGGTCTTCTTTAAGGAACACGAAAAACACAT
** * *
1743455 CAATCTTCTGACAGGGTTTCTGTTAAAGGCATTTTGTTTAATCAGAAT-TTCTTTGGTATTTATG
125 CAATCTTCAAACAGAGTTTCTGTTAAA-G-----T-TTAAATCAGAATGTTCTTTGGTATTTATG
* * *** *
1743519 TTTGTACGAGTTTTAGGCATTTGAATGACTTGGTTTTGTTGAGCATAAGATCTTCTTTAAGTAGC
183 TTAGAACGAGTTTTAGGCATTTGAATGACTCAATTTTGTTGAGCATAAGATCTTCTTTAAGGAGC
*
1743584 ATGAAAACCACATCAATCTTCCAATA-G
248 ATGAAAACCACATCAATCTTCAAATAGG
1743611 -TGTTAAA
1 TTGTTAAA
1743618 AGTATATTAA
Statistics
Matches: 246, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
278 3 0.01
279 132 0.54
280 3 0.01
283 1 0.00
285 97 0.39
286 10 0.04
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (275 bp):
TTGTTAAAGGCATTTGGTTTAATCAATATGTAATTTGGTATTTATGTTAGCACGAGTTTTAGGCA
TTTGAAAGACGTGGTTTTGTCGAGCATAAGGTCTTCTTTAAGGAACACGAAAAACACATCAATCT
TCAAACAGAGTTTCTGTTAAAGTTTAAATCAGAATGTTCTTTGGTATTTATGTTAGAACGAGTTT
TAGGCATTTGAATGACTCAATTTTGTTGAGCATAAGATCTTCTTTAAGGAGCATGAAAACCACAT
CAATCTTCAAATAGG
Found at i:1746365 original size:2 final size:2
Alignment explanation
Indices: 1746358--1746383 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1746348 GTTTATCAGT
1746358 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
1746384 AACCTCTGGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1746490 original size:12 final size:12
Alignment explanation
Indices: 1746473--1746498 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1746463 TTAACTAAAA
1746473 AAGTCTAGGCAT
1 AAGTCTAGGCAT
1746485 AAGTCTAGGCAT
1 AAGTCTAGGCAT
1746497 AA
1 AA
1746499 CTAAAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (12 bp):
AAGTCTAGGCAT
Found at i:1749587 original size:3 final size:3
Alignment explanation
Indices: 1749579--1749608 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1749569 GGTTTGAAGT
1749579 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1749609 AAGGGTAATT
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1750687 original size:21 final size:21
Alignment explanation
Indices: 1750650--1750689 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1750640 ACCTTCAAGC
*
1750650 TTAAATTAGATTTAAAATTTT
1 TTAAATTAGATTAAAAATTTT
1750671 TTAATATTA-ATTAAAAATT
1 TTAA-ATTAGATTAAAAATT
1750690 AAAAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTAAATTAGATTAAAAATTTT
Found at i:1750989 original size:3 final size:3
Alignment explanation
Indices: 1750981--1751007 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1750971 AGAACCCTCA
1750981 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1751008 ATTCTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1754739 original size:9 final size:9
Alignment explanation
Indices: 1754727--1754774 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1754717 TAAATATATC
1754727 ATATTAATT
1 ATATTAATT
1754736 ATATTAATT
1 ATATTAATT
1754745 ATATT-ATT
1 ATATTAATT
1754753 -T-TT-ATAT
1 ATATTAAT-T
*
1754760 ATATTAAAT
1 ATATTAATT
1754769 ATATTA
1 ATATTA
1754775 TGCTCATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 4 0.12
9 23 0.68
10 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTAATT
Found at i:1754783 original size:24 final size:24
Alignment explanation
Indices: 1754735--1754783 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1754725 TCATATTAAT
* ** *
1754735 TATATTAATTATATTATTTTTATA
1 TATATTAAATATATTATGCTCATA
1754759 TATATTAAATATATTATGCTCATA
1 TATATTAAATATATTATGCTCATA
1754783 T
1 T
1754784 TAAATCTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
TATATTAAATATATTATGCTCATA
Found at i:1765555 original size:23 final size:24
Alignment explanation
Indices: 1765524--1765571 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
1765514 CTTAAAAAAA
1765524 ATTTAAAATTAATTTATTTA-AATT
1 ATTTAAAATTAA-TTATTTATAATT
*
1765548 ATTT-AAATTTATTATTTATAATT
1 ATTTAAAATTAATTATTTATAATT
1765571 A
1 A
1765572 AAAATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 11 0.50
24 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTAAAATTAATTATTTATAATT
Found at i:1765586 original size:21 final size:21
Alignment explanation
Indices: 1765558--1765615 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1765548 ATTTAAATTT
1765558 ATTA-TTTATAATTAAAAATA
1 ATTATTTTATAATTAAAAATA
* * *
1765578 ATTATTTTAT-ATTAATATTT
1 ATTATTTTATAATTAAAAATA
1765598 ATATATTTTATAATTAAA
1 AT-TATTTTATAATTAAA
1765616 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.42
21 13 0.42
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATTTTATAATTAAAAATA
Found at i:1765618 original size:21 final size:21
Alignment explanation
Indices: 1765550--1765619 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
1765540 TTTAAATTAT
1765550 TTAAATTTAT-TA-TTTATAA
1 TTAAATTTATATATTTTATAA
**
1765569 TTAAAAATA-ATTATTTTAT-A
1 TTAAATTTATA-TATTTTATAA
1765589 TTAATATTTATATATTTTATAA
1 TTAA-ATTTATATATTTTATAA
1765611 TTAAATTTA
1 TTAAATTTA
1765620 AATAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 7 0.17
20 7 0.17
21 21 0.51
22 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTTATATATTTTATAA
Found at i:1765678 original size:13 final size:13
Alignment explanation
Indices: 1765660--1765684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1765650 ATTTTAATTG
1765660 ATAAAAAATATTA
1 ATAAAAAATATTA
1765673 ATAAAAAATATT
1 ATAAAAAATATT
1765685 TTTAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAAAAATATTA
Found at i:1768658 original size:22 final size:22
Alignment explanation
Indices: 1768633--1768696 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 22
1768623 AAAAATATTT
1768633 TTATTTAAATTTAATTATAAAA
1 TTATTTAAATTTAATTATAAAA
*
1768655 TTATATAAATATTAA-TATAAAA
1 TTATTTAAAT-TTAATTATAAAA
1768677 TAATATTTTAATATTTAATT
1 T--TA-TTTAA-ATTTAATT
1768697 TGAATCAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 17 0.50
23 4 0.12
24 2 0.06
25 8 0.24
26 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTTAAATTTAATTATAAAA
Found at i:1770545 original size:15 final size:16
Alignment explanation
Indices: 1770516--1770545 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1770506 TATTAAATCA
1770516 TAAAAATAATATAATT
1 TAAAAATAATATAATT
1770532 TAAAAATAAT-TAAT
1 TAAAAATAATATAAT
1770546 ATATTATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAATAATATAATT
Found at i:1771525 original size:25 final size:25
Alignment explanation
Indices: 1771496--1771550 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1771486 TTTGAGTATG
* *
1771496 ATAAAAAAAATAATATATATATTAT
1 ATAAAAAAAATAAAATATATATAAT
* * *
1771521 ATAAATATATTAAAATATATATAAT
1 ATAAAAAAAATAAAATATATATAAT
1771546 ATAAA
1 ATAAA
1771551 TTATTAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAAAAAAAATAAAATATATATAAT
Found at i:1771538 original size:16 final size:16
Alignment explanation
Indices: 1771519--1771568 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1771509 TATATATATT
1771519 ATATAAATATATTAAA
1 ATATAAATATATTAAA
*
1771535 ATATATATA-ATATAAA
1 ATATAAATATAT-TAAA
* *
1771551 TTATTAATATATTAAA
1 ATATAAATATATTAAA
1771567 AT
1 AT
1771569 TTATATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAATATATTAAA
Found at i:1771551 original size:25 final size:24
Alignment explanation
Indices: 1771510--1771562 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
1771500 AAAAAATAAT
*
1771510 ATATATATTATATAAATATATTAAA
1 ATATATATAATATAAAT-TATTAAA
*
1771535 ATATATATAATATAAATTATTAAT
1 ATATATATAATATAAATTATTAAA
1771559 ATAT
1 ATAT
1771563 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATATATAATATAAATTATTAAA
Found at i:1771560 original size:32 final size:36
Alignment explanation
Indices: 1771505--1771576 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 36
1771495 GATAAAAAAA
1771505 ATAATATATATATTATATAAATATATTAAAATATAT
1 ATAATATATATATTATATAAATATATTAAAATATAT
*
1771541 ATAATATA-A-ATTAT-T-AATATATTAAAATTTAT
1 ATAATATATATATTATATAAATATATTAAAATATAT
1771573 ATAA
1 ATAA
1771577 ATTTATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 20 0.57
33 1 0.03
34 5 0.14
35 1 0.03
36 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
ATAATATATATATTATATAAATATATTAAAATATAT
Found at i:1771585 original size:27 final size:29
Alignment explanation
Indices: 1771502--1771586 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 29
1771492 TATGATAAAA
*
1771502 AAAATA-ATATATATATTATATAAATATATT
1 AAAATATATATATAAATT-TAT-AATATATT
*
1771532 AAAATATATATAATATAAATTATTAATATATT
1 AAAATATATAT-ATA-AATTTA-TAATATATT
1771564 AAAAT-T-TATATAAATTTATAATA
1 AAAATATATATATAAATTTATAATA
1771587 ATTTTATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 3 0.06
30 9 0.19
31 5 0.10
32 18 0.38
33 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATATATATATAAATTTATAATATATT
Found at i:1771593 original size:21 final size:21
Alignment explanation
Indices: 1771568--1771607 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1771558 TATATTAAAA
1771568 TTTATATA-AATTTATAATAAT
1 TTTATATATAA-TTATAATAAT
1771589 TTTATATATAATTATAATA
1 TTTATATATAATTATAATA
1771608 CGTAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATATATAATTATAATAAT
Found at i:1771881 original size:18 final size:20
Alignment explanation
Indices: 1771844--1771882 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1771834 ATAAATTTTT
1771844 TAAAAATAATATATTAAATA
1 TAAAAATAATATATTAAATA
1771864 TAAAAATAAT-TA-TAAATA
1 TAAAAATAATATATTAAATA
1771882 T
1 T
1771883 CAGTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAATATATTAAATA
Found at i:1772111 original size:18 final size:17
Alignment explanation
Indices: 1772088--1772123 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1772078 GATACAACAT
1772088 AAAATAATATAATACTAA
1 AAAATAATATAATA-TAA
1772106 AAAATAATATAATATAA
1 AAAATAATATAATATAA
1772123 A
1 A
1772124 TATATGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAATATAATATAA
Found at i:1777535 original size:16 final size:15
Alignment explanation
Indices: 1777511--1777565 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1777501 CTATTTCGAT
*
1777511 TTTAGATTACTTTAAA
1 TTTAAATTA-TTTAAA
1777527 TTTAAATTATTTAAA
1 TTTAAATTATTTAAA
1777542 -TT--A-T-TTTAAA
1 TTTAAATTATTTAAA
1777552 TTTAAATTATTTAA
1 TTTAAATTATTTAA
1777566 GTTCGGACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
12 1 0.03
13 1 0.03
14 3 0.09
15 11 0.33
16 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTAAATTATTTAAA
Found at i:1777539 original size:25 final size:25
Alignment explanation
Indices: 1777511--1777565 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1777501 CTATTTCGAT
*
1777511 TTTAGATTACTTTAAATTTAAATTA
1 TTTAAATTACTTTAAATTTAAATTA
*
1777536 TTTAAATTATTTTAAATTTAAATTA
1 TTTAAATTACTTTAAATTTAAATTA
1777561 TTTAA
1 TTTAA
1777566 GTTCGGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTAAATTACTTTAAATTTAAATTA
Found at i:1777551 original size:10 final size:9
Alignment explanation
Indices: 1777526--1777565 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1777516 ATTACTTTAA
1777526 ATTTAAATT
1 ATTTAAATT
1777535 ATTTAAATT
1 ATTTAAATT
*
1777544 ATTTTAA--
1 ATTTAAATT
1777551 ATTTAAATT
1 ATTTAAATT
1777560 ATTTAA
1 ATTTAA
1777566 GTTCGGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 6 0.22
9 21 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTAAATT
Found at i:1777698 original size:15 final size:15
Alignment explanation
Indices: 1777669--1777711 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 15
1777659 TATTTGATAA
1777669 ATTTAAATT-AAATT
1 ATTTAAATTAAAATT
1777683 ATTTAAATTAAAATT
1 ATTTAAATTAAAATT
1777698 ATTTTAAAATTAAA
1 A-TTT-AAATTAAA
1777712 TCATTTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.35
15 6 0.23
16 3 0.12
17 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATTAAAATT
Found at i:1777712 original size:16 final size:15
Alignment explanation
Indices: 1777670--1777717 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1777660 ATTTGATAAA
1777670 TTTAAATTAAATTA-
1 TTTAAATTAAATTAT
1777684 TTTAAATTAAAATTAT
1 TTTAAATT-AAATTAT
*
1777700 TTTAAAATTAAATCAT
1 TTT-AAATTAAATTAT
1777716 TT
1 TT
1777718 GGAATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.27
15 6 0.20
16 11 0.37
17 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAATTAAATTAT
Found at i:1778721 original size:27 final size:26
Alignment explanation
Indices: 1778691--1778744 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1778681 ATAAATAATA
*
1778691 TTAAAATT-TTTTACATGTATCATTTTT
1 TTAAAATTATTTTAAATG-AT-ATTTTT
*
1778718 TTAATATTATTTTAAATGATATTTTT
1 TTAAAATTATTTTAAATGATATTTTT
1778744 T
1 T
1778745 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 9 0.38
28 8 0.33
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (26 bp):
TTAAAATTATTTTAAATGATATTTTT
Found at i:1778995 original size:22 final size:22
Alignment explanation
Indices: 1778970--1779014 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1778960 TTTGATTGAC
*
1778970 TTTATAATTTTTTAAGAAT-TAA
1 TTTAAAATTTTTTAA-AATATAA
1778992 TTTAAAATTTTTTAAAATATAA
1 TTTAAAATTTTTTAAAATATAA
1779014 T
1 T
1779015 AATTATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAAAATTTTTTAAAATATAA
Found at i:1779833 original size:2 final size:2
Alignment explanation
Indices: 1779826--1779851 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1779816 CAATTTCCCG
1779826 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
1779852 TGAGTTCACT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1784610 original size:26 final size:26
Alignment explanation
Indices: 1784574--1784626 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1784564 TAAAAAAAAA
*
1784574 TAAATTAAATTTAGTT-ATTATTAAAT
1 TAAATTAAATTTA-TTAAATATTAAAT
*
1784600 TAAATTTAATTTATTAAATATTAAAT
1 TAAATTAAATTTATTAAATATTAAAT
1784626 T
1 T
1784627 TTAATGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TAAATTAAATTTATTAAATATTAAAT
Found at i:1784622 original size:21 final size:20
Alignment explanation
Indices: 1784573--1784627 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
1784563 ATAAAAAAAA
1784573 ATAAATTAAATTTAGTTATT
1 ATAAATTAAATTTAGTTATT
*
1784593 ATTAAATTAAATTTAATTTATT
1 A-TAAATTAAATTT-AGTTATT
1784615 A-AATATTAAATTT
1 ATAA-ATTAAATTT
1784628 TAATGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 3 0.10
21 21 0.68
22 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAAATTAAATTTAGTTATT
Found at i:1784637 original size:21 final size:21
Alignment explanation
Indices: 1784592--1784667 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
1784582 ATTTAGTTAT
*
1784592 TATTAA-ATTAAA-TTTAATT
1 TATTAATATTAAATTTTAATG
1784611 TATTAAATATTAAATTTTAATG
1 TATT-AATATTAAATTTTAATG
* *
1784633 T-TTAAT-TTAAATAATTTATTT
1 TATTAATATTAAAT--TTTAATG
1784654 TAATTAATATTAAA
1 T-ATTAATATTAAA
1784668 AAATTTCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 10 0.22
20 5 0.11
21 14 0.30
22 7 0.15
23 5 0.11
24 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
TATTAATATTAAATTTTAATG
Found at i:1784691 original size:18 final size:18
Alignment explanation
Indices: 1784668--1784707 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1784658 TAATATTAAA
* *
1784668 AAATTTCAATTAAAATTT
1 AAATTTAAATTAAAATAT
1784686 AAATTTAAATTAAAATAT
1 AAATTTAAATTAAAATAT
1784704 AAAT
1 AAAT
1784708 AACCAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTAAATTAAAATAT
Found at i:1784887 original size:22 final size:22
Alignment explanation
Indices: 1784858--1784916 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1784848 AAGAAAATTG
1784858 ATTT-AATTATTATTAAATTAA
1 ATTTAAATTATTATTAAATTAA
*
1784879 ATTTAAATTATTAAATAAATTAA
1 ATTTAAATTATT-ATTAAATTAA
*
1784902 A-TTAAAATATT-TTAA
1 ATTTAAATTATTATTAA
1784917 TACTTAGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 4 0.12
22 16 0.48
23 10 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAAATTATTATTAAATTAA
Found at i:1784890 original size:19 final size:17
Alignment explanation
Indices: 1784866--1784905 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
1784856 TGATTTAATT
1784866 ATTATTAAATTAAATTTAA
1 ATTATTAAA-TAAA-TTAA
1784885 ATTATTAAATAAATTAA
1 ATTATTAAATAAATTAA
1784902 ATTA
1 ATTA
1784906 AAATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATTAAATAAATTAA
Found at i:1784918 original size:23 final size:23
Alignment explanation
Indices: 1784862--1784909 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1784852 AAATTGATTT
* *
1784862 AATTATT-ATTAAATTAAATTTA
1 AATTATTAAATAAATTAAATTAA
1784884 AATTATTAAATAAATTAAATTAA
1 AATTATTAAATAAATTAAATTAA
1784907 AAT
1 AAT
1784910 ATTTTAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTATTAAATAAATTAAATTAA
Found at i:1785001 original size:45 final size:47
Alignment explanation
Indices: 1784913--1785006 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 47
1784903 TTAAAATATT
* *
1784913 TTAATACTTAGACAATTTATATATTTGATCAATTTTTTTAATTTTTAA
1 TTAATACTTAGAAAATCTATATATTTGATCAATTTTTTTAA-TTTTAA
1784961 TTAATACTTA-AAAATCTAT-TAATTT-ATC-ATTTTTTTAATTTTAA
1 TTAATACTTAGAAAATCTATAT-ATTTGATCAATTTTTTTAATTTTAA
1785005 TT
1 TT
1785007 TTTTAATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 8 0.19
45 10 0.23
46 4 0.09
47 11 0.26
48 10 0.23
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (47 bp):
TTAATACTTAGAAAATCTATATATTTGATCAATTTTTTTAATTTTAA
Found at i:1789101 original size:19 final size:19
Alignment explanation
Indices: 1789062--1789120 Score: 109
Period size: 19 Copynumber: 3.1 Consensus size: 19
1789052 GACACAATAC
1789062 TTTAAGAAAAATGAAGAAAT
1 TTTAAGAAAAATGAAG-AAT
1789082 TTTAAGAAAAATGAAGAAT
1 TTTAAGAAAAATGAAGAAT
1789101 TTTAAGAAAAATGAAGAAT
1 TTTAAGAAAAATGAAGAAT
1789120 T
1 T
1789121 GAAGTAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (19 bp):
TTTAAGAAAAATGAAGAAT
Found at i:1790676 original size:31 final size:31
Alignment explanation
Indices: 1790641--1790700 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
1790631 GGTAACTTTT
1790641 ATCATCGATATCAACCGTTATTAACATGTCC
1 ATCATCGATATCAACCGTTATTAACATGTCC
1790672 ATCATCGATATCAACCGTTATTAACATGT
1 ATCATCGATATCAACCGTTATTAACATGT
1790701 GAGTGACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (31 bp):
ATCATCGATATCAACCGTTATTAACATGTCC
Found at i:1792439 original size:17 final size:17
Alignment explanation
Indices: 1792417--1792481 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
1792407 ATAATTCCAA
*
1792417 ATCATTTTTATTTCATT
1 ATCATTTTTATTTAATT
* *
1792434 ATCA-TTTAATTTTATT
1 ATCATTTTTATTTAATT
** *
1792450 AAAATTATTATTTAATT
1 ATCATTTTTATTTAATT
1792467 AAT-ATTTTTATTTAA
1 -ATCATTTTTATTTAA
1792482 ATTTAATTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
16 12 0.32
17 24 0.65
18 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATCATTTTTATTTAATT
Found at i:1793170 original size:24 final size:24
Alignment explanation
Indices: 1793143--1793194 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1793133 TCGCCATCTT
1793143 CTTCCCCTTCACCGGCTCCCAAGG
1 CTTCCCCTTCACCGGCTCCCAAGG
** *
1793167 CTTCTTCTTCACCTGCTCCCAAGG
1 CTTCCCCTTCACCGGCTCCCAAGG
1793191 CTTC
1 CTTC
1793195 TTCGCCTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.46, G:0.13, T:0.29
Consensus pattern (24 bp):
CTTCCCCTTCACCGGCTCCCAAGG
Found at i:1793195 original size:24 final size:24
Alignment explanation
Indices: 1793149--1793197 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1793139 TCTTCTTCCC
1793149 CTTCACCGGCTCCCAAGGCTTCTT
1 CTTCACCGGCTCCCAAGGCTTCTT
*
1793173 CTTCACCTGCTCCCAAGGCTTCTT
1 CTTCACCGGCTCCCAAGGCTTCTT
1793197 C
1 C
1793198 GCCTTCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.43, G:0.14, T:0.31
Consensus pattern (24 bp):
CTTCACCGGCTCCCAAGGCTTCTT
Found at i:1794683 original size:30 final size:31
Alignment explanation
Indices: 1794649--1794709 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1794639 AAAATATTAA
*
1794649 TATTAATATAAAAATATT-TTTTAAATTTTT
1 TATTAATATAAAAATATTAATTTAAATTTTT
* *
1794679 TATTAATTTATAAATATTAATTTAAATTTTT
1 TATTAATATAAAAATATTAATTTAAATTTTT
1794710 AAACGAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTAATATAAAAATATTAATTTAAATTTTT
Found at i:1802277 original size:19 final size:18
Alignment explanation
Indices: 1802240--1802288 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
1802230 ACATTACATG
*
1802240 TTATATAAATAATTAAAA
1 TTATATTAATAATTAAAA
* *
1802258 TTTATATTAATATTTTAAA
1 -TTATATTAATAATTAAAA
*
1802277 TTAAATTAATAA
1 TTATATTAATAA
1802289 AACTTTTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATATTAATAATTAAAA
Found at i:1803332 original size:17 final size:18
Alignment explanation
Indices: 1803310--1803344 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1803300 AAAAAGTTAA
1803310 AATTTT-ATATATTAAAT
1 AATTTTAATATATTAAAT
1803327 AATTTTAGATATATTAAA
1 AATTTTA-ATATATTAAA
1803345 AGGTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTTTAATATATTAAAT
Found at i:1803516 original size:26 final size:26
Alignment explanation
Indices: 1803473--1803542 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
1803463 AACTTACACA
* *
1803473 ATAACTTAAATTAAAAATAATATTTAAT
1 ATAATTTAAATT--AAATAATATATAAT
** *
1803501 ATAATTTAAATTAAATTTTATATATT
1 ATAATTTAAATTAAATAATATATAAT
*
1803527 ATATTTTAAATTAAAT
1 ATAATTTAAATTAAAT
1803543 TTTAGTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 25 0.69
28 11 0.31
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATTTAAATTAAATAATATATAAT
Found at i:1803520 original size:12 final size:12
Alignment explanation
Indices: 1803505--1803546 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
1803495 TTTAATATAA
1803505 TTTAAATTAAAT
1 TTTAAATTAAAT
*
1803517 TTTATATATTATAT
1 TTTA-A-ATTAAAT
1803531 TTTAAATTAAAT
1 TTTAAATTAAAT
1803543 TTTA
1 TTTA
1803547 GTTTTTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 14 0.54
13 2 0.08
14 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTAAATTAAAT
Found at i:1804293 original size:15 final size:15
Alignment explanation
Indices: 1804275--1804307 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1804265 GTTGTTGGAT
1804275 TTTTATTAT-TTATTA
1 TTTTATTATGTT-TTA
1804290 TTTTATTATGTTTTA
1 TTTTATTATGTTTTA
1804305 TTT
1 TTT
1804308 GTTGAATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATTATGTTTTA
Found at i:1808547 original size:5 final size:5
Alignment explanation
Indices: 1808537--1808567 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1808527 TTTTCATCCA
*
1808537 ATTCT ATTCT ACTCT ATTCT ATTCT ATTCT A
1 ATTCT ATTCT ATTCT ATTCT ATTCT ATTCT A
1808568 GGCATCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTCT
Found at i:1809406 original size:2 final size:2
Alignment explanation
Indices: 1809399--1809438 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1809389 ATGTCAGTGA
1809399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1809439 TCATCTCAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1816860 original size:16 final size:16
Alignment explanation
Indices: 1816839--1816869 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1816829 TTCAATATTA
1816839 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
1816855 AATAAATATTTAATA
1 AATAAATATTAAATA
1816870 AAAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:1816871 original size:20 final size:20
Alignment explanation
Indices: 1816848--1816890 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1816838 AAATAAATAT
*
1816848 TAAATATAATAAATATTTAA
1 TAAAAATAATAAATATTTAA
* **
1816868 TAAAAATATTTTATATTTAA
1 TAAAAATAATAAATATTTAA
1816888 TAA
1 TAA
1816891 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATAATAAATATTTAA
Found at i:1820087 original size:23 final size:22
Alignment explanation
Indices: 1820042--1820083 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1820032 ATTTTTTATT
1820042 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1820064 TAAATATTAATTA-AAAAATA
1 TAAAT-TTAATTATAAAAATA
1820084 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1820339 original size:23 final size:23
Alignment explanation
Indices: 1820313--1820368 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1820303 ATTCGTATTT
1820313 TTTTATATATTTAAAATATT-ATA
1 TTTTATATATTT-AAATATTAATA
1820336 TTTTATATA--TAAATATTAATA
1 TTTTATATATTTAAATATTAATA
1820357 TATTTATATATT
1 T-TTTATATATT
1820369 CGTATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.24
21 5 0.17
22 8 0.28
23 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATATATTTAAATATTAATA
Found at i:1820351 original size:20 final size:22
Alignment explanation
Indices: 1820326--1820367 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1820316 TATATATTTA
1820326 AAATATT-ATAT-TTTATATAT
1 AAATATTAATATATTTATATAT
1820346 AAATATTAATATATTTATATAT
1 AAATATTAATATATTTATATAT
1820368 TCGTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATTAATATATTTATATAT
Found at i:1820698 original size:2 final size:2
Alignment explanation
Indices: 1820691--1820730 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1820681 TGGGGGTATG
1820691 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
1820731 AAACTATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1821017 original size:27 final size:27
Alignment explanation
Indices: 1820964--1821018 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1820954 TATTTTGAAG
* *
1820964 TTTTTAAATTTAATTATAAAAATAAAA
1 TTTTAAAATTTAATAATAAAAATAAAA
*
1820991 TTTTAAAATTTTAATAATATAAA-AAAA
1 TTTTAAAA-TTTAATAATAAAAATAAAA
1821018 T
1 T
1821019 AATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTTAAAATTTAATAATAAAAATAAAA
Found at i:1822709 original size:108 final size:108
Alignment explanation
Indices: 1822569--1822791 Score: 419
Period size: 108 Copynumber: 2.1 Consensus size: 108
1822559 AGATTATGGG
*
1822569 GGGTGGTTGGTTGATCCACCAGATGTCGAGGACGCGTGAGTTTAGCCATGTCTTTCATCCTTCAC
1 GGGTGGTTGGTTGATCCACCAGATGTCAAGGACGCGTGAGTTTAGCCATGTCTTTCATCCTTCAC
1822634 TCTCCCTTAAATATGGTACCAATATCGGGGCATATCAACCGGA
66 TCTCCCTTAAATATGGTACCAATATCGGGGCATATCAACCGGA
*
1822677 GGGTGGTTGGTTGATCCACCAGATGTCAAGGACGTGTGAGTTTAGCCATGTCTTTCATCCTTCAC
1 GGGTGGTTGGTTGATCCACCAGATGTCAAGGACGCGTGAGTTTAGCCATGTCTTTCATCCTTCAC
*
1822742 TCTCCCTTAAATATGGTTCCAATATCGGGGCATATCAACCGGA
66 TCTCCCTTAAATATGGTACCAATATCGGGGCATATCAACCGGA
1822785 GGGTGGT
1 GGGTGGT
1822792 CGCTTGAAGA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 112 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (108 bp):
GGGTGGTTGGTTGATCCACCAGATGTCAAGGACGCGTGAGTTTAGCCATGTCTTTCATCCTTCAC
TCTCCCTTAAATATGGTACCAATATCGGGGCATATCAACCGGA
Found at i:1828331 original size:20 final size:20
Alignment explanation
Indices: 1828306--1828349 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1828296 CATACCGATC
1828306 TCAGATATCGACATGAAACA
1 TCAGATATCGACATGAAACA
*
1828326 TCAGATCTCGACATGAAACA
1 TCAGATATCGACATGAAACA
1828346 TCAG
1 TCAG
1828350 CGGCTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAGATATCGACATGAAACA
Found at i:1833470 original size:22 final size:21
Alignment explanation
Indices: 1833445--1833488 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1833435 TTGATTTTTT
1833445 TTAATAGAAGAATAGATTACTA
1 TTAATAGAA-AATAGATTACTA
* **
1833467 TTAATGGAATTTAGATTACTA
1 TTAATAGAAAATAGATTACTA
1833488 T
1 T
1833489 AAAAGTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (21 bp):
TTAATAGAAAATAGATTACTA
Found at i:1833813 original size:24 final size:23
Alignment explanation
Indices: 1833786--1833830 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1833776 AACAGAAGAA
1833786 AAGAAAAAAAGAGATAAAGAAAGT
1 AAGAAAAAAAGAG-TAAAGAAAGT
* *
1833810 AAGATAAAGAGAGTAAAGAAA
1 AAGAAAAAAAGAGTAAAGAAA
1833831 TATTCTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
AAGAAAAAAAGAGTAAAGAAAGT
Found at i:1834440 original size:15 final size:17
Alignment explanation
Indices: 1834420--1834454 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1834410 TATAACGAAC
1834420 ATAA-TTTT-AATATAT
1 ATAATTTTTAAATATAT
1834435 ATAATTTTTAAATATAT
1 ATAATTTTTAAATATAT
1834452 ATA
1 ATA
1834455 TATATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 4 0.22
17 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATTTTTAAATATAT
Found at i:1834860 original size:3 final size:3
Alignment explanation
Indices: 1834852--1834879 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1834842 CAATACACAG
1834852 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1834880 CAAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1840031 original size:2 final size:2
Alignment explanation
Indices: 1840026--1840057 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1840016 TCCATTGTCA
1840026 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1840058 TTATTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1840640 original size:17 final size:17
Alignment explanation
Indices: 1840618--1840650 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1840608 AATATTTTTC
1840618 ATTTTGTTAA-AAAAATT
1 ATTTTG-TAACAAAAATT
1840635 ATTTTGTAACAAAAAT
1 ATTTTGTAACAAAAAT
1840651 CTCATCTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTTTGTAACAAAAATT
Found at i:1840854 original size:16 final size:13
Alignment explanation
Indices: 1840848--1840877 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1840838 TTTAAATCTG
1840848 AATTAATTTAAAT
1 AATTAATTTAAAT
1840861 AATTAATTTAAAAT
1 AATTAATTT-AAAT
1840875 AAT
1 AAT
1840878 CAAACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTAATTTAAAT
Found at i:1840866 original size:13 final size:14
Alignment explanation
Indices: 1840848--1841043 Score: 78
Period size: 15 Copynumber: 13.2 Consensus size: 14
1840838 TTTAAATCTG
1840848 AATTAATTT-AAAT
1 AATTAATTTAAAAT
1840861 AATTAATTTAAAAT
1 AATTAATTTAAAAT
* ** *
1840875 AATCAAACTAAAAA
1 AATTAATTTAAAAT
*
1840889 AATATAATATTAAACTT
1 AAT-TAAT-TTAAA-AT
1840906 AATTAATTTAAAATT
1 AATTAATTTAAAA-T
* *
1840921 AACTGATTT--AAT
1 AATTAATTTAAAAT
*
1840933 -ATTAAATTT-AATT
1 AATT-AATTTAAAAT
1840946 AATTCGAATTTAAAAT
1 AATT--AATTTAAAAT
*
1840962 AATATAAAATTAAAATT
1 AAT-T-AATTTAAAA-T
* *
1840979 ACTTAAAATTAAAAT
1 AATT-AATTTAAAAT
* *
1840994 ATCTTAACTTAAAAT
1 A-ATTAATTTAAAAT
* *
1841009 AACTAAAATTAAAAT
1 AA-TTAATTTAAAAT
1841024 AATTTAAATTTAAAAAT
1 AA-TT-AATTT-AAAAT
1841041 AAT
1 AAT
1841044 ATAAAATATT
Statistics
Matches: 140, Mismatches: 27, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
11 2 0.01
12 5 0.04
13 13 0.09
14 20 0.14
15 45 0.32
16 41 0.29
17 14 0.10
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (14 bp):
AATTAATTTAAAAT
Found at i:1840921 original size:21 final size:21
Alignment explanation
Indices: 1840860--1840961 Score: 57
Period size: 21 Copynumber: 4.7 Consensus size: 21
1840850 TTAATTTAAA
1840860 TAATTAATTTAAAATAATCAAACT
1 TAATTAATTTAAAAT--T-AAACT
* ** * *
1840884 AAAAAAATATAATATTAAACT
1 TAATTAATTTAAAATTAAACT
1840905 TAATTAATTTAAAATT-AACT
1 TAATTAATTTAAAATTAAACT
* * *
1840925 GATTTAATATT-AAATTTAA-T
1 TAATTAAT-TTAAAATTAAACT
1840945 TAATTCGAATTTAAAAT
1 TAATT--AATTTAAAAT
1840962 AATATAAAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
20 19 0.32
21 22 0.37
22 8 0.14
24 10 0.17
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATTAATTTAAAATTAAACT
Found at i:1840922 original size:15 final size:15
Alignment explanation
Indices: 1840835--1840937 Score: 63
Period size: 15 Copynumber: 6.9 Consensus size: 15
1840825 GAATTTAAAA
1840835 TAATTT-AAATCTGAAT
1 TAATTTAAAAT-T-AAT
1840851 TAATTT-AAA-TAAT
1 TAATTTAAAATTAAT
1840864 TAATTTAAAA-TAAT
1 TAATTTAAAATTAAT
* ** *
1840878 CAAACTAAAA-AAAT
1 TAATTTAAAATTAAT
*
1840892 ATAATATTAAACTTAAT
1 -TAAT-TTAAAATTAAT
*
1840909 TAATTTAAAATTAAC
1 TAATTTAAAATTAAT
* *
1840924 TGATTTAATATTAA
1 TAATTTAAAATTAA
1840938 ATTTAATTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.13
14 18 0.26
15 23 0.33
16 17 0.24
17 3 0.04
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (15 bp):
TAATTTAAAATTAAT
Found at i:1840974 original size:16 final size:16
Alignment explanation
Indices: 1840955--1841060 Score: 92
Period size: 15 Copynumber: 6.6 Consensus size: 16
1840945 TAATTCGAAT
1840955 TTAAAATAATATAAAA
1 TTAAAATAATATAAAA
*
1840971 TTAAAATTACT-TAAAA
1 TTAAAA-TAATATAAAA
* * *
1840987 TTAAAAT-ATCTTAAC
1 TTAAAATAATATAAAA
*
1841002 TTAAAATAA-CTAAAA
1 TTAAAATAATATAAAA
* *
1841017 TTAAAATAATTTAAAT
1 TTAAAATAATATAAAA
1841033 TTAAAAATAATATAAAATA
1 TT-AAAATAATAT-AAA-A
1841052 TTAAAATAA
1 TTAAAATAA
1841061 CTAAATTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
14 1 0.01
15 24 0.33
16 24 0.33
17 12 0.16
18 10 0.14
19 2 0.03
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAATAATATAAAA
Found at i:1841007 original size:15 final size:15
Alignment explanation
Indices: 1840955--1841065 Score: 87
Period size: 16 Copynumber: 6.9 Consensus size: 15
1840945 TAATTCGAAT
*
1840955 TTAAAATAATATAAAA
1 TTAAAATAA-CTAAAA
*
1840971 TTAAAATTACTTAAAA
1 TTAAAATAAC-TAAAA
* * *
1840987 TTAAAATATCTTAAC
1 TTAAAATAACTAAAA
1841002 TTAAAATAACTAAAA
1 TTAAAATAACTAAAA
* *
1841017 TTAAAATAATTTAAAT
1 TTAAAATAA-CTAAAA
*
1841033 TTAAAAATAATATAAAATA
1 TT-AAAATAA-CT-AAA-A
1841052 TTAAAATAACTAAA
1 TTAAAATAACTAAA
1841066 TTCAATTTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
15 24 0.32
16 30 0.39
17 10 0.13
18 10 0.13
19 2 0.03
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATAACTAAAA
Found at i:1841057 original size:18 final size:17
Alignment explanation
Indices: 1841002--1841065 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
1840992 ATATCTTAAC
*
1841002 TTAAAATAACT-AAA-A
1 TTAAAATAATTAAAATA
*
1841017 TTAAAATAATTTAAAT-
1 TTAAAATAATTAAAATA
1841033 TTAAAAATAATATAAAATA
1 TT-AAAATAAT-TAAAATA
*
1841052 TTAAAATAACTAAA
1 TTAAAATAATTAAA
1841066 TTCAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.24
16 5 0.12
17 12 0.29
18 12 0.29
19 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAATTAAAATA
Found at i:1844485 original size:3 final size:3
Alignment explanation
Indices: 1844477--1844502 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1844467 AGAGAGAGAG
1844477 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
1844503 GAAGCTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1847683 original size:2 final size:2
Alignment explanation
Indices: 1847676--1847714 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1847666 AATTTATCTA
1847676 AT 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 AT A
1847715 AAATATGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1847957 original size:67 final size:66
Alignment explanation
Indices: 1847849--1847975 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 66
1847839 ATACAATAAT
* * * * *
1847849 ATTTAATAAATTTAAGATTTTAATTTTAATATTTATAATTTTTTTATTTTTAAATTATTATAGTA
1 ATTTAATAAAGTTAAAATTTGAATATCAATATTTATAA-TTTTTTATTTTTAAATTATTATAGTA
1847914 AC
65 AC
1847916 ATTTAATAAAGTTAAAATTTGAATATCAATATTTATAATTTTTTATTTTTAAATTATTAT
1 ATTTAATAAAGTTAAAATTTGAATATCAATATTTATAATTTTTTATTTTTAAATTATTAT
1847976 GATAGGAAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
66 22 0.40
67 33 0.60
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (66 bp):
ATTTAATAAAGTTAAAATTTGAATATCAATATTTATAATTTTTTATTTTTAAATTATTATAGTAA
C
Found at i:1864029 original size:29 final size:30
Alignment explanation
Indices: 1863997--1864071 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
1863987 TTATATAATT
* * *
1863997 GTGCAATTTTGTGCTTAA-TTGTTGAGAAA
1 GTGCAATTTTGTGATTAATTTGTGGAAAAA
*
1864026 GTGCAATTTTATGATTAATTTGTGGAAAAA
1 GTGCAATTTTGTGATTAATTTGTGGAAAAA
*
1864056 GT-CAATCTTGTGATTA
1 GTGCAATTTTGTGATTA
1864072 GTTGAGTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (30 bp):
GTGCAATTTTGTGATTAATTTGTGGAAAAA
Done.