Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 52 of 52
Found at i:8465620 original size:18 final size:18
Alignment explanation
Indices: 8465599--8465649 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
8465589 GTTTATAATA
8465599 TTAATATTTATATAAATT
1 TTAATATTTATATAAATT
8465617 TTAATATATTA-AT-AA-T
1 TTAATAT-TTATATAAATT
8465633 TT-ATA-TTATATAAATT
1 TTAATATTTATATAAATT
8465649 T
1 T
8465650 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 5 0.17
16 5 0.17
17 2 0.07
18 9 0.31
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATATTTATATAAATT
Found at i:8466287 original size:42 final size:42
Alignment explanation
Indices: 8466223--8466302 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
8466213 GGAAGAAGAA
* * *
8466223 GACGACGACGAAGATGATGATGATGACGGTGAAGAGGACGAC
1 GACGACGACGAAGATGACGATGAAGACGGAGAAGAGGACGAC
* *
8466265 GACGACGAGGACGATGACGATGAAGACGGAGAAGAGGA
1 GACGACGACGAAGATGACGATGAAGACGGAGAAGAGGA
8466303 TGATGATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.38, C:0.14, G:0.40, T:0.09
Consensus pattern (42 bp):
GACGACGACGAAGATGACGATGAAGACGGAGAAGAGGACGAC
Found at i:8466408 original size:6 final size:6
Alignment explanation
Indices: 8466373--8466452 Score: 54
Period size: 6 Copynumber: 13.3 Consensus size: 6
8466363 CGATGAGGAT
* * * * * * *
8466373 GATGAC GAGGAC GAGGAT GATGAG GGTGAC GATGAC GACGGC GATGAC
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
* * *
8466421 GATGAT GACGAC GAT-AGC GACGAC GATGAC GA
1 GATGAC GATGAC GATGA-C GATGAC GATGAC GA
8466453 AGGTGAAGAG
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
5 1 0.02
6 53 0.96
7 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.40, T:0.12
Consensus pattern (6 bp):
GATGAC
Found at i:8467757 original size:2 final size:2
Alignment explanation
Indices: 8467750--8467774 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8467740 CATAGGGCAA
8467750 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
8467775 AGAAAGAATG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8468670 original size:18 final size:18
Alignment explanation
Indices: 8468636--8468673 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8468626 TAAGAACAGA
*
8468636 GGCTTTGGCATTGGCTTT
1 GGCTTTGGCATTAGCTTT
8468654 GGCTTTGGC-TTCAGCTTT
1 GGCTTTGGCATT-AGCTTT
8468672 GG
1 GG
8468674 AGACAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.05, C:0.18, G:0.34, T:0.42
Consensus pattern (18 bp):
GGCTTTGGCATTAGCTTT
Found at i:8494122 original size:24 final size:25
Alignment explanation
Indices: 8494068--8494132 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
8494058 CTAAGAATAT
*
8494068 ATTATACGTTTAATAAATAGAAAGCA
1 ATTATATGTTTAATAAATAGAAA-CA
8494094 A--ATATGTTTAATAAATAGAAA-A
1 ATTATATGTTTAATAAATAGAAACA
* *
8494116 ATTATATATTTATTAAA
1 ATTATATGTTTAATAAA
8494133 ATACATTAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
24 31 0.91
26 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTATATGTTTAATAAATAGAAACA
Found at i:8494251 original size:22 final size:22
Alignment explanation
Indices: 8494226--8494299 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 22
8494216 AAAAAAGAGG
8494226 AATTTTTTTAAAAAAAATGAAT
1 AATTTTTTTAAAAAAAATGAAT
* * ** *
8494248 AATTTACTTTAAGAAAGGTAAAT
1 AATTT-TTTTAAAAAAAATGAAT
* *
8494271 ACTTTTTTT-AAGAAAATGAAT
1 AATTTTTTTAAAAAAAATGAAT
8494292 AATTTTTT
1 AATTTTTT
8494300 ATGATATATT
Statistics
Matches: 38, Mismatches: 13, Indels: 3
0.70 0.24 0.06
Matches are distributed among these distances:
21 14 0.37
22 8 0.21
23 16 0.42
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (22 bp):
AATTTTTTTAAAAAAAATGAAT
Found at i:8495349 original size:2 final size:2
Alignment explanation
Indices: 8495342--8495379 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8495332 CAACGGGAAA
8495342 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
8495380 TCAAATTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8497043 original size:2 final size:2
Alignment explanation
Indices: 8497030--8497075 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
8497020 TACTGAATAC
*
8497030 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8497072 AT AT
1 AT AT
8497076 GATCATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8498924 original size:12 final size:12
Alignment explanation
Indices: 8498903--8498938 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
8498893 ATGGCTACTC
*
8498903 TATATATATATA
1 TATATGTATATA
8498915 TATATGTATATA
1 TATATGTATATA
*
8498927 TATACGTATATA
1 TATATGTATATA
8498939 GGGGGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (12 bp):
TATATGTATATA
Found at i:8499544 original size:2 final size:2
Alignment explanation
Indices: 8499537--8499562 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8499527 GGAAATATTA
8499537 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
8499563 TAATTGAAGT
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):
AT
Found at i:8500937 original size:20 final size:20
Alignment explanation
Indices: 8500902--8500947 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
8500892 TTAAAAATTC
* *
8500902 AAAAATTATTTAAATTGATT
1 AAAAATTATTTAAATTAATA
8500922 AAAAATTAATTT-AATTAATA
1 AAAAATT-ATTTAAATTAATA
8500942 AAAAAT
1 AAAAAT
8500948 AAATAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAATTATTTAAATTAATA
Found at i:8501923 original size:2 final size:2
Alignment explanation
Indices: 8501911--8501946 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
8501901 GTAACATTAT
8501911 TA TA T- 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 TA TA TA T
8501947 TCTTTTGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8502447 original size:21 final size:21
Alignment explanation
Indices: 8502423--8502462 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8502413 TTTTTTAATC
8502423 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
8502444 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
8502463 CCGTCTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:8504251 original size:7 final size:7
Alignment explanation
Indices: 8504239--8504266 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
8504229 ACCAAGAAAG
8504239 CAATAGC
1 CAATAGC
8504246 CAATAGC
1 CAATAGC
8504253 CAATAGC
1 CAATAGC
8504260 CAATAGC
1 CAATAGC
8504267 TATGTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
CAATAGC
Found at i:8505502 original size:9 final size:9
Alignment explanation
Indices: 8505490--8505514 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
8505480 AAAAAATTTA
8505490 AAAATTATT
1 AAAATTATT
8505499 AAAATTATT
1 AAAATTATT
8505508 AAAATTA
1 AAAATTA
8505515 AAATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAATTATT
Found at i:8509475 original size:20 final size:22
Alignment explanation
Indices: 8509436--8509484 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
8509426 CTTAATGCTT
8509436 TTTTTATAATTATATTAATATA
1 TTTTTATAATTATATTAATATA
*
8509458 TTTTTAT-A-TATTTTAATATA
1 TTTTTATAATTATATTAATATA
*
8509478 TATTTAT
1 TTTTTAT
8509485 TTTTGATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATAATTATATTAATATA
Found at i:8509477 original size:12 final size:10
Alignment explanation
Indices: 8509453--8509517 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
8509443 AATTATATTA
8509453 ATATATTTTT
1 ATATATTTTT
*
8509463 ATATATTTTA
1 ATATATTTTT
*
8509473 ATATA-TATT
1 ATATATTTTT
*
8509482 -TAT-TTTTG
1 ATATATTTTT
8509490 ATATATTTATGTT
1 ATATA-TT-T-TT
8509503 ATATATTTTT
1 ATATATTTTT
8509513 ATATA
1 ATATA
8509518 GTATTAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
8 5 0.12
9 5 0.12
10 21 0.49
11 3 0.07
12 3 0.07
13 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
ATATATTTTT
Found at i:8509508 original size:15 final size:14
Alignment explanation
Indices: 8509456--8509514 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 14
8509446 TATATTAATA
*
8509456 TATTTTTATATA-T
1 TATTTATATATATT
*
8509469 T-TTAATATATATT
1 TATTTATATATATT
*
8509482 TATTTTTGATATATT
1 TATTTAT-ATATATT
*
8509497 TATGTTATATATTTT
1 TAT-TTATATATATT
8509512 TAT
1 TAT
8509515 ATAGTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 3 0.08
15 19 0.53
16 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
TATTTATATATATT
Found at i:8522146 original size:2 final size:2
Alignment explanation
Indices: 8522139--8522166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8522129 ATCATTTAAC
8522139 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
8522167 GCAATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8524132 original size:4 final size:4
Alignment explanation
Indices: 8524123--8524157 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
8524113 TTTGGAGTTT
8524123 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
8524158 ATATTAGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:8524423 original size:26 final size:26
Alignment explanation
Indices: 8524352--8524431 Score: 70
Period size: 32 Copynumber: 2.8 Consensus size: 26
8524342 TTTGAAATTT
* * *
8524352 ATATTTATATTTATATAACTTTTAAT
1 ATATTTATATTTATATAAATTTAAAA
8524378 ATATTAATAATAAATATTATATAAATTTAAAA
1 ATATT--T-AT--AT-TTATATAAATTTAAAA
*
8524410 ATATTTATATTTATATTAATTT
1 ATATTTATATTTATATAAATTT
8524432 TTAATATCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
26 16 0.36
27 2 0.05
28 1 0.02
29 4 0.09
30 1 0.02
31 2 0.05
32 18 0.41
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATTTATATTTATATAAATTTAAAA
Found at i:8528375 original size:2 final size:2
Alignment explanation
Indices: 8528368--8528406 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8528358 AGGTAAACAT
8528368 GA GA GA 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 GA GA GA G
8528407 GAGTAAAGCC
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8530712 original size:2 final size:2
Alignment explanation
Indices: 8530707--8530765 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
8530697 CTTATTTAAT
*
8530707 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8530749 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
8530766 GAGCCGAATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8531737 original size:23 final size:22
Alignment explanation
Indices: 8531693--8531742 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
8531683 ATATGCAGTA
*
8531693 AATTTTGATATATGAATTTTTC
1 AATTTTGATATATGAATATTTC
*
8531715 ATATTTTAGATAT-TTAATATTTC
1 A-ATTTT-GATATATGAATATTTC
8531738 AATTT
1 AATTT
8531743 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 14 0.58
24 5 0.21
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
AATTTTGATATATGAATATTTC
Found at i:8531884 original size:23 final size:23
Alignment explanation
Indices: 8531840--8531884 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
8531830 TTAAATTTGA
*
8531840 TATTCAAATATATAGTTAATTTT
1 TATTCAAATATATAATTAATTTT
* * *
8531863 TATTTAAATTTATAATTCATTT
1 TATTCAAATATATAATTAATTT
8531885 AAAAAAGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTCAAATATATAATTAATTTT
Found at i:8533486 original size:2 final size:2
Alignment explanation
Indices: 8533479--8533510 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8533469 TATAAATAAC
8533479 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
8533511 TTCTACAAAT
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:8533625 original size:3 final size:3
Alignment explanation
Indices: 8533617--8533645 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8533607 CTTTACTGCT
8533617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8533646 GAAATGTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:8534843 original size:2 final size:2
Alignment explanation
Indices: 8534836--8534862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8534826 ATTTTCATTC
8534836 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
8534863 ACCTACATTA
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:8538497 original size:2 final size:2
Alignment explanation
Indices: 8538492--8538517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8538482 AGAGAGTTGC
8538492 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
8538518 TAGAAGAAAT
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):
AT
Found at i:8539950 original size:18 final size:17
Alignment explanation
Indices: 8539921--8539965 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
8539911 TGATAGCACG
*
8539921 ATAATAATAAAATATAAGT
1 ATAAT-ATAAAATA-AAAT
8539940 ATAATATAAAATAAAAT
1 ATAATATAAAATAAAAT
8539957 ATAAATATA
1 AT-AATATA
8539966 TATATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATATAAAATAAAAT
Found at i:8539952 original size:23 final size:25
Alignment explanation
Indices: 8539921--8539970 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
8539911 TGATAGCACG
*
8539921 ATAATAATAAAATATAAGTATA-AT
1 ATAATAATAAAATATAAATATATAT
8539945 ATAA-AATAAAATATAAATATATAT
1 ATAATAATAAAATATAAATATATAT
8539969 AT
1 AT
8539971 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAATAATAAAATATAAATATATAT
Found at i:8540021 original size:33 final size:32
Alignment explanation
Indices: 8539953--8540029 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
8539943 ATATAAAATA
*
8539953 AAATATAAATA-TATATATTTTAAATTTATAT
1 AAATATAAATATTATATATTTAAAATTTATAT
8539984 -AATATAAATTATTA-ATATATTAAAATTTATAT
1 AAATATAAA-TATTATATAT-TTAAAATTTATAT
8540016 AAATATAAAATATT
1 AAATAT-AAATATT
8540030 TTAATTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 8 0.20
31 6 0.15
32 14 0.35
33 9 0.22
34 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AAATATAAATATTATATATTTAAAATTTATAT
Found at i:8540024 original size:17 final size:17
Alignment explanation
Indices: 8539974--8540026 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
8539964 TATATATTTT
8539974 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
8539989 AAA-TTAT-TAATATATTA
1 AAATTTATATAA-ATA-TA
8540006 AAATTTATATAAATATA
1 AAATTTATATAAATATA
8540023 AAAT
1 AAAT
8540027 ATTTTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 1 0.03
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:8551857 original size:2 final size:2
Alignment explanation
Indices: 8551850--8551886 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8551840 ATAGAAGGTG
8551850 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8551887 TTTAGTAACT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:8559620 original size:3 final size:3
Alignment explanation
Indices: 8559612--8559646 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
8559602 TTGAAATTAT
* *
8559612 ATC ATC ATC ATC ATC ATC GTC ATC ATC GTC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
8559647 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:8562199 original size:2 final size:2
Alignment explanation
Indices: 8562192--8562232 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8562182 TTTTACCTGA
8562192 AT 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 AT A
8562233 CATTTTCCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8565592 original size:21 final size:22
Alignment explanation
Indices: 8565563--8565608 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
8565553 TGTTCAGACA
** *
8565563 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
8565585 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
8565606 AGT
1 AGT
8565609 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:8567542 original size:28 final size:27
Alignment explanation
Indices: 8567493--8567558 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
8567483 CATTTTTTTG
8567493 GTCAAAAATGGTGGTTATTTTGTG-TTT
1 GTCAAAAATGGTGGTTATTTTG-GATTT
8567520 GTCAAAAATGGTGGTT-TCCTTTGGATTT
1 GTCAAAAATGGTGGTTAT--TTTGGATTT
*
8567548 GTCAAATATGG
1 GTCAAAAATGG
8567559 AGGCTTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 1 0.03
27 17 0.49
28 17 0.49
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (27 bp):
GTCAAAAATGGTGGTTATTTTGGATTT
Found at i:8567907 original size:3 final size:3
Alignment explanation
Indices: 8567899--8567955 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
8567889 GTTTGGATGA
*
8567899 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8567947 AAT AGAT AA
1 AAT A-AT AA
8567956 GGTAAAGAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:8568191 original size:2 final size:2
Alignment explanation
Indices: 8568184--8568222 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8568174 TTCAACTAGC
8568184 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
8568223 ATTAAGATGT
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:8570663 original size:2 final size:2
Alignment explanation
Indices: 8570656--8570689 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8570646 TGGTTGATGA
8570656 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
8570690 GAGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 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:8572150 original size:2 final size:2
Alignment explanation
Indices: 8572145--8572176 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8572135 AAGTCGTAGA
*
8572145 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8572177 TATGAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8573140 original size:6 final size:6
Alignment explanation
Indices: 8573129--8573158 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
8573119 TAACCGGTCA
8573129 TCACTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT
8573159 CGTGAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
TCACTT
Found at i:8573655 original size:2 final size:2
Alignment explanation
Indices: 8573648--8573692 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
8573638 AATTTGGTTT
8573648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8573690 TA T
1 TA T
8573693 TCTATGAGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8590774 original size:17 final size:18
Alignment explanation
Indices: 8590754--8590793 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
8590744 GCCTACTTTT
*
8590754 AACAATAAAGAAGAAAA-
1 AACAACAAAGAAGAAAAG
*
8590771 AACAACAAAGAGGAAAAG
1 AACAACAAAGAAGAAAAG
8590789 AACAA
1 AACAA
8590794 AATTGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.72, C:0.10, G:0.15, T:0.03
Consensus pattern (18 bp):
AACAACAAAGAAGAAAAG
Found at i:8604751 original size:2 final size:2
Alignment explanation
Indices: 8604744--8604775 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8604734 TTACCTATGA
*
8604744 AT AT AT AT AT AA 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
8604776 TCATAGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8604828 original size:2 final size:2
Alignment explanation
Indices: 8604821--8604867 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
8604811 TTGAATTATG
8604821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8604863 TA TA T
1 TA TA T
8604868 GCTTATAGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8610324 original size:2 final size:2
Alignment explanation
Indices: 8610317--8610343 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8610307 CAGGAAATAG
8610317 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
8610344 TTGCTTCAAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:8617876 original size:2 final size:2
Alignment explanation
Indices: 8617869--8617894 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8617859 TTTCAAAGGT
8617869 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
8617895 ATGTAACCGT
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:8627548 original size:2 final size:2
Alignment explanation
Indices: 8627541--8627576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8627531 TCCTAGGAAA
8627541 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
8627577 GATACCTCTT
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:8629743 original size:7 final size:7
Alignment explanation
Indices: 8629731--8629757 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
8629721 ACAACAAACC
8629731 AAAGGCG
1 AAAGGCG
8629738 AAAGGCG
1 AAAGGCG
8629745 AAAGGCG
1 AAAGGCG
8629752 AAAGGC
1 AAAGGC
8629758 TTATTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.41, T:0.00
Consensus pattern (7 bp):
AAAGGCG
Found at i:8632115 original size:39 final size:39
Alignment explanation
Indices: 8632068--8632168 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
8632058 AATCATAAGT
** *
8632068 AAAGTAAACAACACCTAGATGCACCCAATTCACATAAAC
1 AAAGTAAACAACATATAGATGCACCCAATCCACATAAAC
8632107 AAAGTAAACAACATATAGATGCACCCAATCCACATAAAC
1 AAAGTAAACAACATATAGATGCACCCAATCCACATAAAC
8632146 AAAGTAAACAACATATAGATGCA
1 AAAGTAAACAACATATAGATGCA
8632169 ATGAAAACAC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.51, C:0.24, G:0.09, T:0.16
Consensus pattern (39 bp):
AAAGTAAACAACATATAGATGCACCCAATCCACATAAAC
Found at i:8642865 original size:1 final size:1
Alignment explanation
Indices: 8642859--8642934 Score: 80
Period size: 1 Copynumber: 76.0 Consensus size: 1
8642849 AAATCTTCAC
* * ** * * * *
8642859 TTTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTGGTTTTTTTCTTTTTTCTTTGTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8642924 TTTTTTTTTTT
1 TTTTTTTTTTT
8642935 CCAATTGCCA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:8642906 original size:36 final size:34
Alignment explanation
Indices: 8642860--8642935 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
8642850 AATCTTCACT
*
8642860 TTTTTTTTTTTGTTTTTT-TTTG--TT-TTTTTT
1 TTTTTTTTTTTCTTTTTTCTTTGTTTTGTTTTTT
**
8642890 TTGGTTTTTTTCTTTTTTCTTTGTTTTGTTTTTT
1 TTTTTTTTTTTCTTTTTTCTTTGTTTTGTTTTTT
8642924 TTTTTTTTTTTC
1 TTTTTTTTTTTC
8642936 CAATTGCCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 15 0.41
31 4 0.11
33 2 0.05
34 16 0.43
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (34 bp):
TTTTTTTTTTTCTTTTTTCTTTGTTTTGTTTTTT
Found at i:8654707 original size:40 final size:40
Alignment explanation
Indices: 8654661--8654769 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 40
8654651 TACTATTTGA
*
8654661 GTGGCTATGCCAATCCACAGAAATTTAAATATGCAGTTGG
1 GTGGCTATGCCAATCCACAGAAATTTAAATATGCAATTGG
* * *
8654701 GTGGCTATGCTAATCCAC-GAAAATCAAATATGCAATTGG
1 GTGGCTATGCCAATCCACAGAAATTTAAATATGCAATTGG
* *
8654740 GTGGC-AGTGCCAA-CCACATAAATGTAAATA
1 GTGGCTA-TGCCAATCCACAGAAATTTAAATA
8654770 GAAGAGAACG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 5 0.09
39 36 0.62
40 17 0.29
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (40 bp):
GTGGCTATGCCAATCCACAGAAATTTAAATATGCAATTGG
Found at i:8660947 original size:2 final size:2
Alignment explanation
Indices: 8660942--8660971 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8660932 ACACACACGC
8660942 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
8660972 CAATAAAATT
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:8661081 original size:2 final size:2
Alignment explanation
Indices: 8661074--8661099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8661064 TTAATATGAA
8661074 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
8661100 TTATTAAAGT
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):
AT
Found at i:8666237 original size:50 final size:50
Alignment explanation
Indices: 8666172--8666390 Score: 246
Period size: 50 Copynumber: 4.4 Consensus size: 50
8666162 GTTGATTATC
* * * * *
8666172 CTTCATCAACTTTTGACAATAAAGAGAGATGGTCATAATTATTGACTATC
1 CTTCACCAACCTTTGACAATAAAGAGAGATGGTCATAATTGTTGACGATT
* * *
8666222 CTTCACTAACCTTTGACAATAGAA-AGAGGTGGTCGTAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATA-AAGAGAGATGGTCATAATTGTTGACGATT
* ** *
8666272 CTTCACCAACCTTTGACAATAGAGAGAGGCGGTCGTAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAAAGAGAGATGGTCATAATTGTTGACGATT
* * * *
8666322 TTTCACCAACCTTTGATAATAGAGAGA-AGTGG-CTATTATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAAAGAGAGA-TGGTC-ATAATTGTTGACGATT
8666372 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
8666391 ATGTAGCCAT
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.01
50 142 0.97
51 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAAAGAGAGATGGTCATAATTGTTGACGATT
Found at i:8666333 original size:100 final size:99
Alignment explanation
Indices: 8666172--8666390 Score: 278
Period size: 100 Copynumber: 2.2 Consensus size: 99
8666162 GTTGATTATC
* * * * *
8666172 CTTCATCAACTTTTGACAATAAAGAGAGATGGTCATAATTATTGACTATCCTTCACTAACCTTTG
1 CTTCACCAACCTTTGACAATAAAGAGAGACGGTCATAATTATTGACGATCCTTCACCAACCTTTG
*
8666237 ACAATAGAAAGAGGTGGTCGTA-ATTGTTGACGATT
66 ACAATAGAAAGAAGTGG-C-TATATTGTTGACGATT
* * * * **
8666272 CTTCACCAACCTTTGACAATAGAGAGAGGCGGTCGTAATTGTTGACGATTTTTCACCAACCTTTG
1 CTTCACCAACCTTTGACAATAAAGAGAGACGGTCATAATTATTGACGATCCTTCACCAACCTTTG
* *
8666337 ATAATAGAGAGAAGTGGCTATTATTGTTGACGATT
66 ACAATAGAAAGAAGTGGCTA-TATTGTTGACGATT
8666372 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
8666391 ATGTAGCCAT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
98 2 0.02
99 1 0.01
100 100 0.97
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (99 bp):
CTTCACCAACCTTTGACAATAAAGAGAGACGGTCATAATTATTGACGATCCTTCACCAACCTTTG
ACAATAGAAAGAAGTGGCTATATTGTTGACGATT
Found at i:8670722 original size:50 final size:50
Alignment explanation
Indices: 8670643--8670874 Score: 302
Period size: 50 Copynumber: 4.6 Consensus size: 50
8670633 AGTTGTTGCC
* * * * *
8670643 ATTGTTGACTATCCTTCACTAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * * * *
8670693 ATTGTCGATGATTCTTTACCAACCTTTGACAATAGAGAGATGTGGTCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
8670743 GTTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTTGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
8670793 ATTGTTGACGATTCTTCACCAACTTTTGACAATAAAGAGAGGTTGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
8670843 ATTGTTGACGATTTTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
8670875 ATGTGGTCAC
Statistics
Matches: 160, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 160 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:8679860 original size:1 final size:1
Alignment explanation
Indices: 8679856--8679899 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
8679846 CTTAAAAATT
* * * *
8679856 AAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8679900 TGAAGGCAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:8680321 original size:12 final size:12
Alignment explanation
Indices: 8680301--8680344 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
8680291 GCAAACATTA
8680301 CATGAATATATT
1 CATGAATATATT
*
8680313 CATGTATATA-T
1 CATGAATATATT
*
8680324 AATCGAATATATT
1 CAT-GAATATATT
8680337 CATGAATA
1 CATGAATA
8680345 ATTAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (12 bp):
CATGAATATATT
Found at i:8680354 original size:22 final size:23
Alignment explanation
Indices: 8680329--8680377 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
8680319 TATATAATCG
* *
8680329 AATATATTCATGAATAATTAA-A
1 AATATATTCATAAATAATAAATA
*
8680351 AATATATTTATAAATAATAAATA
1 AATATATTCATAAATAATAAATA
8680374 AATA
1 AATA
8680378 AATAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AATATATTCATAAATAATAAATA
Found at i:8680395 original size:18 final size:18
Alignment explanation
Indices: 8680368--8680405 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
8680358 TTATAAATAA
8680368 TAAATAAATAAATAAATT
1 TAAATAAATAAATAAATT
* *
8680386 TAAATGAATAAATATATT
1 TAAATAAATAAATAAATT
8680404 TA
1 TA
8680406 TTAATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAATAAATAAATAAATT
Found at i:8680434 original size:15 final size:15
Alignment explanation
Indices: 8680414--8680479 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
8680404 TATTAATTTT
8680414 AAATATAAAATAATA
1 AAATATAAAATAATA
*
8680429 AAATATAAATATTATTA
1 AAATATAAA-A-TAATA
*
8680446 ATTATATTATAAATAAATA
1 A-AATA-TA-AAAT-AATA
8680465 AAATAT-AAATAATA
1 AAATATAAAATAATA
8680479 A
1 A
8680480 TATTAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 1 0.02
17 6 0.15
18 7 0.17
19 7 0.17
20 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATATAAAATAATA
Found at i:8680438 original size:40 final size:38
Alignment explanation
Indices: 8680371--8680513 Score: 118
Period size: 39 Copynumber: 3.7 Consensus size: 38
8680361 TAAATAATAA
*
8680371 ATAA-ATAAATAAATTTAAATGAATAAATATATTTATTAATT
1 ATAATATAAATAAA-TAAAAT--ATAAATATA-TTATTAATT
*
8680412 TTAAATATAAA-ATAATAAAATAT-AA-ATATTATTAATT
1 AT-AATATAAATA-AATAAAATATAAATATATTATTAATT
* *
8680449 ATATTATAAATAAATAAAATATAAATAATAATATTAATT
1 ATAATATAAATAAATAAAATATAAAT-ATATTATTAATT
*
8680488 AT-ATCATAATTAAATAATAA-ATAAAT
1 ATAAT-ATAAATAAATAA-AATATAAAT
8680514 TTAAAATAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
36 17 0.20
37 13 0.15
38 4 0.05
39 32 0.37
40 4 0.05
41 1 0.01
42 8 0.09
43 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (38 bp):
ATAATATAAATAAATAAAATATAAATATATTATTAATT
Found at i:8680474 original size:11 final size:12
Alignment explanation
Indices: 8680359--8680513 Score: 58
Period size: 11 Copynumber: 12.6 Consensus size: 12
8680349 AAAATATATT
8680359 TATAAATAATAA
1 TATAAATAATAA
8680371 -ATAAATAAATAAA
1 TATAAAT-AAT-AA
*
8680384 TTTAAATGAATAAA
1 TATAAAT-AAT-AA
** *
8680398 TATATTTATTAA
1 TATAAATAATAA
*
8680410 TTTTAAAT-ATAA
1 -TATAAATAATAA
*
8680422 AAT-AATAA-AA
1 TATAAATAATAA
8680432 TATAAATATTATTAA
1 TATAAATA--A-TAA
* *
8680447 T-TATATTATAA
1 TATAAATAATAA
8680458 -ATAAATAA-AA
1 TATAAATAATAA
8680468 TATAAATAATAA
1 TATAAATAATAA
8680480 TATTAATTATATCATAA
1 TA-TAA--ATA--ATAA
8680497 T-TAAATAATAA
1 TATAAATAATAA
8680508 -ATAAAT
1 TATAAAT
8680514 TTAAAATAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 39
0.66 0.10 0.24
Matches are distributed among these distances:
10 9 0.08
11 37 0.35
12 13 0.12
13 15 0.14
14 19 0.18
15 9 0.08
17 5 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (12 bp):
TATAAATAATAA
Found at i:8680479 original size:50 final size:50
Alignment explanation
Indices: 8680414--8680513 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
8680404 TATTAATTTT
* *
8680414 AAATATAAAATAATAAAATATAAATAT-TATTAATTATATTATAAATAAATA
1 AAATATAAAATAATAAAAT-TAAATATATA-TAATTAAATAATAAATAAATA
* *
8680465 AAATAT-AAATAATAATATTAATTATATCATAATTAAATAATAAATAAAT
1 AAATATAAAATAATAAAATTAAATATAT-ATAATTAAATAATAAATAAAT
8680514 TTAAAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
49 6 0.14
50 30 0.70
51 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (50 bp):
AAATATAAAATAATAAAATTAAATATATATAATTAAATAATAAATAAATA
Found at i:8682204 original size:12 final size:11
Alignment explanation
Indices: 8682182--8682215 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
8682172 TTTGCAGGTT
8682182 ATACTATACTA
1 ATACTATACTA
8682193 ATACTAATACTA
1 ATACT-ATACTA
*
8682205 ATACTTTACTA
1 ATACTATACTA
8682216 GTCTCTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (11 bp):
ATACTATACTA
Found at i:8690073 original size:2 final size:2
Alignment explanation
Indices: 8690003--8690055 Score: 54
Period size: 2 Copynumber: 26.0 Consensus size: 2
8689993 ATTATTTTGG
* * *
8690003 AT AT AT AT AT AT AT AT AT AT AT AT GT CAT AC A- ACT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT AT
8690046 AT AT AT AT AT
1 AT AT AT AT AT
8690056 TAATATAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:8695042 original size:54 final size:54
Alignment explanation
Indices: 8694961--8695069 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
8694951 TGTAGATTCT
8694961 TTCTGTGCTGTCTCTGCCTTCTGATTTTCAAGTTATTTGTTGCTCGGTCTTCCA
1 TTCTGTGCTGTCTCTGCCTTCTGATTTTCAAGTTATTTGTTGCTCGGTCTTCCA
* *
8695015 TTCTGTGCTGTCTTTGCCTTCTGATTTTCAAGTTATTTGTTGCTTGGTCTTCCA
1 TTCTGTGCTGTCTCTGCCTTCTGATTTTCAAGTTATTTGTTGCTCGGTCTTCCA
8695069 T
1 T
8695070 GGCCTTCCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.09, C:0.22, G:0.18, T:0.50
Consensus pattern (54 bp):
TTCTGTGCTGTCTCTGCCTTCTGATTTTCAAGTTATTTGTTGCTCGGTCTTCCA
Found at i:8698662 original size:2 final size:2
Alignment explanation
Indices: 8698655--8698683 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8698645 TATCAATAAC
8698655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8698684 GTAAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8699539 original size:3 final size:3
Alignment explanation
Indices: 8699533--8699570 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8699523 TCCTTTAAAT
8699533 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
8699571 TCATTTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:8705488 original size:2 final size:2
Alignment explanation
Indices: 8705481--8705512 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8705471 CTTGATGGTG
8705481 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
8705513 GAAAGTTCCC
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:8707151 original size:21 final size:20
Alignment explanation
Indices: 8707121--8707162 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
8707111 TTAATTAGTA
8707121 TTTTATTTAATATATTTTAT
1 TTTTATTTAATATATTTTAT
* *
8707141 TTTTAATTTAATTTTTTTTAT
1 TTTT-ATTTAATATATTTTAT
8707162 T
1 T
8707163 CTTGATCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTAATATATTTTAT
Found at i:8707290 original size:35 final size:37
Alignment explanation
Indices: 8707251--8707341 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 37
8707241 AATATCATGC
8707251 ATAAAATATATAAAATACTTAT-AAAAAA-ATCATAT
1 ATAAAATATATAAAATACTTATAAAAAAACATCATAT
8707286 ATAAAATATATAAAATACTTATAAAAAAAAACATCATAT
1 ATAAAATATATAAAATACTTAT--AAAAAAACATCATAT
8707325 ATAAAATAT-TGAAAATA
1 ATAAAATATAT-AAAATA
8707342 GGTGAGGGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
35 22 0.43
38 7 0.14
39 22 0.43
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.30
Consensus pattern (37 bp):
ATAAAATATATAAAATACTTATAAAAAAACATCATAT
Found at i:8714383 original size:2 final size:2
Alignment explanation
Indices: 8714376--8714410 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8714366 GCAAGATTCC
8714376 TA TA 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 TA TA T
8714411 TACGCAAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8714962 original size:3 final size:3
Alignment explanation
Indices: 8714954--8714979 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8714944 AGAGAAAGGT
8714954 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
8714980 GTCGCAACGT
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:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:8717299 original size:23 final size:24
Alignment explanation
Indices: 8717273--8717330 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 24
8717263 TGGACATGTT
8717273 AAAAATGCATGAAACATAAT-AAA
1 AAAAATGCATGAAACATAATAAAA
8717296 AAAAATGCATGAAACATAATAAAA
1 AAAAATGCATGAAACATAATAAAA
8717320 AAAAATGCATG
1 AAAAATGCATG
8717331 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (24 bp):
AAAAATGCATGAAACATAATAAAA
Found at i:8718293 original size:20 final size:20
Alignment explanation
Indices: 8718242--8718316 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
8718232 AAAAAGACAT
*
8718242 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
* *
8718261 GAATATATAGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
8718282 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
8718302 AATGTATCGATACAT
1 AATGTATCGATACAT
8718317 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:8718314 original size:40 final size:39
Alignment explanation
Indices: 8718239--8718316 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
8718229 GGTAAAAAGA
* *
8718239 CATAATGTATCGATACATTGTAGAATATATAGATACATT
1 CATAATGTATCGATACATTGAAAAATATATAGATACATT
* * *
8718278 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATAGATACAT
8718317 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATAGATACATT
Found at i:8718524 original size:3 final size:3
Alignment explanation
Indices: 8718516--8718559 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
8718506 AGTGTCTACA
*
8718516 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A
8718560 CCTCATGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8720904 original size:22 final size:21
Alignment explanation
Indices: 8720860--8720913 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
8720850 TTATAATAAT
*
8720860 TATTATAAAAT-ATATAATTA
1 TATTATAAAATAAAATAATTA
*
8720880 TATTATAAAATAAAAATTATTA
1 TATTATAAAAT-AAAATAATTA
*
8720902 TATAATAAAATA
1 TATTATAAAATA
8720914 TTATTTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
22 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTATAAAATAAAATAATTA
Found at i:8720918 original size:18 final size:18
Alignment explanation
Indices: 8720858--8720918 Score: 72
Period size: 17 Copynumber: 3.3 Consensus size: 18
8720848 AATTATAATA
8720858 ATTATTATAAAATATATAAT
1 ATTATTATAAAATA-A-AAT
8720878 -TATATTATAAAATAAAA-
1 AT-TATTATAAAATAAAAT
*
8720895 ATTATTATATAATAAAAT
1 ATTATTATAAAATAAAAT
8720913 ATTATT
1 ATTATT
8720919 TAGGTTGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
17 14 0.38
18 9 0.24
19 2 0.05
20 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATTATAAAATAAAAT
Found at i:8726737 original size:6 final size:6
Alignment explanation
Indices: 8726726--8726762 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
8726716 ACAATTCTCT
*
8726726 TCAACA TCAACA TCAACA TCAACG TCAACA TCAACA T
1 TCAACA TCAACA TCAACA TCAACA TCAACA TCAACA T
8726763 GGATCATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (6 bp):
TCAACA
Found at i:8741416 original size:31 final size:30
Alignment explanation
Indices: 8741375--8741436 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
8741365 TGATATATAT
8741375 TATATT-AAAA-ATTTAAAAATATGTTATAAA
1 TATATTAAAAATATTTAAAAA-AT-TTATAAA
8741405 TATATATAAAAATATTTAAAAAATTTATAAA
1 TATAT-TAAAAATATTTAAAAAATTTATAAA
8741436 T
1 T
8741437 CTAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 5 0.17
31 9 0.31
32 6 0.21
33 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATATTAAAAATATTTAAAAAATTTATAAA
Found at i:8741435 original size:21 final size:23
Alignment explanation
Indices: 8741380--8741435 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
8741370 TATATTATAT
8741380 TAAAAA-TT-TAAAAATATGTTA
1 TAAAAATTTATAAAAATATGTTA
* *
8741401 TAAATATATATAAAAATAT-TTA
1 TAAAAATTTATAAAAATATGTTA
8741423 -AAAAATTTATAAA
1 TAAAAATTTATAAA
8741436 TCTAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.55
22 4 0.14
23 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAAATTTATAAAAATATGTTA
Found at i:8751604 original size:494 final size:493
Alignment explanation
Indices: 8750676--8751648 Score: 1635
Period size: 494 Copynumber: 2.0 Consensus size: 493
8750666 ACAAATGATA
8750676 CCTTTTCAAAAGGGAAATTTCATGAAGTTTTTATAAAAAATATTTGCAAAATTTGAAAAAAAAAA
1 CCTTTTCAAAAGGGAAATTTCATGAAGTTTTTATAAAAAATATTTGCAAAATTTGAAAAAAAAAA
* * * *
8750741 TCATGTAATAGGCCTAAATAGCCCAACCAAAATATATTTTGTTGATTTTAGGGATTCTAAACAGT
66 TCATGTAATAGGCCTAAATAGCCCAACCAAAATACATTTTATTGATTCTAGGGATTCTAAACAGC
*
8750806 TTAGGTTTGAAACTTGTAACTCCCTTATCCAAAATGGTCGAGGGGCAAATAAGACTCCGTTAAAA
131 TTAGGTTTGAAACTTGTAACTCCCTCATCCAAAATGGTCGAGGGGCAAATAAGACTCCGTTAAAA
*
8750871 GATATTTTGACACATTTTTAACAAAAAATATTAAAAAATTCATGAATTTTTTTTGGGATGTTAAA
196 GATATTTTGACACATTTTTAACAAAAAATATTAAAAAATTCATGAATTTTTTTTGAGATGTTAAA
* * *
8750936 ATGATTTTTCAATATGCAACAGTAGCACTACCGGCAGAGAATAGTGCAAAGCGTTGGATATTTTG
261 ATGATTTTTCAATATGCAACAGTAGCACTACCAGCAGAGAATAGAGCAAAGCATTGGATATTTTG
* *
8751001 GTTTTCTTGGTGTTTACAGGTCCAAACTCGAGTTATGGACATTCGAACATTTGAGACTAATGGGA
326 GTTTTCTTGGTGTTTACAGGTCCAAACTCGAGTCATGGACATTCGAACATTTGAGACTAATGAGA
* * *
8751066 TAGAGTGGCATAAGTTTCATGAACTCATTTGCATAACTTCGGAGTTGTTTGGAATAATGAAATAT
391 TAGAGTGGCATAAGTTTCATGAACTCATTTGCATAACCTCGGAGTAGTTTGGAATAATGAAATAG
8751131 CCCGTTGATCATACCACTCAAGGTGGTATGATCATACC
456 CCCGTTGATCATACCACTCAAGGTGGTATGATCATACC
*
8751169 CCTTTTCAAAAGGGGAATTTCATGAAGTTTTTATAAAAAATATTTGCAAAATTTG-AAAAAAAAA
1 CCTTTTCAAAAGGGAAATTTCATGAAGTTTTTATAAAAAATATTTGCAAAATTTGAAAAAAAAAA
* *
8751233 TCATGTAGTAGGCCTAAATAGCCCAACCAAAATACATTTTATTGATTCTAGGGATTCTAGACAGC
66 TCATGTAATAGGCCTAAATAGCCCAACCAAAATACATTTTATTGATTCTAGGGATTCTAAACAGC
* *
8751298 TTAGGTTTGAAAACTTGTAACTCCCTCATCCGAAATGGTCGATGGGCAAATAAGACTCCGTTAAA
131 TTAGGTTTG-AAACTTGTAACTCCCTCATCCAAAATGGTCGAGGGGCAAATAAGACTCCGTT-AA
* * * * *
8751363 AAGATATTTTGACACATTTTTAACAAAAAATATTAGAAAATTCGTGAGTTTTTTTTTAGATTTTA
194 AAGATATTTTGACACATTTTTAACAAAAAATATTAAAAAATTCATGAATTTTTTTTGAGATGTTA
* * *
8751428 AAATGATTTTTCAATATGCAACAGT-GATACTGCCAGCAGGGAATAGAGCAAAGCATTGGATATT
259 AAATGATTTTTCAATATGCAACAGTAG-CACTACCAGCAGAGAATAGAGCAAAGCATTGGATATT
*
8751492 TTGGTTTTCTTGGTGTTTACAGGTCCAAACTTGAGTCATGGACATTCGAACATTTGAGACTAATG
323 TTGGTTTTCTTGGTGTTTACAGGTCCAAACTCGAGTCATGGACATTCGAACATTTGAGACTAATG
*
8751557 AGATAGAGTGGCATAAGTTTCATGAACTCATTTGCATAACCTCGGAGTAGTTTGGAATGATGAAA
388 AGATAGAGTGGCATAAGTTTCATGAACTCATTTGCATAACCTCGGAGTAGTTTGGAATAATGAAA
*
8751622 TAGCCCGTTGATCATATCACTCAAGGT
453 TAGCCCGTTGATCATACCACTCAAGGT
8751649 TTTAGCTTAA
Statistics
Matches: 447, Mismatches: 30, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
492 77 0.17
493 104 0.23
494 266 0.60
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (493 bp):
CCTTTTCAAAAGGGAAATTTCATGAAGTTTTTATAAAAAATATTTGCAAAATTTGAAAAAAAAAA
TCATGTAATAGGCCTAAATAGCCCAACCAAAATACATTTTATTGATTCTAGGGATTCTAAACAGC
TTAGGTTTGAAACTTGTAACTCCCTCATCCAAAATGGTCGAGGGGCAAATAAGACTCCGTTAAAA
GATATTTTGACACATTTTTAACAAAAAATATTAAAAAATTCATGAATTTTTTTTGAGATGTTAAA
ATGATTTTTCAATATGCAACAGTAGCACTACCAGCAGAGAATAGAGCAAAGCATTGGATATTTTG
GTTTTCTTGGTGTTTACAGGTCCAAACTCGAGTCATGGACATTCGAACATTTGAGACTAATGAGA
TAGAGTGGCATAAGTTTCATGAACTCATTTGCATAACCTCGGAGTAGTTTGGAATAATGAAATAG
CCCGTTGATCATACCACTCAAGGTGGTATGATCATACC
Found at i:8756859 original size:2 final size:2
Alignment explanation
Indices: 8756854--8756882 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8756844 GTCGTTCATT
8756854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8756883 TAATTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8760425 original size:36 final size:36
Alignment explanation
Indices: 8760352--8760425 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
8760342 TGGGGACAAA
* * *
8760352 GGTAGTGACTCAGCCTAGTTTTGAGACTCAGATTGT
1 GGTAGTGACTCAGCCTAGTTTCGAGACTCAAAATGT
* * *
8760388 GGTAGTGACTTAGCTTGGTTTCGAGACTCAAAATGT
1 GGTAGTGACTCAGCCTAGTTTCGAGACTCAAAATGT
8760424 GG
1 GG
8760426 CAATGACAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (36 bp):
GGTAGTGACTCAGCCTAGTTTCGAGACTCAAAATGT
Done.