Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 1 of 15
Found at i:5073 original size:16 final size:16
Alignment explanation
Indices: 5040--5086 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
5030 GTTTGGGCAG
* **
5040 GTTCGGGTTTGGATTC
1 GTTCGGGTTCGGGCTC
5056 GTTCGGGTTCGGGCTC
1 GTTCGGGTTCGGGCTC
*
5072 GTTCGAGTTCGGGCT
1 GTTCGGGTTCGGGCT
5087 TTTTTGGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.04, C:0.19, G:0.40, T:0.36
Consensus pattern (16 bp):
GTTCGGGTTCGGGCTC
Found at i:5162 original size:16 final size:16
Alignment explanation
Indices: 5057--5163 Score: 90
Period size: 16 Copynumber: 6.7 Consensus size: 16
5047 TTTGGATTCG
* **
5057 TTCGGGTTCGGGCTCG
1 TTCGGGTTCAGGCTTT
* *
5073 TTCGAGTTCGGGCTTT
1 TTCGGGTTCAGGCTTT
* *
5089 TTTGGGTTCAAGCTTT
1 TTCGGGTTCAGGCTTT
* *
5105 TTTGGGTTC-GGATTTT
1 TTCGGGTTCAGG-CTTT
*
5121 TTCGGGTTCAGGCCTT
1 TTCGGGTTCAGGCTTT
*
5137 TTCGGATTCAGGCTTT
1 TTCGGGTTCAGGCTTT
*
5153 TTCGAGTTCAG
1 TTCGGGTTCAG
5164 ATTCAACTTC
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
15 1 0.01
16 70 0.96
17 2 0.03
ACGTcount: A:0.08, C:0.18, G:0.31, T:0.43
Consensus pattern (16 bp):
TTCGGGTTCAGGCTTT
Found at i:5279 original size:8 final size:8
Alignment explanation
Indices: 5266--5292 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5256 CTTTAAAAAG
5266 TAAATTAT
1 TAAATTAT
5274 TAAATTAT
1 TAAATTAT
5282 TAAATTAT
1 TAAATTAT
5290 TAA
1 TAA
5293 TTTTTAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAATTAT
Found at i:5409 original size:18 final size:18
Alignment explanation
Indices: 5370--5409 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5360 ATATTTATAT
*
5370 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
5388 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
5406 ATAA
1 ATAA
5410 TCTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:5981 original size:13 final size:13
Alignment explanation
Indices: 5946--5981 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5936 GCAGAGATTG
5946 ATTTATTTTTGTA
1 ATTTATTTTTGTA
5959 ATTTGATTTTTGTA
1 ATTT-ATTTTTGTA
5973 ATTT-TTTTT
1 ATTTATTTTT
5982 AATTCTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 4 0.18
14 13 0.59
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
ATTTATTTTTGTA
Found at i:7541 original size:535 final size:537
Alignment explanation
Indices: 6486--7560 Score: 1393
Period size: 535 Copynumber: 2.0 Consensus size: 537
6476 AAGATTCAGT
* * * *
6486 AGTAGTTACTTCTATTAATAGGTATACATTTGTTTCATTTAAAATTAGAGGAAAAAAAAGTAAAT
1 AGTAGTTACTTCTATTAACAGGTATACATTTATTTCATTTAAAATGAAAGGAAAAAAAAGTAAAT
* * *
6551 TTCATTATTGCAAATCTAAAATTATATTGGTTCTTTTAAATAAAAGTGAAGTAAAATGACTGCAA
66 TTCATAATTACAAATCTAAAATTATATTGGTTC-----------AGTGAAGTAAAATGACTACAA
* * *
6616 AATATTGAATTAATAAAATTATATATTATTTTAAAAGTTGATTTATCTTTTATTAAAGTTATTCT
120 AACATTGAATTAATAAAATTATATATTATTTTAAAAGTTGATTTATCTTTTATCAAAGTTATGCT
* * *
6681 TATTAATTTTTTTTAATTTGTAATATTATTTTGAAGATTTGTTCACTTTGTAATATAATTATCTA
185 TATTAATTTGTTTTAATTGGTAATACTATTTTGAAGATTTGTTCACTTTGTAATATAATTATCTA
* * * *
6746 CCTTTTTTAAAAAATAATAATACACTAACAAAATCAATCTTTAATTTCATATTTGAAATAATAAT
250 CCTTTTTTAAAAAATAATAATACACTAACAAAATCAATCATAAATTTCATATTTGAAACAACAAT
* * * * *
6811 TAAAGTGATTTAAATCAAGCATATTTGATGTAATGGTTCTTTTTTTTTTTCAAATTCATGTCAAC
315 TAAAGTGATTTAAATCAAACATATCTAATGTAATGGTTCTTTTTTTTCTTCAAAGTCATGTCAAC
*
6876 TTGATTTTGAATTAATAACAGTTTAGTTTTTAATTTTTTATATTGACATAGATTTAAAGATTTTA
380 TTGATTTTGAATTAATAACAGTTTAGTTTTTAATTATTTATATTGACATAGATTTAAAGATTTTA
* *
6941 TATACCATGATTATTTAAACATTAAAGTAATACTAATTATTTTGCTGTTGCTATATATAATAATA
445 TATACCATGATTATTCAAACATTAAAGTAATACTAATTATTTTGCTATTGC-ATATATAATAATA
7006 AT-CTTAAAACTAAAAATGAAGTAATAGC
509 ATACTTAAAACTAAAAATGAAGTAATAGC
* * *
7034 AGTAGTTATTTCTATTAACAGGTATATATTTATTTCATTTAAAATGAAAGTAAAAAAAA-TAAAT
1 AGTAGTTACTTCTATTAACAGGTATACATTTATTTCATTTAAAATGAAAGGAAAAAAAAGTAAAT
* * * *
7098 TTCATAATTACAAATTTAAAATTATATTGGTTC-GTGAAGTAAAATGATTATAAAACATTTAATT
66 TTCATAATTACAAATCTAAAATTATATTGGTTCAGTGAAGTAAAATGACTACAAAACATTGAATT
* * *
7162 AATAACATTATATATTATTTTAGAAGTTGATTTATCTTTTATCAAATTTATGCTTATTAATTTGT
131 AATAAAATTATATATTATTTTAAAAGTTGATTTATCTTTTATCAAAGTTATGCTTATTAATTTGT
* * * *
7227 TTTAATTGGTAATACTATTTTGAA-AGTTTGTTCACTTTGTAGTATAGTTATTTA-TTTTTTTAA
196 TTTAATTGGTAATACTATTTTGAAGA-TTTGTTCACTTTGTAATATAATTATCTACCTTTTTT--
* * * * *
7290 AAAAAAATAATATTATACTAATAAAATTAATCATAAATCTT-ATGTTTGAAACAACAATTGAAA-
258 -AAAAAATAATAATACACTAACAAAATCAATCATAAAT-TTCATATTTGAAACAACAATT-AAAG
7353 TGATTTAAATCAAACATATCTAATGTAATGG-TCTATTTCTTTTCTT-AAAGTCATGTCAACTTG
320 TGATTTAAATCAAACATATCTAATGTAATGGTTCT-TTT-TTTTCTTCAAAGTCATGTCAACTTG
*
7416 ATTTTGAGTTAATAACAGTTTAAG-TTTTAATTATTTATCATTGACATAGATTTGAAA-ATTTTA
383 ATTTTGAATTAATAACAGTTT-AGTTTTTAATTATTTAT-ATTGACATAGATTT-AAAGATTTTA
* * *
7479 TATACCATTATTGTTCAAACATTAATA-TAATATTAATTATTTTGCTATTGCTATATATAATAAT
445 TATACCATGATTATTCAAACATTAA-AGTAATACTAATTATTTTGCTATTGC-ATATATAATAAT
*
7543 AA-GCTTAAAACTAAAAAT
508 AATACTTAAAACTAAAAAT
7561 AACGTAGTTT
Statistics
Matches: 466, Mismatches: 48, Indels: 36
0.85 0.09 0.07
Matches are distributed among these distances:
534 7 0.02
535 132 0.28
536 3 0.01
537 126 0.27
538 107 0.23
539 4 0.01
547 35 0.08
548 52 0.11
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (537 bp):
AGTAGTTACTTCTATTAACAGGTATACATTTATTTCATTTAAAATGAAAGGAAAAAAAAGTAAAT
TTCATAATTACAAATCTAAAATTATATTGGTTCAGTGAAGTAAAATGACTACAAAACATTGAATT
AATAAAATTATATATTATTTTAAAAGTTGATTTATCTTTTATCAAAGTTATGCTTATTAATTTGT
TTTAATTGGTAATACTATTTTGAAGATTTGTTCACTTTGTAATATAATTATCTACCTTTTTTAAA
AAATAATAATACACTAACAAAATCAATCATAAATTTCATATTTGAAACAACAATTAAAGTGATTT
AAATCAAACATATCTAATGTAATGGTTCTTTTTTTTCTTCAAAGTCATGTCAACTTGATTTTGAA
TTAATAACAGTTTAGTTTTTAATTATTTATATTGACATAGATTTAAAGATTTTATATACCATGAT
TATTCAAACATTAAAGTAATACTAATTATTTTGCTATTGCATATATAATAATAATACTTAAAACT
AAAAATGAAGTAATAGC
Found at i:9538 original size:2 final size:2
Alignment explanation
Indices: 9531--9566 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9521 AGCAAACCAA
9531 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
9567 TAATAAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12789 original size:25 final size:25
Alignment explanation
Indices: 12752--12807 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
12742 AAGTGGGTAG
* *
12752 TTTTTATAATTTTTAATTTT-GAAT
1 TTTTTAAAATTTTTAATTTTAAAAT
12776 TTTTTAAAATTTTTTAATTTTAAAAT
1 TTTTTAAAA-TTTTTAATTTTAAAAT
12802 TTTTTA
1 TTTTTA
12808 GTCAAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.29
25 11 0.39
26 9 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTAAAATTTTTAATTTTAAAAT
Found at i:12796 original size:16 final size:16
Alignment explanation
Indices: 12777--12807 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12767 ATTTTGAATT
12777 TTTTAAAATTTTTTAA
1 TTTTAAAATTTTTTAA
12793 TTTTAAAATTTTTTA
1 TTTTAAAATTTTTTA
12808 GTCAAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAAATTTTTTAA
Found at i:13121 original size:20 final size:20
Alignment explanation
Indices: 13072--13121 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
13062 ATATCAACTT
*
13072 AATAA-ATAAAATTAATTAA
1 AATAATATAAAAATAATTAA
* *
13091 AATATTTTAAAAAT-ATTAA
1 AATAATATAAAAATAATTAA
13110 CAATAATATAAA
1 -AATAATATAAA
13122 CTTAAAGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAATATAAAAATAATTAA
Found at i:13735 original size:12 final size:14
Alignment explanation
Indices: 13708--13739 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
13698 TGATGTACAA
13708 TTTAAATTTAATTT
1 TTTAAATTTAATTT
13722 TTTAAA-TT-ATTT
1 TTTAAATTTAATTT
13734 TTTAAA
1 TTTAAA
13740 ACAGATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 2 0.11
14 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAAATTTAATTT
Found at i:14506 original size:34 final size:34
Alignment explanation
Indices: 14460--14644 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
14450 GTAAAAACCA
*
14460 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
14494 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
14528 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
14562 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
14596 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
14629 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
14645 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:18737 original size:19 final size:19
Alignment explanation
Indices: 18710--18772 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
18700 TCACGTGTAC
* *
18710 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
18729 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
18748 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
18767 AGTACC
1 AGTACC
18773 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:19123 original size:34 final size:34
Alignment explanation
Indices: 19077--19259 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
19067 GTAAAAACCA
*
19077 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
19111 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
19145 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
19179 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
19213 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
19246 CCATTTAATCAACA
1 CCATTTAATCAACA
19260 CTTATTCCGA
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:19596 original size:3 final size:3
Alignment explanation
Indices: 19590--19618 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19580 TATTATTGGT
19590 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
19619 CAGTAGTCTC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:22813 original size:8 final size:8
Alignment explanation
Indices: 22800--22841 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
22790 AATTGAAGCC
22800 TTCTTTTT
1 TTCTTTTT
**
22808 TTCTTTCC
1 TTCTTTTT
22816 TT-TTTTT
1 TTCTTTTT
22823 TTC-TTTT
1 TTCTTTTT
22830 TTCTTTTT
1 TTCTTTTT
22838 TTCT
1 TTCT
22842 CTCTCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTCTTTTT
Found at i:22823 original size:15 final size:16
Alignment explanation
Indices: 22798--22841 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
22788 TCAATTGAAG
22798 CCTTCTTTTTTTCTTT
1 CCTTCTTTTTTTCTTT
22814 CCTT-TTTTTTTCTTT
1 CCTTCTTTTTTTCTTT
*
22829 -TTTCTTTTTTTCT
1 CCTTCTTTTTTTCT
22842 CTCTCTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 20 0.77
16 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
CCTTCTTTTTTTCTTT
Found at i:22825 original size:11 final size:11
Alignment explanation
Indices: 22804--22852 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
22794 GAAGCCTTCT
22804 TTTTTTCTTTCC
1 TTTTTTCTTT-C
22816 TTTTTT-TTTC
1 TTTTTTCTTTC
22826 TTTTTTCTTT-
1 TTTTTTCTTTC
* *
22836 TTTTCTCTCTC
1 TTTTTTCTTTC
22847 TTTTTT
1 TTTTTT
22853 AACAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 15 0.47
11 11 0.34
12 6 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:22835 original size:17 final size:15
Alignment explanation
Indices: 22798--22852 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
22788 TCAATTGAAG
22798 CCTTCTTTTTTTCTTT
1 CCTT-TTTTTTTCTTT
22814 CCTTTTTTTTTCTTT
1 CCTTTTTTTTTCTTT
* *
22829 -TTTCTTTTTTTCTCT
1 CCTT-TTTTTTTCTTT
22844 CTCTTTTTT
1 C-CTTTTTT
22853 AACAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.06
15 21 0.64
16 8 0.24
17 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
CCTTTTTTTTTCTTT
Found at i:24933 original size:24 final size:24
Alignment explanation
Indices: 24905--24950 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
24895 ATTTATATAT
24905 TTTATA-ATTTAATTTAAATAAAAA
1 TTTATATATTTAA-TTAAATAAAAA
*
24929 TTTATATATTTTATTAAATAAA
1 TTTATATATTTAATTAAATAAA
24951 TAATGATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATATTTAATTAAATAAAAA
Found at i:35948 original size:5 final size:5
Alignment explanation
Indices: 35911--35947 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
35901 TCTCTGTTTC
*
35911 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCCCT TC
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TC
35948 CAGTTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
TCTCT
Found at i:36270 original size:2 final size:2
Alignment explanation
Indices: 36263--36293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36253 CATGATATTG
36263 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
36294 ATTGCAATAG
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:38455 original size:21 final size:21
Alignment explanation
Indices: 38417--38456 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38407 CATTAGTTAG
* * *
38417 ATGAAAGAATGTATTTTTTGA
1 ATGAAAAAATATAATTTTTGA
38438 ATGAAAAAATATAATTTTT
1 ATGAAAAAATATAATTTTT
38457 AATAACCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGAAAAAATATAATTTTTGA
Found at i:38594 original size:18 final size:18
Alignment explanation
Indices: 38566--38608 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38556 TCAAAATTTT
*
38566 CATTTCACTTATTCCACC
1 CATTCCACTTATTCCACC
* *
38584 TATTCCACTTATTTCACC
1 CATTCCACTTATTCCACC
38602 CATTCCA
1 CATTCCA
38609 TTCCATTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (18 bp):
CATTCCACTTATTCCACC
Found at i:39015 original size:21 final size:21
Alignment explanation
Indices: 38991--39042 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
38981 AAATGTATCT
38991 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
39012 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
39033 TTGGATGAAA
1 TTGGATGAAA
39043 AAACGTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:42454 original size:21 final size:21
Alignment explanation
Indices: 42414--42455 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42404 GCATTAGTTG
* **
42414 GATGAAAAAATGTATTTTTTA
1 GATGAAAAAATGAAACTTTTA
42435 GATGAAAAAATGAAACTTTTA
1 GATGAAAAAATGAAACTTTTA
42456 ATAATTAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (21 bp):
GATGAAAAAATGAAACTTTTA
Found at i:44437 original size:2 final size:2
Alignment explanation
Indices: 44430--44466 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44420 AGAATGGATG
44430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44467 ATTCCAATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44901 original size:33 final size:33
Alignment explanation
Indices: 44790--44921 Score: 149
Period size: 34 Copynumber: 3.9 Consensus size: 33
44780 GTTATTGTTA
* * * *
44790 ATTTGATAATTTATTATTATTGACTAAATAAGAG
1 ATTTGATAATTTATCATTGTTGATTAAAT-GGAG
*
44824 ATTTGATAATTTGTCATTGTTGATTAAAT-GAG
1 ATTTGATAATTTATCATTGTTGATTAAATGGAG
* *
44856 TAATTTGGTAATTTATCATTGTTGATTAGATGGAG
1 --ATTTGATAATTTATCATTGTTGATTAAATGGAG
* *
44891 ATTTGATAATTTACCATTGTTAATTAAATGG
1 ATTTGATAATTTATCATTGTTGATTAAATGG
44922 GTGATTTGGT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
32 3 0.04
33 27 0.32
34 51 0.61
35 3 0.04
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (33 bp):
ATTTGATAATTTATCATTGTTGATTAAATGGAG
Found at i:44902 original size:67 final size:68
Alignment explanation
Indices: 44788--44932 Score: 184
Period size: 67 Copynumber: 2.1 Consensus size: 68
44778 TTGTTATTGT
* * ** *
44788 TAATTTGATAATTTATTATTATTGACTAAATAAGAGATTTGATAATTTGTCATTGTTGATTAAAT
1 TAATTTGGTAATTTATCATTATTGACTAAATAAGAGATTTGATAATTTACCATTGTTAATTAAAT
44853 GAG
66 GAG
* * * *
44856 TAATTTGGTAATTTATCATTGTTGATTAGAT-GGAGATTTGATAATTTACCATTGTTAATTAAAT
1 TAATTTGGTAATTTATCATTATTGACTAAATAAGAGATTTGATAATTTACCATTGTTAATTAAAT
*
44920 GGG
66 GAG
*
44923 TGATTTGGTA
1 TAATTTGGTA
44933 GTTTTTACCA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
67 40 0.61
68 26 0.39
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (68 bp):
TAATTTGGTAATTTATCATTATTGACTAAATAAGAGATTTGATAATTTACCATTGTTAATTAAAT
GAG
Found at i:45255 original size:19 final size:19
Alignment explanation
Indices: 45231--45267 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
45221 TTAGTTGTCG
45231 AGGCACTATTCACGTATAT
1 AGGCACTATTCACGTATAT
45250 AGGCACTATTCACGTATA
1 AGGCACTATTCACGTATA
45268 CGGTACTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (19 bp):
AGGCACTATTCACGTATAT
Found at i:49389 original size:22 final size:22
Alignment explanation
Indices: 49361--49407 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
49351 GATTAAATGG
*
49361 TGATTTGGTAGTTTGCCATTAT
1 TGATTTGGTAGCTTGCCATTAT
* *
49383 TGATTTGGTGGCTTGCCATTGT
1 TGATTTGGTAGCTTGCCATTAT
49405 TGA
1 TGA
49408 CAAAATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.11, G:0.28, T:0.47
Consensus pattern (22 bp):
TGATTTGGTAGCTTGCCATTAT
Found at i:53008 original size:20 final size:20
Alignment explanation
Indices: 52983--53035 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
52973 GTTGCTTGCA
52983 TGTATCGATACATTTAATAG
1 TGTATCGATACATTTAATAG
53003 TGTATCGATACATTTAATAG
1 TGTATCGATACATTTAATAG
53023 TGTATCGATACAT
1 TGTATCGATACAT
53036 CTGGGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTAATAG
Found at i:53090 original size:13 final size:13
Alignment explanation
Indices: 53072--53099 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
53062 ATACAAAGAT
53072 CAATGTATCGATA
1 CAATGTATCGATA
53085 CAATGTATCGATA
1 CAATGTATCGATA
53098 CA
1 CA
53100 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:53177 original size:33 final size:33
Alignment explanation
Indices: 53140--53206 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
53130 AGTAGCTTAA
53140 ATTGTATCAATACAAAAAAATATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
* * ***
53173 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
53206 A
1 A
53207 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCAATACAAAAAAATATGTATCGATAC
Found at i:53180 original size:13 final size:13
Alignment explanation
Indices: 53162--53186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53152 CAAAAAAATA
53162 TGTATCGATACAT
1 TGTATCGATACAT
53175 TGTATCGATACA
1 TGTATCGATACA
53187 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:56435 original size:62 final size:62
Alignment explanation
Indices: 56335--56461 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
56325 CTATTTGGAA
56335 ACTAAAATGGCTTTTATCTAATCTTTTATCTTCCTTTTTTTCTAGAAAATAATTTTACTAAG
1 ACTAAAATGGCTTTTATCTAATCTTTTATCTTCCTTTTTTTCTAGAAAATAATTTTACTAAG
*
56397 ACTAAAATGGCTTTTATCTAATCTTTTATCTTCGTTTTTTTCTAGAAAATAATTTTACTAAG
1 ACTAAAATGGCTTTTATCTAATCTTTTATCTTCCTTTTTTTCTAGAAAATAATTTTACTAAG
56459 ACT
1 ACT
56462 CCAAAATTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (62 bp):
ACTAAAATGGCTTTTATCTAATCTTTTATCTTCCTTTTTTTCTAGAAAATAATTTTACTAAG
Found at i:61743 original size:18 final size:18
Alignment explanation
Indices: 61702--61785 Score: 93
Period size: 18 Copynumber: 4.8 Consensus size: 18
61692 TATTGGGGTT
61702 GAAAATCTATGATTAC--A
1 GAAAATCTATGATT-CTTA
*
61719 G-AAATCTATGATTTTTA
1 GAAAATCTATGATTCTTA
*
61736 GAAAATCTGTGATTCTTA
1 GAAAATCTATGATTCTTA
* *
61754 GAAAATCTAAGATTCCTA
1 GAAAATCTATGATTCTTA
*
61772 AAAAATCTATGATT
1 GAAAATCTATGATT
61786 GCTAAAAGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 12 0.21
17 3 0.05
18 41 0.73
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (18 bp):
GAAAATCTATGATTCTTA
Found at i:65312 original size:2 final size:2
Alignment explanation
Indices: 65305--65331 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65295 CCAATACCCA
65305 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
65332 ACATATGAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:72287 original size:2 final size:2
Alignment explanation
Indices: 72282--72306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72272 TCTCTCTCAG
72282 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 A
72307 TACCCAGATT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:73062 original size:6 final size:6
Alignment explanation
Indices: 73051--73076 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
73041 TTAACCTTAG
73051 TTTAAT TTTAAT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TT
73077 ATTATGAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:76864 original size:16 final size:16
Alignment explanation
Indices: 76843--76873 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76833 TCCCCCAAAA
*
76843 TAAAATAAAAGCCTCT
1 TAAAATAAAAACCTCT
76859 TAAAATAAAAACCTC
1 TAAAATAAAAACCTC
76874 GGTCAGCTCA
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:0.55, C:0.19, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAATAAAAACCTCT
Found at i:81119 original size:13 final size:13
Alignment explanation
Indices: 81101--81160 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 13
81091 ATTTGTAAAA
81101 AAAAAAATATTTT
1 AAAAAAATATTTT
*
81114 AAAAAATATTTTTT
1 AAAAAA-ATATTTT
*
81128 AAAAAACT-TATTT
1 AAAAAAATAT-TTT
*
81141 -AAAAAA-ATTTA
1 AAAAAAATATTTT
81152 AAAAAAATA
1 AAAAAAATA
81161 ATTAATACCT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 2 0.05
12 13 0.34
13 11 0.29
14 12 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAAAATATTTT
Found at i:81119 original size:14 final size:14
Alignment explanation
Indices: 81100--81147 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
81090 TATTTGTAAA
81100 AAAAAAAATATTTT
1 AAAAAAAATATTTT
* *
81114 AAAAAATATTTTTT
1 AAAAAAAATATTTT
**
81128 AAAAAACTTA-TTT
1 AAAAAAAATATTTT
81141 AAAAAAA
1 AAAAAAA
81148 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAAAAATATTTT
Found at i:87005 original size:2 final size:2
Alignment explanation
Indices: 87000--87029 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
86990 ATATATATAT
87000 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
87030 GAGTGGGACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:88327 original size:2 final size:2
Alignment explanation
Indices: 88320--88355 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
88310 TCTGACTCTG
88320 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
88356 CAATGTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88616 original size:16 final size:15
Alignment explanation
Indices: 88591--88623 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
88581 AAAGAAAATG
88591 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
88606 AAAAGAAAAAAAAGAA
1 AAAA-AAAAAAAAGAA
88622 AA
1 AA
88624 GCAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:90657 original size:20 final size:21
Alignment explanation
Indices: 90610--90683 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
90600 TTTAACAATT
*
90610 TGTATCGATACAATAAG-GTAA
1 TGTATCGATAC-ATAAGTGAAA
*
90631 TGCATCGATACATAAGTG-AA
1 TGTATCGATACATAAGTGAAA
* **
90651 TATATCGATACATACTTGAAA
1 TGTATCGATACATAAGTGAAA
90672 TGTATCGATACA
1 TGTATCGATACA
90684 GGACCATGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 21 0.47
21 24 0.53
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAAGTGAAA
Found at i:94274 original size:3 final size:3
Alignment explanation
Indices: 94266--94314 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
94256 CTAAACTTTT
*
94266 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
94314 A
1 A
94315 AAGTAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:95476 original size:2 final size:2
Alignment explanation
Indices: 95469--95511 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
95459 CTTATTAATT
*
95469 AG AG AG AG AG AG AA 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 AG AG AG
95511 A
1 A
95512 AATCAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:97221 original size:12 final size:12
Alignment explanation
Indices: 97204--97229 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
97194 CTAGAAGTTG
97204 TACACATATCTA
1 TACACATATCTA
97216 TACACATATCTA
1 TACACATATCTA
97228 TA
1 TA
97230 ATCATGGCTG
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:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (12 bp):
TACACATATCTA
Found at i:97371 original size:2 final size:2
Alignment explanation
Indices: 97364--97390 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
97354 AAGAAAATTA
97364 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
97391 CATTCTTGTA
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:99694 original size:71 final size:71
Alignment explanation
Indices: 99578--99716 Score: 208
Period size: 71 Copynumber: 2.0 Consensus size: 71
99568 CTGCTGTAAG
** * *
99578 ATACATTGTAGACCTATAATGGGATCCAAGTTGCCTTTAACGAAAATTAATAAGTCGTCTGCAAA
1 ATACATTACAGACCTATAATGGAATCCAAGTTGCCTTTAACGAAAATTAATAAGTCATCTGCAAA
99643 ACACAA
66 ACACAA
* *
99649 ATACATTACAGACCTATAATGGAATCCAAGTTG-CTTATAGCGAAAATTAATAAGTCATTTGCAA
1 ATACATTACAGACCTATAATGGAATCCAAGTTGCCTT-TAACGAAAATTAATAAGTCATCTGCAA
99713 AACA
65 AACA
99717 TGAATGTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 3 0.05
71 58 0.95
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (71 bp):
ATACATTACAGACCTATAATGGAATCCAAGTTGCCTTTAACGAAAATTAATAAGTCATCTGCAAA
ACACAA
Found at i:103613 original size:3 final size:3
Alignment explanation
Indices: 103605--103640 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
103595 TATTTAATTC
103605 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
103641 TCTAAATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:104033 original size:2 final size:2
Alignment explanation
Indices: 104026--104050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104016 CCAACAACTT
104026 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
104051 ACTGAAATCA
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:107225 original size:2 final size:2
Alignment explanation
Indices: 107218--107246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
107208 TAAATACGTG
107218 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
107247 CCACAAGTTA
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:111038 original size:17 final size:18
Alignment explanation
Indices: 111016--111051 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
111006 GGTTTTAGAA
111016 GAAGCGGAAAGG-AAGGG
1 GAAGCGGAAAGGAAAGGG
*
111033 GAAGCGGAAGGGAAAGGG
1 GAAGCGGAAAGGAAAGGG
111051 G
1 G
111052 GGGGGCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.39, C:0.06, G:0.56, T:0.00
Consensus pattern (18 bp):
GAAGCGGAAAGGAAAGGG
Found at i:114448 original size:4 final size:4
Alignment explanation
Indices: 114439--114465 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
114429 CTCACTTCAA
114439 CTTC CTTC CTTC CTTC CTTC CTTC CTT
1 CTTC CTTC CTTC CTTC CTTC CTTC CTT
114466 AATGTATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (4 bp):
CTTC
Found at i:124015 original size:2 final size:2
Alignment explanation
Indices: 124003--124056 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
123993 TGGAAGCTTG
*
124003 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124045 AT AT AT AT AT AT
1 AT AT AT AT AT AT
124057 TAGTAGTACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:124844 original size:2 final size:2
Alignment explanation
Indices: 124837--124870 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
124827 CTTTGCCACT
* *
124837 TA TA TA TA TA TA CA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124871 GTTTTATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:124855 original size:12 final size:12
Alignment explanation
Indices: 124838--124870 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
124828 TTTGCCACTT
124838 ATATATATATAC
1 ATATATATATAC
124850 ATATATATATAC
1 ATATATATATAC
124862 ATATATATA
1 ATATATATA
124871 GTTTTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:125598 original size:2 final size:2
Alignment explanation
Indices: 125591--125621 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
125581 ACCAAAGGCT
125591 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 G
125622 CAATGGAGCA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:129502 original size:2 final size:2
Alignment explanation
Indices: 129495--129556 Score: 63
Period size: 2 Copynumber: 31.5 Consensus size: 2
129485 GAAACAACAA
* * *
129495 AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT GT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
129536 TT AT AT AC AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
129557 GTAGTATAGT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:129646 original size:3 final size:3
Alignment explanation
Indices: 129638--129662 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
129628 AATTAGAATA
129638 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
129663 TTGAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:136423 original size:7 final size:7
Alignment explanation
Indices: 136411--136435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
136401 GACCCGCTAT
136411 AAAATGC
1 AAAATGC
136418 AAAATGC
1 AAAATGC
136425 AAAATGC
1 AAAATGC
136432 AAAA
1 AAAA
136436 AACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAATGC
Found at i:137526 original size:2 final size:2
Alignment explanation
Indices: 137521--137566 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
137511 ACACACACAC
137521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
137563 AT AT
1 AT AT
137567 TCATGCTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147565 original size:8 final size:8
Alignment explanation
Indices: 147552--147582 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
147542 AGTATGAAAG
*
147552 ATATATAT
1 ATATATAC
147560 ATATATAC
1 ATATATAC
147568 ATATATAC
1 ATATATAC
147576 ATATATA
1 ATATATA
147583 AGAAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAC
Found at i:151499 original size:6 final size:6
Alignment explanation
Indices: 151485--151514 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
151475 TAATGGCTGA
*
151485 GGAGGG GGAGAG GGAGGG GGAGGG GGAGGG
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG
151515 CGGCGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:153054 original size:2 final size:2
Alignment explanation
Indices: 153049--153078 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
153039 TAGAAAAAAC
153049 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
153079 AGGATAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153675 original size:2 final size:2
Alignment explanation
Indices: 153668--153708 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
153658 TGCGACTACA
153668 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
153709 CGTTTTTCCA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:154010 original size:2 final size:2
Alignment explanation
Indices: 154003--154029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
153993 GTATCAATAA
154003 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
154030 GAGAGAGAGA
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:154034 original size:2 final size:2
Alignment explanation
Indices: 154029--154058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
154019 ATATATATAT
154029 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
154059 TTCTCAGTAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:156629 original size:22 final size:22
Alignment explanation
Indices: 156603--156656 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
156593 TACAAGATAA
*
156603 GTTTATCTAACACACCTAAGAT
1 GTTTACCTAACACACCTAAGAT
* *
156625 GTTTACCTAACACACCTGATAT
1 GTTTACCTAACACACCTAAGAT
156647 GTTTACCTAA
1 GTTTACCTAA
156657 TATATCATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (22 bp):
GTTTACCTAACACACCTAAGAT
Found at i:156706 original size:37 final size:38
Alignment explanation
Indices: 156649--156726 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
156639 CCTGATATGT
* * *
156649 TTACCTAATATATCATCTAACACACTTAATAT-ATTAC
1 TTACCTAACATACCACCTAACACACTTAATATGATTAC
*
156686 TTACCTAACATACCACCTAACACACTTAATATGCTTAC
1 TTACCTAACATACCACCTAACACACTTAATATGATTAC
156724 TTA
1 TTA
156727 ATACACTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (38 bp):
TTACCTAACATACCACCTAACACACTTAATATGATTAC
Found at i:161308 original size:22 final size:22
Alignment explanation
Indices: 161283--161340 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
161273 TACAAGATAA
*
161283 GTTTACCTAACATA-CTTAATAT
1 GTTTACCTAACACATC-TAATAT
*
161305 GTTTATCTAACACATCTAATAT
1 GTTTACCTAACACATCTAATAT
*
161327 GTTTACTTAACACA
1 GTTTACCTAACACA
161341 CCACCTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (22 bp):
GTTTACCTAACACATCTAATAT
Found at i:161414 original size:22 final size:21
Alignment explanation
Indices: 161364--161418 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
161354 TTAATATATT
161364 ACATACTTAATATATCACCTA
1 ACATACTTAATATATCACCTA
* * *
161385 ACACACTTAATATGCTTACCTA
1 ACATACTTAATAT-ATCACCTA
*
161407 AGATACTTAATA
1 ACATACTTAATA
161419 AAGATATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
ACATACTTAATATATCACCTA
Found at i:164998 original size:14 final size:14
Alignment explanation
Indices: 164951--165000 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
164941 AGTAGTAAAT
164951 TTAATTTTTTTATA
1 TTAATTTTTTTATA
* **
164965 TTTA-TTTGATATA
1 TTAATTTTTTTATA
164978 TCT-ATTTTTTTATA
1 T-TAATTTTTTTATA
164992 TTAATTTTT
1 TTAATTTTT
165001 GAATTATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTAATTTTTTTATA
Found at i:170766 original size:65 final size:64
Alignment explanation
Indices: 170636--170766 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 64
170626 CTTTATCTGA
** * *
170636 TTCGATCTTCTTCTCTAAACACAATGCATCTGCCTAATCGAACCATATATATATATATATATAT
1 TTCGATCTTCTTCTCTAAACACAACCCATCTGCCTAATCAAAACATATATATATATATATATAT
* * * *
170700 TTCGATCTTCTTCTCTAAACAACACCCCATTTGCCTAATTAAAACGTATATATATATATATATAT
1 TTCGATCTTCTTCTCTAAAC-ACAACCCATCTGCCTAATCAAAACATATATATATATATATATAT
170765 TT
1 TT
170767 GTTGTGAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 20 0.34
65 38 0.66
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (64 bp):
TTCGATCTTCTTCTCTAAACACAACCCATCTGCCTAATCAAAACATATATATATATATATATAT
Found at i:176256 original size:24 final size:25
Alignment explanation
Indices: 176207--176256 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
176197 GCCACTCATT
176207 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGG-T-TTTTG
176234 TGTTTGTCAAAAATGGTGGTTTT
1 TGTTTGTCAAAAATGGTGGTTTT
176257 CTTTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 1 0.04
27 19 0.83
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.48
Consensus pattern (25 bp):
TGTTTGTCAAAAATGGTGGTTTTTG
Found at i:178817 original size:2 final size:2
Alignment explanation
Indices: 178810--178843 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
178800 TCATAAAGAA
178810 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
178844 TCAAGTAATG
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:181849 original size:6 final size:6
Alignment explanation
Indices: 181833--181892 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
181823 CGAGAAAATA
* * * *
181833 AGAGAC AGAGAG CGAGAG AGAGAG CGAGAG AGAGAG AGAGAG AGAGCG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
*
181881 AGAGAG AAAGAG
1 AGAGAG AGAGAG
181893 CATAAAAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.47, C:0.07, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAGAG
Found at i:181850 original size:8 final size:8
Alignment explanation
Indices: 181833--181892 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
181823 CGAGAAAATA
*
181833 AGAGACAG
1 AGAGAGAG
*
181841 AGAGCGAG
1 AGAGAGAG
181849 AGAGAGAG
1 AGAGAGAG
*
181857 CGAGAGAG
1 AGAGAGAG
181865 AGAGAGAG
1 AGAGAGAG
*
181873 AGAGAGCG
1 AGAGAGAG
*
181881 AGAGAGAA
1 AGAGAGAG
181889 AGAG
1 AGAG
181893 CATAAAAAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.47, T:0.00
Consensus pattern (8 bp):
AGAGAGAG
Found at i:181852 original size:10 final size:10
Alignment explanation
Indices: 181848--181887 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
181838 CAGAGAGCGA
181848 GAGAGAGAGC
1 GAGAGAGAGC
*
181858 GAGAGAGAGAGA
1 --GAGAGAGAGC
181870 GAGAGAGAGC
1 GAGAGAGAGC
181880 GAGAGAGA
1 GAGAGAGA
181888 AAGAGCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
12 9 0.35
ACGTcount: A:0.45, C:0.05, G:0.50, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGC
Found at i:181854 original size:12 final size:12
Alignment explanation
Indices: 181834--181887 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
181824 GAGAAAATAA
*
181834 GAGACAGAGAGC
1 GAGAGAGAGAGC
181846 GAGAGAGAGAGC
1 GAGAGAGAGAGC
181858 GAGAGAGAGA--
1 GAGAGAGAGAGC
181868 GAGAGAGAGAGC
1 GAGAGAGAGAGC
181880 GAGAGAGA
1 GAGAGAGA
181888 AAGAGCATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
10 10 0.26
12 29 0.74
ACGTcount: A:0.44, C:0.07, G:0.48, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAGC
Found at i:183145 original size:2 final size:2
Alignment explanation
Indices: 183138--183182 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
183128 TACATTATGG
* **
183138 AT AT AT AT AT AT AT AT AC AT -T AT GG 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
183179 AT AT
1 AT AT
183183 GTAAACGTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:183157 original size:25 final size:25
Alignment explanation
Indices: 183125--183179 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
183115 ATTTTGAAAA
183125 ATATACATTATGGATATATATATAT
1 ATATACATTATGGATATATATATAT
183150 ATATACATTATGGATATATATATAT
1 ATATACATTATGGATATATATATAT
183175 ATATA
1 ATATA
183180 TATGTAAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (25 bp):
ATATACATTATGGATATATATATAT
Found at i:185086 original size:2 final size:2
Alignment explanation
Indices: 185081--185121 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
185071 ATATATATAT
185081 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
185122 ACACAACACG
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:188284 original size:16 final size:16
Alignment explanation
Indices: 188265--188306 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
188255 ATAAATATAT
188265 TAAATTTTATATAATA
1 TAAATTTTATATAATA
*
188281 TAAATTATTA-ATAATT
1 TAAATT-TTATATAATA
*
188297 TAAAATTTAT
1 TAAATTTTAT
188307 TTAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:188327 original size:28 final size:27
Alignment explanation
Indices: 188295--188348 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
188285 TTATTAATAA
*
188295 TTTAAAATTTATT-TAAATATATAAATTT
1 TTTAAAA-TTATTATAAA-ATAAAAATTT
*
188323 TTTAATATTATTATAAAATAAAAATT
1 TTTAAAATTATTATAAAATAAAAATT
188349 ATAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTAAAATTATTATAAAATAAAAATTT
Found at i:198272 original size:3 final size:3
Alignment explanation
Indices: 198264--198306 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
198254 TTACTTAAGG
198264 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
198307 AAAAAGATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:199906 original size:2 final size:2
Alignment explanation
Indices: 199899--199937 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
199889 AAACGCCCAC
199899 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
199938 CGCAACCCTC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:206531 original size:7 final size:7
Alignment explanation
Indices: 206521--206546 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
206511 TATAAATATT
206521 AAATTTA
1 AAATTTA
206528 AAATTTA
1 AAATTTA
206535 AAATTTA
1 AAATTTA
206542 AAATT
1 AAATT
206547 ATTAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:206531 original size:14 final size:14
Alignment explanation
Indices: 206514--206553 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
206504 ATAAAATTAT
206514 AAATATTAAATTTA
1 AAATATTAAATTTA
206528 AAAT-TTAAAATTTA
1 AAATATT-AAATTTA
206542 AAATTATTAAAT
1 AAA-TATTAAAT
206554 ATTATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 5 0.22
16 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTAAATTTA
Found at i:210213 original size:13 final size:14
Alignment explanation
Indices: 210195--210224 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
210185 TCTATCACTC
210195 TTTTTTTTTAAA-T
1 TTTTTTTTTAAAGT
210208 TTTTTTTTTAAAGT
1 TTTTTTTTTAAAGT
210222 TTT
1 TTT
210225 CTTCTCTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTAAAGT
Found at i:218551 original size:2 final size:2
Alignment explanation
Indices: 218544--218584 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
218534 TTCTTTTCCT
218544 TA TA TA 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 TA TA TA T
218585 GTATTAAGAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:219997 original size:35 final size:35
Alignment explanation
Indices: 219924--219989 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
219914 AAGAATAATA
* *
219924 AAATTATTTTATTTAAAAATTTATTTTTATATCAT
1 AAATTATTTTATTTAAAAATTTATATTTAAATCAT
219959 AAATT-TTTT-TTTAAAAATTTTATATTTAAAT
1 AAATTATTTTATTTAAAAA-TTTATATTTAAAT
219990 TATTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.29
34 15 0.54
35 5 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (35 bp):
AAATTATTTTATTTAAAAATTTATATTTAAATCAT
Found at i:221967 original size:31 final size:31
Alignment explanation
Indices: 221932--221992 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
221922 ATATTATCTA
221932 ATTTATTGATATAATATAGATAGATATATAT
1 ATTTATTGATATAATATAGATAGATATATAT
221963 ATTTATTGATATAATATAGATAGATATATA
1 ATTTATTGATATAATATAGATAGATATATA
221993 CATTGTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (31 bp):
ATTTATTGATATAATATAGATAGATATATAT
Found at i:227906 original size:2 final size:2
Alignment explanation
Indices: 227899--227928 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
227889 TTCAAAAACA
227899 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
227929 TTTTGCAAAC
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:228531 original size:33 final size:34
Alignment explanation
Indices: 228476--228609 Score: 209
Period size: 33 Copynumber: 4.0 Consensus size: 34
228466 CCATGCCACG
228476 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
1 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
*
228510 TCTATTGCCTTA-TAGCTCTAATTCTTGGAGATT
1 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
* * *
228543 TCTATTCCCTTATTAGCTTTAATTCTTAGAGATA
1 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
*
228577 TCTATTGCCTTA-TAGCTCTAATTCTCGGAGATA
1 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
228610 CTACAATTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 49 0.54
34 41 0.46
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (34 bp):
TCTATTGCCTTATTAGCTCTAATTCTTGGAGATA
Found at i:228584 original size:67 final size:67
Alignment explanation
Indices: 228476--228608 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
228466 CCATGCCACG
* * *
228476 TCTATTGCCTTATTAGCTCTAATTCTTGGAGATATCTATTGCCTTATAGCTCTAATTCTTGGAGA
1 TCTATTCCCTTATTAGCTCTAATTCTTAGAGATATCTATTGCCTTATAGCTCTAATTCTCGGAGA
228541 TT
66 TT
*
228543 TCTATTCCCTTATTAGCTTTAATTCTTAGAGATATCTATTGCCTTATAGCTCTAATTCTCGGAGA
1 TCTATTCCCTTATTAGCTCTAATTCTTAGAGATATCTATTGCCTTATAGCTCTAATTCTCGGAGA
228608 T
66 T
228609 ACTACAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (67 bp):
TCTATTCCCTTATTAGCTCTAATTCTTAGAGATATCTATTGCCTTATAGCTCTAATTCTCGGAGA
TT
Found at i:229028 original size:22 final size:22
Alignment explanation
Indices: 229003--229070 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
228993 GATTTAATTG
229003 ATTATAATCATTATATCAATCT
1 ATTATAATCATTATATCAATCT
* *
229025 ATTATTAT-A-TATGATTTAAT-T
1 ATTATAATCATTAT-A-TCAATCT
229046 GATTATAATCATTATATCAATCT
1 -ATTATAATCATTATATCAATCT
229069 AT
1 AT
229071 CACCAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 24 0.67
23 3 0.08
24 3 0.08
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTATAATCATTATATCAATCT
Found at i:229043 original size:44 final size:44
Alignment explanation
Indices: 228982--229070 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
228972 ATCGGTTACT
*
228982 TTATTATTTATGATTTAATTGATTATAATCATTATATCAATCTA
1 TTATTATATATGATTTAATTGATTATAATCATTATATCAATCTA
229026 TTATTATATATGATTTAATTGATTATAATCATTATATCAATCTA
1 TTATTATATATGATTTAATTGATTATAATCATTATATCAATCTA
229070 T
1 T
229071 CACCAATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (44 bp):
TTATTATATATGATTTAATTGATTATAATCATTATATCAATCTA
Found at i:232671 original size:36 final size:36
Alignment explanation
Indices: 232624--232723 Score: 182
Period size: 36 Copynumber: 2.8 Consensus size: 36
232614 CATAACTTTG
232624 AATTCGAATGTCATTTGTGATGTCTATGCGCCTTCA
1 AATTCGAATGTCATTTGTGATGTCTATGCGCCTTCA
*
232660 AATTCGAATGTCATTTGTGATGTCTATGCGCCTTCG
1 AATTCGAATGTCATTTGTGATGTCTATGCGCCTTCA
*
232696 AATTCGAATGTCATTTGTAATGTCTATG
1 AATTCGAATGTCATTTGTGATGTCTATG
232724 GACCTTGTGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (36 bp):
AATTCGAATGTCATTTGTGATGTCTATGCGCCTTCA
Found at i:232983 original size:120 final size:122
Alignment explanation
Indices: 232761--233002 Score: 416
Period size: 120 Copynumber: 2.0 Consensus size: 122
232751 ATCTCTTGAT
*
232761 GGAAATTTTGAACCTGAAAGAAGTAATGGCCGGAAACTGGTGTGTGGCTAGTGACTGTTGTAATG
1 GGAAAATTTGAACCTGAAAGAAGTAATGGCCGGAAAC--GTGTGTGGCTAGTGACTGTTGTAATG
* * *
232826 CAGGTGTGCATTTACTTGCAGAAGAGGGATTTTATAAAGCTCAGTAACAATAAAATGAC
64 CAGGTGTGCATTTACTTGCAGAAGAGGGATTTCATAAAGCTAAGTAACAAGAAAATGAC
232885 GGAAAATTTGAACCTGAAAGAAGTAATGGCCGGAAAC-TG-GTGGCTAGTGACTGTTGTAATGCA
1 GGAAAATTTGAACCTGAAAGAAGTAATGGCCGGAAACGTGTGTGGCTAGTGACTGTTGTAATGCA
232948 GGTGTGCATTTACTTGCAGAAGAGGGATTTCATAAAGCTAAGTAACAAGAAAATG
66 GGTGTGCATTTACTTGCAGAAGAGGGATTTCATAAAGCTAAGTAACAAGAAAATG
233003 GCGCTTACCA
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
120 76 0.67
121 2 0.02
124 36 0.32
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (122 bp):
GGAAAATTTGAACCTGAAAGAAGTAATGGCCGGAAACGTGTGTGGCTAGTGACTGTTGTAATGCA
GGTGTGCATTTACTTGCAGAAGAGGGATTTCATAAAGCTAAGTAACAAGAAAATGAC
Found at i:246088 original size:2 final size:2
Alignment explanation
Indices: 246081--246106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
246071 AATTACTAGC
246081 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
246107 TGTTTAGGGA
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:249750 original size:2 final size:2
Alignment explanation
Indices: 249743--249775 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
249733 CTTTGTCTAG
249743 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 T
249776 TATTGAAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:250435 original size:2 final size:2
Alignment explanation
Indices: 250428--250460 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
250418 TTTACGTTAT
250428 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 T
250461 CATCGAACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256302 original size:21 final size:22
Alignment explanation
Indices: 256276--256317 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
256266 ATTGTATTTA
256276 TTTAT-AAATTAAAATAATTAT
1 TTTATAAAATTAAAATAATTAT
*
256297 TTTATAAAATTAAAATTATTA
1 TTTATAAAATTAAAATAATTA
256318 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTATAAAATTAAAATAATTAT
Found at i:256839 original size:29 final size:28
Alignment explanation
Indices: 256792--256854 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
256782 ATATAAAGTA
* *
256792 TAAAATTTAATTAATATAT-TTTAAAATT
1 TAAAAATTAATTAAAATATATTT-AAATT
256820 TAAAAATTAATATAAAATATATTTAAATT
1 TAAAAATTAAT-TAAAATATATTTAAATT
256849 TAAAAA
1 TAAAAA
256855 CGACAGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 10 0.32
29 18 0.58
30 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAAATTAATTAAAATATATTTAAATT
Found at i:266656 original size:2 final size:2
Alignment explanation
Indices: 266649--266677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
266639 ATGAGTGTAA
266649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
266678 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270948 original size:2 final size:2
Alignment explanation
Indices: 270941--270968 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
270931 CTGCACAATT
270941 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
270969 AATTATGAAA
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:273821 original size:29 final size:29
Alignment explanation
Indices: 273782--273840 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
273772 ATTAAAATTT
* * **
273782 TTATTAATTATATAATATTTTAAATATAA
1 TTATTAATTATAAAAAATAATAAATATAA
*
273811 TTATTTATTATAAAAAATAATAAATATAA
1 TTATTAATTATAAAAAATAATAAATATAA
273840 T
1 T
273841 ATAATCGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTATTAATTATAAAAAATAATAAATATAA
Found at i:276363 original size:29 final size:29
Alignment explanation
Indices: 276330--276400 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
276320 ATTTATATAC
*
276330 ATATAAAATATTTTAAATATAATTAT-AAT
1 ATATAAAATATTATAAATATAA-TATGAAT
276359 ATATAAAA-ATATATAAATATAATATGAAT
1 ATATAAAATAT-TATAAATATAATATGAAT
* *
276388 ATGTAAATTATTA
1 ATATAAAATATTA
276401 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 29 0.81
30 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATATAAAATATTATAAATATAATATGAAT
Found at i:294041 original size:15 final size:16
Alignment explanation
Indices: 294002--294042 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
293992 AGGATGCATA
294002 TTTCATAAA-TATATT
1 TTTCATAAATTATATT
* *
294017 TTTAAAAAATTAT-TT
1 TTTCATAAATTATATT
294032 TTTCATAAATT
1 TTTCATAAATT
294043 TTACAAATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTCATAAATTATATT
Found at i:297028 original size:15 final size:15
Alignment explanation
Indices: 297008--297037 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
296998 TGGTTGCTAA
297008 AAATTTTTAGACACT
1 AAATTTTTAGACACT
297023 AAATTTTTAGACACT
1 AAATTTTTAGACACT
297038 TTTACTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AAATTTTTAGACACT
Found at i:306721 original size:70 final size:71
Alignment explanation
Indices: 306639--306780 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
306629 ACGTTATGTC
* *
306639 AAATATATAAAATTCATATATTGACT-CGATG-TCATATATGCTAGTAACTAGAAATTAATTAAT
1 AAATAAATAAAATTCATATATTGACTGCCATGCT-ATATATGCTAGTAACTAGAAATTAATTAAT
306702 TAACGTG
65 TAACGTG
* *
306709 AAATAAATAAAATTCATGTATTGACTGCCCTGCTATATATGCTAGTAACTAGAAATTAATTAATT
1 AAATAAATAAAATTCATATATTGACTGCCATGCTATATATGCTAGTAACTAGAAATTAATTAATT
306774 AACGTG
66 AACGTG
306780 A
1 A
306781 CCTAGCAGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
70 24 0.36
71 41 0.62
72 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (71 bp):
AAATAAATAAAATTCATATATTGACTGCCATGCTATATATGCTAGTAACTAGAAATTAATTAATT
AACGTG
Found at i:316116 original size:14 final size:14
Alignment explanation
Indices: 316097--316139 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
316087 AAAATTTCCT
316097 ATTTAAATATATAA
1 ATTTAAATATATAA
316111 ATTTAAATATA-AA
1 ATTTAAATATATAA
* *
316124 TTTATAAATATTTAA
1 ATT-TAAATATATAA
316139 A
1 A
316140 AATAGAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 18 0.75
15 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTAAATATATAA
Found at i:316197 original size:94 final size:100
Alignment explanation
Indices: 316018--316358 Score: 290
Period size: 105 Copynumber: 3.4 Consensus size: 100
316008 TTATTAAATT
* * * *
316018 TTTAAATTTAAATTAATAAATATCTAAAAATAGAG-TCTTCATGATATTAATCTATTTTAAAATT
1 TTTAAATTTAAATTAATAAATATTTAAAAATAGAGTTC-ACATGATATTAATCCACTTTAAAATT
* *
316082 AACACAAAATTTCCTATTT-AAA-T-A-TA-T-A-AA
65 AATA-AAAATTTCATATTTAAAAGTAATTATTAATAA
* * * *
316112 TTTAAATATAAATTTATAAATATTTAAAAATAGAGTTCACATAATATTAATCCACATTAAAATTA
1 TTTAAATTTAAATTAATAAATATTTAAAAATAGAGTTCACATGATATTAATCCACTTTAAAATTA
*
316177 ATAAAATTTTCATATCTTAAAATGTAATTTTATTAATTAA
66 ATAAAAATTTCATAT-TTAAAA-GTAA--TTATTAA-TAA
* * * *
316217 TTTAAATTTAAATTAATAAATATTTTAAAATAGAATTCACATGATATTAAACGACTTTAAAATTA
1 TTTAAATTTAAATTAATAAATATTTAAAAATAGAGTTCACATGATATTAATCCACTTTAAAATTA
* * * *
316282 AT-AAACTTTCCTTTTTAATATA-TAATTTTATTAATTTA
66 ATAAAAATTTCATATTTAA-A-AGTAA--TTATTAA-TAA
* * *
316320 TTTGAATTTAAATAAACTAACTATTTAAAAATAGA-TTCA
1 TTTAAATTTAAATTAA-TAAATATTTAAAAATAGAGTTCA
316359 GCATTAATAA
Statistics
Matches: 204, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
93 10 0.05
94 58 0.28
95 5 0.02
97 1 0.00
98 1 0.00
101 2 0.01
102 1 0.00
103 38 0.19
104 26 0.13
105 62 0.30
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (100 bp):
TTTAAATTTAAATTAATAAATATTTAAAAATAGAGTTCACATGATATTAATCCACTTTAAAATTA
ATAAAAATTTCATATTTAAAAGTAATTATTAATAA
Found at i:316236 original size:105 final size:102
Alignment explanation
Indices: 316110--316367 Score: 309
Period size: 105 Copynumber: 2.5 Consensus size: 102
316100 TAAATATATA
* * *
316110 AATTTAAATATAAATTTATAAATATTTAAAAATAGAGTTCACATAATATTAATCCACATTAAAAT
1 AATTTAAATTTAAATTAATAAATATTTAAAAATAGA-TTCACATAATATTAAACCACATTAAAAT
* *
316175 TAATAAAATTTTCATATCTTAAAATGTAATTTTATTAATT
65 TAAT-AAACTTTCAT-TCTTAAAATATAATTTTATTAATT
* * * *
316215 AATTTAAATTTAAATTAATAAATATTTTAAAATAGAATTCACATGATATTAAACGACTTTAAAAT
1 AATTTAAATTTAAATTAATAAATATTTAAAAATAG-ATTCACATAATATTAAACCACATTAAAAT
* * *
316280 TAATAAACTTTCCTTTTTAATATATAATTTTATTAATT
65 TAATAAACTTTCATTCTTAAAATATAATTTTATTAATT
* * * *
316318 TATTTGAATTTAAATAAACTAACTATTTAAAAATAGATTCAGCATTAATA
1 AATTTAAATTTAAATTAA-TAAATATTTAAAAATAGATTCA-CA-TAATA
316368 AAACTTCCCA
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
103 41 0.31
104 25 0.19
105 64 0.49
106 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (102 bp):
AATTTAAATTTAAATTAATAAATATTTAAAAATAGATTCACATAATATTAAACCACATTAAAATT
AATAAACTTTCATTCTTAAAATATAATTTTATTAATT
Found at i:316365 original size:83 final size:84
Alignment explanation
Indices: 316278--316438 Score: 227
Period size: 84 Copynumber: 1.9 Consensus size: 84
316268 CGACTTTAAA
* * * * * *
316278 ATTAAT-AAACTTTCCTTTTTAATATATAATTTTATTAATTTATTTGAATTTAAATAAACTAACT
1 ATTAATAAAACTTCCCATTTAAATATATAATGTTATTAATTTATTTAAATTTAAATAAA-TAAAT
316342 AT-TTAAAAATAGATTCAGC
65 ATATTAAAAATAGATTCAGC
*
316361 ATTAATAAAACTTCCCATTTAAATATATAATGTTATTAATTTATTTAAATTTAAATTAATAAATA
1 ATTAATAAAACTTCCCATTTAAATATATAATGTTATTAATTTATTTAAATTTAAATAAATAAATA
*
316426 TATTTAAAATAGA
66 TATTAAAAATAGA
316439 GTCTTCGTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 12 0.18
84 56 0.82
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (84 bp):
ATTAATAAAACTTCCCATTTAAATATATAATGTTATTAATTTATTTAAATTTAAATAAATAAATA
TATTAAAAATAGATTCAGC
Found at i:316463 original size:188 final size:189
Alignment explanation
Indices: 316193--316546 Score: 500
Period size: 188 Copynumber: 1.9 Consensus size: 189
316183 TTTTCATATC
* *
316193 TTAAAATGTAATTTTATTAATTAATTTAAATTTAAATTAATAAATATTTTAAAATAGAATTCACA
1 TTAAAATATAATGTTATTAATTAATTTAAATTTAAATTAATAAATATTTTAAAATAGAATTCACA
*
316258 TGATATTAAACGACTTTAAAATTAATAAACTTTCC-TTTTT-AATATATAA-TTTTATTAATTTA
66 TGATATTAAACGACTTTAAAATTAATAAACTATCCATTTTTAAATATATAATTTTTATTAATTTA
* * *
316320 TTTGAATTTAAATAAACTAACTATTTAAAAATAGATTCAGCATTAATAAAACTTCCCAT
131 TTTAAATTTAAATAAACTAAATATTAAAAAATAGATTCAGCATTAATAAAACTTCCCAT
* *
316379 TTAAATATATAATGTTATTAATTTATTTAAATTTAAATTAATAAATATATTTAAAATAG-AGTCT
1 TTAAA-ATATAATGTTATTAATTAATTTAAATTTAAATTAATAAATAT-TTTAAAATAGAATTC-
* * * * * *
316443 TCGTTATATTAAATGACTTTAAAATTAATAAACTATCCATTTTTCAAATATGTAATTTTTATTAC
63 ACATGATATTAAACGACTTTAAAATTAATAAACTATCCATTTTT-AAATATATAATTTTTATTAA
**
316508 TTTATTTAAATTTAAATGTACTAAATATTAAAAAATAGA
127 TTTATTTAAATTTAAATAAACTAAATATTAAAAAATAGA
316547 GTCACATAAA
Statistics
Matches: 145, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
186 5 0.03
187 42 0.29
188 43 0.30
189 5 0.03
191 8 0.06
192 42 0.29
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (189 bp):
TTAAAATATAATGTTATTAATTAATTTAAATTTAAATTAATAAATATTTTAAAATAGAATTCACA
TGATATTAAACGACTTTAAAATTAATAAACTATCCATTTTTAAATATATAATTTTTATTAATTTA
TTTAAATTTAAATAAACTAAATATTAAAAAATAGATTCAGCATTAATAAAACTTCCCAT
Done.