Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 136 of 199
Found at i:39611879 original size:21 final size:23
Alignment explanation
Indices: 39611834--39611880 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39611824 TCACCTGCAA
* *
39611834 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39611857 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39611878 TAA
1 TAA
39611881 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39614231 original size:12 final size:13
Alignment explanation
Indices: 39614203--39614253 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
39614193 ATAGGTGCGT
* *
39614203 AAAAAAAAGTTCA
1 AAAAAAAAATTGA
39614216 AAAAAAAAATTGA
1 AAAAAAAAATTGA
39614229 AAAAAAAAATTGA
1 AAAAAAAAATTGA
39614242 AAAAAAAAATTG
1 AAAAAAAAATTG
39614254 CATACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:39619547 original size:22 final size:23
Alignment explanation
Indices: 39619522--39619581 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
39619512 TGGACTGAAT
39619522 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
39619544 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
39619566 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
39619582 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:39619549 original size:4 final size:4
Alignment explanation
Indices: 39619531--39619564 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
39619521 TATAAAAATT
39619531 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
39619565 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:39620989 original size:18 final size:18
Alignment explanation
Indices: 39620963--39621001 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39620953 TTTCTTCAAC
* *
39620963 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
39620981 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
39620999 TTC
1 TTC
39621002 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:39623355 original size:22 final size:23
Alignment explanation
Indices: 39623330--39623389 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
39623320 TGGACTGAAT
39623330 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
39623352 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
39623374 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
39623390 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:39623357 original size:4 final size:4
Alignment explanation
Indices: 39623339--39623372 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
39623329 TATAAAAATT
39623339 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
39623373 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:39625300 original size:18 final size:17
Alignment explanation
Indices: 39625247--39625306 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
39625237 GCACTCTTTC
*
39625247 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
39625266 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
**
39625283 TGTTTCTTTTTCTGTTTT
1 T-TTTCTTTTTCAATTTT
39625301 TTTTCT
1 TTTTCT
39625307 CTCGTCACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.26
18 19 0.54
19 7 0.20
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:39626250 original size:14 final size:14
Alignment explanation
Indices: 39626231--39626265 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39626221 CTAGCTCTCT
*
39626231 TTTTTTTTTCACAA
1 TTTTTTTTTCAAAA
39626245 TTTTTTTTTCAAAA
1 TTTTTTTTTCAAAA
39626259 TTTTTTT
1 TTTTTTT
39626266 ACAACTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTCAAAA
Found at i:39626325 original size:12 final size:12
Alignment explanation
Indices: 39626307--39626353 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
39626297 TGGAAACTAG
39626307 TTTTTTTTCGAAA
1 TTTTTTTTCG-AA
39626320 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
39626331 TTTTTTTTCGAG
1 TTTTTTTTCGAA
39626343 TTTTTTTTCGA
1 TTTTTTTTCGA
39626354 GAAACTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 10 0.31
12 14 0.44
13 8 0.25
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:39629676 original size:26 final size:26
Alignment explanation
Indices: 39629647--39629696 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
39629637 AAATCGTAGC
39629647 TTCGAAAAAAAAAGT-TAAAAAAAAGT
1 TTCGAAAAAAAAA-TCTAAAAAAAAGT
39629673 TTCGAAAAAAAAATCTAAAAAAAA
1 TTCGAAAAAAAAATCTAAAAAAAA
39629697 AAGAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (26 bp):
TTCGAAAAAAAAATCTAAAAAAAAGT
Found at i:39629720 original size:13 final size:13
Alignment explanation
Indices: 39629704--39629729 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39629694 AAAAAGAAGG
39629704 AAAAAAAATTGCA
1 AAAAAAAATTGCA
39629717 AAAAAAAATTGCA
1 AAAAAAAATTGCA
39629730 TACGGTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGCA
Found at i:39632009 original size:24 final size:25
Alignment explanation
Indices: 39631982--39632035 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
39631972 ATGAGTGATA
*
39631982 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
39632006 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
39632030 AAAAAA
1 AAAAAA
39632036 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:39639618 original size:11 final size:11
Alignment explanation
Indices: 39639602--39639635 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39639592 ATTGGAGTAA
39639602 CAAAAAAAAAT
1 CAAAAAAAAAT
39639613 CAAAAAAAAATT
1 CAAAAAAAAA-T
*
39639625 CGAAAAAAAAT
1 CAAAAAAAAAT
39639636 TGATTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:39639621 original size:13 final size:13
Alignment explanation
Indices: 39639603--39639678 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
39639593 TTGGAGTAAC
39639603 AAAAAAAAA-TC-
1 AAAAAAAAATTCA
39639614 AAAAAAAAATTCGA
1 AAAAAAAAATTC-A
* *
39639628 AAAAAAATTGATTGA
1 AAAAAAA--AATTCA
39639643 AAAAAAAAATTCA
1 AAAAAAAAATTCA
* * *
39639656 AAAAAATAAGTGA
1 AAAAAAAAATTCA
39639669 AAAAAAAAAT
1 AAAAAAAAAT
39639679 CGAGCAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 9 0.18
12 2 0.04
13 22 0.43
14 7 0.14
15 8 0.16
16 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:39639674 original size:29 final size:29
Alignment explanation
Indices: 39639614--39639677 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
39639604 AAAAAAAATC
* * **
39639614 AAAAAAAAATTCGAAAAAAAATTGATTGA
1 AAAAAAAAATTCAAAAAAAAAGTGATAAA
39639643 AAAAAAAAATTCAAAAAAATAAGTGA-AAA
1 AAAAAAAAATTCAAAAAAA-AAGTGATAAA
39639672 AAAAAA
1 AAAAAA
39639678 TCGAGCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (29 bp):
AAAAAAAAATTCAAAAAAAAAGTGATAAA
Found at i:39639689 original size:30 final size:30
Alignment explanation
Indices: 39639653--39639732 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
39639643 AAAAAAAAAT
* *
39639653 TCAAAAAAATAAGTGAAAAAAAAAATCGAG
1 TCAAAAAAAAAAGTGAAAAAAAAAATCAAG
* **
39639683 -CAAAAAAAAAGGGTGACCAAAAAAATCAAG
1 TCAAAAAAAAA-AGTGAAAAAAAAAATCAAG
*
39639713 TTAAAAAAAAAAAGTGAAAA
1 -TCAAAAAAAAAAGTGAAAA
39639733 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
29 9 0.24
30 15 0.39
31 5 0.13
32 9 0.24
ACGTcount: A:0.68, C:0.07, G:0.14, T:0.11
Consensus pattern (30 bp):
TCAAAAAAAAAAGTGAAAAAAAAAATCAAG
Found at i:39640626 original size:18 final size:18
Alignment explanation
Indices: 39640605--39640639 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39640595 AGAAAAGAAA
39640605 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
39640623 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
39640640 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:39643760 original size:12 final size:11
Alignment explanation
Indices: 39643745--39643805 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 11
39643735 AAAAAAAATC
39643745 AAAAAAATTCGAA
1 AAAAAAATT-G-A
39643758 AAAAAAATTGATCA
1 AAAAAAATTG---A
*
39643772 AAAAAAAATTTA
1 -AAAAAAATTGA
*
39643784 AAAAAAAGTGA
1 AAAAAAATTGA
39643795 AAAAAAATTGA
1 AAAAAAATTGA
39643806 GCAAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 19 0.47
12 2 0.05
13 9 0.22
14 1 0.03
15 9 0.22
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:39643787 original size:37 final size:36
Alignment explanation
Indices: 39643735--39643816 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
39643725 TTGGAGTAAC
* *
39643735 AAAAAAAATC-AAAAAAATTCGAAAAAAAAATTGATCA
1 AAAAAAAATCAAAAAAAAGT-G-AAAAAAAATTGAGCA
*
39643772 AAAAAAAATTTAAAAAAAAGTGAAAAAAAATTGAGCA
1 AAAAAAAA-TCAAAAAAAAGTGAAAAAAAATTGAGCA
39643809 AAAAAAAA
1 AAAAAAAA
39643817 AAAAAAGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 30 0.75
38 2 0.05
39 8 0.20
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (36 bp):
AAAAAAAATCAAAAAAAAGTGAAAAAAAATTGAGCA
Found at i:39643819 original size:22 final size:22
Alignment explanation
Indices: 39643794--39643836 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39643784 AAAAAAAGTG
* *
39643794 AAAAAAAATTGAGCAAAAAAAA
1 AAAAAAAAGTGACCAAAAAAAA
*
39643816 AAAAAAAGGTGACCAAAAAAA
1 AAAAAAAAGTGACCAAAAAAA
39643837 TCAAGTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAAAAGTGACCAAAAAAAA
Found at i:39644750 original size:18 final size:18
Alignment explanation
Indices: 39644729--39644763 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39644719 AGAAAAGAAA
39644729 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
39644747 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
39644764 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:39655724 original size:21 final size:23
Alignment explanation
Indices: 39655679--39655725 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39655669 TCACCTGCAA
* *
39655679 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39655702 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39655723 TAA
1 TAA
39655726 TCATAACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39661743 original size:24 final size:25
Alignment explanation
Indices: 39661690--39661743 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
39661680 AACAAATTCT
* *
39661690 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
39661715 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
39661738 TTTTTT
1 TTTTTT
39661744 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:39663321 original size:13 final size:13
Alignment explanation
Indices: 39663303--39663327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39663293 TGGTCATCAT
39663303 GGTGTGAACACAA
1 GGTGTGAACACAA
39663316 GGTGTGAACACA
1 GGTGTGAACACA
39663328 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:39665648 original size:23 final size:23
Alignment explanation
Indices: 39665617--39665662 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39665607 CGTATGCAAT
*
39665617 TTTTTTTTTTGCAATTTTTTTTCC
1 TTTTTTTTTCG-AATTTTTTTTCC
*
39665641 TTTTTTTTTCGGATTTTTTTTC
1 TTTTTTTTTCGAATTTTTTTTC
39665663 AAAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTTTTTTTCGAATTTTTTTTCC
Found at i:39673417 original size:24 final size:22
Alignment explanation
Indices: 39673365--39673419 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
39673355 TTCGGCTACT
*
39673365 GATGTGTTCACACAACAATTAAA
1 GATG-GTTCACACAAAAATTAAA
*
39673388 -AGGGTTCACACTAAAACATTAAA
1 GATGGTTCACAC-AAAA-ATTAAA
39673411 GATGGTTCA
1 GATGGTTCA
39673420 TGAATTCGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGGTTCACACAAAAATTAAA
Found at i:39681738 original size:22 final size:21
Alignment explanation
Indices: 39681706--39681769 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
39681696 TTGGTATTTA
39681706 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
39681727 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
39681749 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39681770 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:39685159 original size:20 final size:19
Alignment explanation
Indices: 39685136--39685200 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39685126 AAGCTCAAAC
39685136 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39685156 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39685176 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39685196 GAGCT
1 GAGCT
39685201 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39691611 original size:15 final size:15
Alignment explanation
Indices: 39691591--39691645 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
39691581 ACTCTCCTCA
*
39691591 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
39691606 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
39691621 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
39691635 TTCTTTT-TCTC
1 TTCTTTTCTCTC
39691646 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:39695676 original size:15 final size:16
Alignment explanation
Indices: 39695656--39695691 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
39695646 TTTTCACTTG
39695656 CTTTTTCTTTT-TCAT
1 CTTTTTCTTTTCTCAT
39695671 CTTTTTCTTTTCTCAT
1 CTTTTTCTTTTCTCAT
39695687 -TTTTT
1 CTTTTT
39695692 TTCACTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTTCTTTTCTCAT
Found at i:39695726 original size:20 final size:20
Alignment explanation
Indices: 39695701--39695744 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39695691 TTTCACTCTA
39695701 TTTTTTCGAATTTTC-TTTCT
1 TTTTTTC-AATTTTCTTTTCT
*
39695721 TTTTTTCATTTTTCTTTTCT
1 TTTTTTCAATTTTCTTTTCT
39695741 TTTT
1 TTTT
39695745 CTCTCATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTCAATTTTCTTTTCT
Found at i:39697963 original size:12 final size:12
Alignment explanation
Indices: 39697937--39697977 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
39697927 ACCGTATACA
39697937 ATTTTTTT-GAT
1 ATTTTTTTCGAT
39697948 -TTTTTTTCGAT
1 ATTTTTTTCGAT
*
39697959 ATTTTTTTC-AA
1 ATTTTTTTCGAT
39697970 ATTTTTTT
1 ATTTTTTT
39697978 TCACGAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 7 0.26
11 12 0.44
12 8 0.30
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
ATTTTTTTCGAT
Found at i:39698314 original size:22 final size:21
Alignment explanation
Indices: 39698282--39698345 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
39698272 TTGGTATTTA
39698282 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
39698303 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
39698325 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39698346 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:39703786 original size:20 final size:20
Alignment explanation
Indices: 39703761--39703809 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
39703751 AAACAAATTA
39703761 AATTTCCAAA-ATAGCAAACC
1 AATTT-CAAATATAGCAAACC
*
39703781 AATTTCAAATTCTAGCAAACC
1 AATTTCAAA-TATAGCAAACC
*
39703802 AATCTCAA
1 AATTTCAA
39703810 CCTGTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 5 0.20
21 16 0.64
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (20 bp):
AATTTCAAATATAGCAAACC
Found at i:39715066 original size:23 final size:23
Alignment explanation
Indices: 39715040--39715087 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
39715030 AACACTTATT
39715040 TTTTTATTTTCACACTCTTGCTC
1 TTTTTATTTTCACACTCTTGCTC
* ** *
39715063 TTTTTCTTTTGTCACTCTTGTTC
1 TTTTTATTTTCACACTCTTGCTC
39715086 TT
1 TT
39715088 ATCTCACTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.08, C:0.23, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTTTATTTTCACACTCTTGCTC
Found at i:39715132 original size:15 final size:15
Alignment explanation
Indices: 39715060--39715153 Score: 57
Period size: 15 Copynumber: 5.9 Consensus size: 15
39715050 CACACTCTTG
39715060 CTCTTTTTCTTTTGTCA
1 CTCTTTTTC-TTT-TCA
*
39715077 CTCTTGTTCTTATCTCA
1 CTCTTTTTCTT-T-TCA
*
39715094 CTCTCCTCATTCTTTTC-
1 CTCT--T-TTTCTTTTCA
*
39715111 TTCCTTTTTCTTTTCA
1 CT-CTTTTTCTTTTCA
* *
39715127 CTCTTTTTGTTTT-T
1 CTCTTTTTCTTTTCA
39715141 CTCTTTTTCTTTT
1 CTCTTTTTCTTTT
39715154 TCTCGCTCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
14 12 0.19
15 18 0.29
16 4 0.06
17 17 0.27
18 4 0.06
19 2 0.03
20 5 0.08
ACGTcount: A:0.05, C:0.27, G:0.03, T:0.65
Consensus pattern (15 bp):
CTCTTTTTCTTTTCA
Found at i:39715144 original size:14 final size:14
Alignment explanation
Indices: 39715114--39715157 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
39715104 TCTTTTCTTC
*
39715114 CTTTTTCTTTTCACT
1 CTTTTTCTTTT-TCT
*
39715129 CTTTTTGTTTTTCT
1 CTTTTTCTTTTTCT
39715143 CTTTTTCTTTTTCT
1 CTTTTTCTTTTTCT
39715157 C
1 C
39715158 GCTCAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (14 bp):
CTTTTTCTTTTTCT
Found at i:39717355 original size:13 final size:12
Alignment explanation
Indices: 39717311--39717355 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
39717301 ACGAGATTGT
*
39717311 AAAAAAAATTTC
1 AAAAAAAAATTC
*
39717323 GAAAAAAAATTC
1 AAAAAAAAATTC
39717335 AAAAAAAAATTC
1 AAAAAAAAATTC
39717347 AAAAAAAAA
1 AAAAAAAAA
39717356 CAAAAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:39717361 original size:11 final size:11
Alignment explanation
Indices: 39717324--39717362 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
39717314 AAAAATTTCG
*
39717324 AAAAAAAATTC
1 AAAAAAAAATC
39717335 AAAAAAAAATTC
1 AAAAAAAAA-TC
39717347 AAAAAAAAA-C
1 AAAAAAAAATC
39717357 AAAAAA
1 AAAAAA
39717363 GTTTGTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 8 0.31
12 11 0.42
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:39717429 original size:18 final size:18
Alignment explanation
Indices: 39717393--39717429 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
39717383 TCCTTTGTGT
* *
39717393 ATTCAGTATTGAAAAAAA
1 ATTCAGAATTAAAAAAAA
39717411 ATTCAGAATTAAAAAAAA
1 ATTCAGAATTAAAAAAAA
39717429 A
1 A
39717430 AGAAGTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (18 bp):
ATTCAGAATTAAAAAAAA
Found at i:39725449 original size:10 final size:10
Alignment explanation
Indices: 39725434--39725466 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
39725424 AAATTGAGTT
39725434 AAAAGAAAAA
1 AAAAGAAAAA
39725444 AAAAGAAAAA
1 AAAAGAAAAA
*
39725454 AAAGGAAAAA
1 AAAAGAAAAA
39725464 AAA
1 AAA
39725467 GTGAAAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:39725472 original size:11 final size:10
Alignment explanation
Indices: 39725434--39725473 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
39725424 AAATTGAGTT
39725434 AAAA-GAAAA
1 AAAAGGAAAA
*
39725443 AAAAAGAAAA
1 AAAAGGAAAA
39725453 AAAAGGAAAA
1 AAAAGGAAAA
39725463 AAAAGTGAAAA
1 AAAAG-GAAAA
39725474 GTCTTGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 4 0.14
10 19 0.68
11 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAGGAAAA
Found at i:39726409 original size:37 final size:37
Alignment explanation
Indices: 39726358--39726428 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
39726348 CATTCTTGTA
39726358 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
39726395 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
39726429 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:39726428 original size:6 final size:6
Alignment explanation
Indices: 39726368--39726417 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
39726358 AAGAGAAAAC
*
39726368 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
39726417 A
1 A
39726418 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:39726510 original size:11 final size:12
Alignment explanation
Indices: 39726478--39726508 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39726468 TTGAGAGAAC
39726478 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39726490 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39726502 TTGAAAA
1 TTGAAAA
39726509 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:39728688 original size:30 final size:30
Alignment explanation
Indices: 39728654--39728750 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
39728644 AGCTCACTCC
39728654 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * *
39728684 TAGCTCAACTTCAGTTTAAGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
39728714 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
39728744 TAGCTCA
1 TAGCTCA
39728751 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:39733011 original size:20 final size:19
Alignment explanation
Indices: 39732980--39733017 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
39732970 GAGCTAATAC
39732980 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
39732999 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
39733018 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:39736735 original size:12 final size:13
Alignment explanation
Indices: 39736720--39736767 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 13
39736710 CAAAAAAAAT
39736720 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
39736733 AAAAAAAATTGATTGA
1 AAAAAAAA-T--TCGA
39736749 AAAAAAAATTC-A
1 AAAAAAAATTCGA
39736761 AAAAAAA
1 AAAAAAA
39736768 GTGAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.27
13 9 0.30
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:39736793 original size:17 final size:17
Alignment explanation
Indices: 39736771--39736810 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39736761 AAAAAAAGTG
39736771 AAAAAAA-ATCGAGCAAA
1 AAAAAAAGAT-GAGCAAA
*
39736788 AAAAAAAGGTGAGCAAA
1 AAAAAAAGATGAGCAAA
39736805 AAAAAA
1 AAAAAA
39736811 TCAAGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.72, C:0.07, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAAAAGATGAGCAAA
Found at i:39744957 original size:22 final size:23
Alignment explanation
Indices: 39744925--39744968 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
39744915 GATTCATTAA
*
39744925 TTTTTAGTTATTT-TAGTTTGTG
1 TTTTTAATTATTTATAGTTTGTG
39744947 TTTTTAATTATTTCATAGTTTG
1 TTTTTAATTATTT-ATAGTTTG
39744969 CACATCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66
Consensus pattern (23 bp):
TTTTTAATTATTTATAGTTTGTG
Found at i:39746949 original size:10 final size:10
Alignment explanation
Indices: 39746934--39746971 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39746924 GCTCGTTTCC
*
39746934 AGCTCACTCG
1 AGCTCAATCG
39746944 AGCTCAAGTC-
1 AGCTCAA-TCG
39746954 AGCTCAATCG
1 AGCTCAATCG
39746964 AGCTCAAT
1 AGCTCAAT
39746972 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39746958 original size:20 final size:20
Alignment explanation
Indices: 39746933--39746970 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39746923 AGCTCGTTTC
*
39746933 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39746953 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39746971 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39746977 original size:20 final size:20
Alignment explanation
Indices: 39746934--39746994 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39746924 GCTCGTTTCC
* * *
39746934 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39746954 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39746974 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39746994 A
1 A
39746995 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39746988 original size:11 final size:10
Alignment explanation
Indices: 39746944--39746990 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39746934 AGCTCACTCG
*
39746944 AGCTCAAGTC
1 AGCTCAATTC
39746954 AGCTCAA-TC
1 AGCTCAATTC
*
39746963 GAGCTCAATTT
1 -AGCTCAATTC
39746974 AGCTACAATTC
1 AGCT-CAATTC
39746985 AGCTCA
1 AGCTCA
39746991 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39748323 original size:13 final size:15
Alignment explanation
Indices: 39748293--39748330 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
39748283 GTTCGTAACG
39748293 AAAAAAAAAAGGAGTC
1 AAAAAAAAAA-GAGTC
39748309 AAAAAAAAAA-A-TC
1 AAAAAAAAAAGAGTC
39748322 AAAAAAAAA
1 AAAAAAAAA
39748331 TTGAGTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
16 10 0.45
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (15 bp):
AAAAAAAAAAGAGTC
Found at i:39748429 original size:13 final size:13
Alignment explanation
Indices: 39748407--39748441 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39748397 AAAAGAGAAG
39748407 AAATTCGAAAAAA
1 AAATTCGAAAAAA
*
39748420 AAATTTGAAAAAA
1 AAATTCGAAAAAA
39748433 AAA-TCGAAA
1 AAATTCGAAA
39748442 TTTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:39749589 original size:48 final size:47
Alignment explanation
Indices: 39749510--39749615 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
39749500 GAGTGTCATG
*
39749510 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
39749558 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
39749606 GAAAAAGAAA
1 GAAAAAGAAA
39749616 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:39751176 original size:10 final size:10
Alignment explanation
Indices: 39751161--39751198 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39751151 GCTCGTTTCC
*
39751161 AGCTCACTCG
1 AGCTCAATCG
39751171 AGCTCAAGTC-
1 AGCTCAA-TCG
39751181 AGCTCAATCG
1 AGCTCAATCG
39751191 AGCTCAAT
1 AGCTCAAT
39751199 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39751185 original size:20 final size:20
Alignment explanation
Indices: 39751160--39751197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39751150 AGCTCGTTTC
*
39751160 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39751180 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39751198 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39751204 original size:20 final size:20
Alignment explanation
Indices: 39751161--39751221 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39751151 GCTCGTTTCC
* * *
39751161 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39751181 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39751201 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39751221 A
1 A
39751222 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39751215 original size:11 final size:10
Alignment explanation
Indices: 39751171--39751217 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39751161 AGCTCACTCG
*
39751171 AGCTCAAGTC
1 AGCTCAATTC
39751181 AGCTCAA-TC
1 AGCTCAATTC
*
39751190 GAGCTCAATTT
1 -AGCTCAATTC
39751201 AGCTACAATTC
1 AGCT-CAATTC
39751212 AGCTCA
1 AGCTCA
39751218 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39755738 original size:10 final size:10
Alignment explanation
Indices: 39755723--39755760 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39755713 GCTCATTTCC
*
39755723 AGCTCACTCG
1 AGCTCAATCG
39755733 AGCTCAAGTC-
1 AGCTCAA-TCG
39755743 AGCTCAATCG
1 AGCTCAATCG
39755753 AGCTCAAT
1 AGCTCAAT
39755761 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39755747 original size:20 final size:20
Alignment explanation
Indices: 39755722--39755759 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39755712 AGCTCATTTC
*
39755722 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39755742 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39755760 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39755766 original size:20 final size:20
Alignment explanation
Indices: 39755723--39755783 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39755713 GCTCATTTCC
* * *
39755723 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39755743 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39755763 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39755783 A
1 A
39755784 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39755777 original size:11 final size:10
Alignment explanation
Indices: 39755733--39755779 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39755723 AGCTCACTCG
*
39755733 AGCTCAAGTC
1 AGCTCAATTC
39755743 AGCTCAA-TC
1 AGCTCAATTC
*
39755752 GAGCTCAATTT
1 -AGCTCAATTC
39755763 AGCTACAATTC
1 AGCT-CAATTC
39755774 AGCTCA
1 AGCTCA
39755780 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39757102 original size:12 final size:11
Alignment explanation
Indices: 39757085--39757117 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
39757075 TCGTAATGTA
39757085 AAAAAAAAAGTC
1 AAAAAAAAA-TC
39757097 AAAAAAAAATC
1 AAAAAAAAATC
39757108 AAAAAAAAAT
1 AAAAAAAAAT
39757118 TTTGAGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:39757217 original size:13 final size:13
Alignment explanation
Indices: 39757195--39757234 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
39757185 AAGAGAGAAG
*
39757195 AAATTCGAAAAAA
1 AAATTTGAAAAAA
39757208 AAATTTGAAAAAA
1 AAATTTGAAAAAA
39757221 AAA-TTGAAAAAA
1 AAATTTGAAAAAA
39757233 AA
1 AA
39757235 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (13 bp):
AAATTTGAAAAAA
Found at i:39757220 original size:12 final size:12
Alignment explanation
Indices: 39757203--39757245 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
39757193 AGAAATTCGA
39757203 AAAAAAAATTTG
1 AAAAAAAATTTG
*
39757215 AAAAAAAAATTG
1 AAAAAAAATTTG
39757227 AAAAAAAA-TT-
1 AAAAAAAATTTG
39757237 AAAAAAAAT
1 AAAAAAAAT
39757246 CGAAGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 19 0.66
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:39757245 original size:10 final size:11
Alignment explanation
Indices: 39757203--39757245 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
39757193 AGAAATTCGA
39757203 AAAAAAAATTTG
1 AAAAAAAA-TTG
39757215 AAAAAAAAATTG
1 -AAAAAAAATTG
39757227 AAAAAAAATT-
1 AAAAAAAATTG
39757237 AAAAAAAAT
1 AAAAAAAAT
39757246 CGAAGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
12 3 0.10
13 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:39759844 original size:10 final size:10
Alignment explanation
Indices: 39759829--39759866 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39759819 GCTCGTTTCC
*
39759829 AGCTCACTCG
1 AGCTCAATCG
39759839 AGCTCAAGTC-
1 AGCTCAA-TCG
39759849 AGCTCAATCG
1 AGCTCAATCG
39759859 AGCTCAAT
1 AGCTCAAT
39759867 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:39759853 original size:20 final size:20
Alignment explanation
Indices: 39759828--39759865 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39759818 AGCTCGTTTC
*
39759828 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
39759848 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
39759866 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:39759872 original size:20 final size:20
Alignment explanation
Indices: 39759829--39759889 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
39759819 GCTCGTTTCC
* * *
39759829 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
39759849 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
39759869 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
39759889 A
1 A
39759890 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:39759883 original size:11 final size:10
Alignment explanation
Indices: 39759839--39759885 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39759829 AGCTCACTCG
*
39759839 AGCTCAAGTC
1 AGCTCAATTC
39759849 AGCTCAA-TC
1 AGCTCAATTC
*
39759858 GAGCTCAATTT
1 -AGCTCAATTC
39759869 AGCTACAATTC
1 AGCT-CAATTC
39759880 AGCTCA
1 AGCTCA
39759886 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:39760606 original size:7 final size:7
Alignment explanation
Indices: 39760594--39760623 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
39760584 ATTTGTAAAG
39760594 GACTTTT
1 GACTTTT
39760601 GACTTTT
1 GACTTTT
39760608 GACTTTT
1 GACTTTT
39760615 GACTTTT
1 GACTTTT
39760622 GA
1 GA
39760624 TCATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
GACTTTT
Found at i:39768836 original size:17 final size:18
Alignment explanation
Indices: 39768814--39768854 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39768804 CGTTTCTTTT
39768814 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
39768831 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
39768849 T-TTTTG
1 TCTTTTG
39768855 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:39768838 original size:24 final size:25
Alignment explanation
Indices: 39768783--39768838 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
39768773 ACAAACAAAT
* *
39768783 TCTTTTTTCATTTTCATCACTCGTT
1 TCTTTTTTCATTTTAATCACTCGTC
39768808 TC-TTTTTC-TTTTGAATCACTC-TC
1 TCTTTTTTCATTTT-AATCACTCGTC
39768831 TCTTTTTT
1 TCTTTTTT
39768839 ATCACTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.26
24 18 0.67
25 2 0.07
ACGTcount: A:0.11, C:0.23, G:0.04, T:0.62
Consensus pattern (25 bp):
TCTTTTTTCATTTTAATCACTCGTC
Found at i:39771108 original size:14 final size:14
Alignment explanation
Indices: 39771089--39771115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39771079 CTAGACCGTA
39771089 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
39771103 TGCAATTTTTTTT
1 TGCAATTTTTTTT
39771116 CCTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:39774234 original size:20 final size:20
Alignment explanation
Indices: 39774211--39774249 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39774201 AAGCTCAAAC
39774211 AAGCTAAAGTAAGCTAAATT
1 AAGCTAAAGTAAGCTAAATT
* * *
39774231 AAGCTCATGTGAGCTAAAT
1 AAGCTAAAGTAAGCTAAAT
39774250 CGAGCTGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AAGCTAAAGTAAGCTAAATT
Found at i:39777771 original size:18 final size:18
Alignment explanation
Indices: 39777750--39777784 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39777740 TTTTTCTTTT
39777750 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
39777768 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
39777785 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:39778697 original size:15 final size:15
Alignment explanation
Indices: 39778664--39778702 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
39778654 TTTAACTTGA
39778664 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
39778680 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
39778695 TTTTTTTT
1 TTTTTTTT
39778703 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 12 0.55
17 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:39778709 original size:12 final size:12
Alignment explanation
Indices: 39778694--39778728 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39778684 TTTTGCTCGA
39778694 TTTTTTTTTCAT
1 TTTTTTTTTCAT
**
39778706 TTTTTTTTGAAT
1 TTTTTTTTTCAT
39778718 TTTTTTTTTCA
1 TTTTTTTTTCA
39778729 ATCAATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTCAT
Found at i:39778750 original size:13 final size:13
Alignment explanation
Indices: 39778680--39778753 Score: 59
Period size: 13 Copynumber: 5.6 Consensus size: 13
39778670 TTGCTCACCT
39778680 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
39778694 TTTTTTTTTC--A
1 TTTTTTTTTCGAA
39778705 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
39778717 TTTTTTTTTTC-AA
1 -TTTTTTTTTCGAA
39778730 TCAATTTTTTTTCGAA
1 T---TTTTTTTTCGAA
39778746 TTTTTTTT
1 TTTTTTTT
39778754 GATTTTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
11 10 0.19
12 4 0.08
13 18 0.35
14 8 0.15
15 9 0.17
16 3 0.06
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:39778758 original size:10 final size:11
Alignment explanation
Indices: 39778732--39778764 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
39778722 TTTTTCAATC
39778732 AATTTTTTTTCG
1 AATTTTTTTT-G
39778744 AATTTTTTTTG
1 AATTTTTTTTG
39778755 -ATTTTTTTTG
1 AATTTTTTTTG
39778765 TTACTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:39780263 original size:20 final size:20
Alignment explanation
Indices: 39780240--39780278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39780230 AAGCTCAAAC
39780240 AAGCTAAAGTAAGCTAAATT
1 AAGCTAAAGTAAGCTAAATT
* * *
39780260 AAGCTCATGTGAGCTAAAT
1 AAGCTAAAGTAAGCTAAAT
39780279 CGAGCTGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AAGCTAAAGTAAGCTAAATT
Found at i:39789713 original size:30 final size:30
Alignment explanation
Indices: 39789679--39789775 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39789669 TAAACTAAAA
*
39789679 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
39789709 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39789739 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
39789768 ATGAGCTA
1 -TGAGCTA
39789776 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:39796216 original size:14 final size:14
Alignment explanation
Indices: 39796198--39796227 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39796188 AAAAGAAGGA
39796198 AAAAAAATAAATTGC
1 AAAAAAA-AAATTGC
39796213 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
39796227 A
1 A
39796228 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:39798500 original size:24 final size:25
Alignment explanation
Indices: 39798473--39798526 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
39798463 ATGAGTGATA
*
39798473 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
39798497 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
39798521 AAAAAA
1 AAAAAA
39798527 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:39802901 original size:20 final size:20
Alignment explanation
Indices: 39802878--39802931 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39802868 AGTTTTTCCC
*
39802878 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
39802898 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
39802918 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
39802932 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:39802913 original size:30 final size:30
Alignment explanation
Indices: 39802878--39802951 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
39802868 AGTTTTTCCC
39802878 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
39802908 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
39802938 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
39802952 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:39802941 original size:20 final size:20
Alignment explanation
Indices: 39802878--39802942 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39802868 AGTTTTTCCC
* * * *
39802878 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
39802898 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
39802917 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
39802938 AGCTC
1 AGCTC
39802943 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:39809562 original size:22 final size:22
Alignment explanation
Indices: 39809532--39809575 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39809522 TTTGGTATTT
39809532 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
* *
39809554 GGGATTTGGTACGAATTGGTAA
1 GGGAATTGGTACGAAATGGTAA
39809576 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39816020 original size:20 final size:20
Alignment explanation
Indices: 39815997--39816043 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39815987 GGGTTAAGAT
*
39815997 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
39816017 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
39816037 TGAGCTG
1 TGAGCTG
39816044 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:39835635 original size:52 final size:52
Alignment explanation
Indices: 39835552--39835652 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
39835542 TAAGGCAACG
* *
39835552 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
39835604 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
39835653 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:39843490 original size:52 final size:52
Alignment explanation
Indices: 39843407--39843507 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
39843397 TAAGGCAACG
* *
39843407 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
39843459 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
39843508 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:39845369 original size:80 final size:79
Alignment explanation
Indices: 39845285--39845456 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
39845275 GGACTAAGAT
*
39845285 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
39845349 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * ** * * * *
39845365 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
39845430 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
39845444 CCGAAGGCATTTG
1 CCGAAGGCATTTG
39845457 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:39845436 original size:39 final size:39
Alignment explanation
Indices: 39845232--39845454 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
39845222 TTGAATGCTG
* * * * *
39845232 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
39845272 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
39845311 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
39845352 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
39845392 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
39845431 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39845455 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 102 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:39845474 original size:79 final size:80
Alignment explanation
Indices: 39845312--39845489 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
39845302 AGATACAAAT
* * * *
39845312 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
39845377 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * *
39845392 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
39845456 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
39845471 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
39845490 TACGTGATTC
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.17
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:39850724 original size:20 final size:20
Alignment explanation
Indices: 39850699--39850749 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39850689 TAACGAGCAC
*
39850699 AATGAGTTGAATTGAGCTCG
1 AATGAGCTGAATTGAGCTCG
* *
39850719 AATGAGCTGACTTGAGCTTG
1 AATGAGCTGAATTGAGCTCG
*
39850739 AGTGAGCTGAA
1 AATGAGCTGAA
39850750 CCGCATGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.27
Consensus pattern (20 bp):
AATGAGCTGAATTGAGCTCG
Found at i:39853359 original size:13 final size:13
Alignment explanation
Indices: 39853341--39853369 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39853331 AATCGGCACA
39853341 AAAATAAATAAAG
1 AAAATAAATAAAG
39853354 AAAATAAATAAAG
1 AAAATAAATAAAG
39853367 AAA
1 AAA
39853370 TCGAAACAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAATAAATAAAG
Found at i:39860679 original size:22 final size:22
Alignment explanation
Indices: 39860651--39860702 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
39860641 TTGTTCTTCA
*
39860651 TTGGAGGGGAGATTAGAGCTGT
1 TTGGAGGGGAGATTAGAGCTAT
39860673 TTGGAGGGGAGATTAGAGCTAT
1 TTGGAGGGGAGATTAGAGCTAT
*
39860695 TTGAAGGG
1 TTGGAGGG
39860703 AGTTGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.44, T:0.27
Consensus pattern (22 bp):
TTGGAGGGGAGATTAGAGCTAT
Found at i:39866033 original size:21 final size:23
Alignment explanation
Indices: 39865988--39866034 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39865978 TCACATGCAA
* *
39865988 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39866011 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39866032 TAA
1 TAA
39866035 TAAATGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39880427 original size:20 final size:20
Alignment explanation
Indices: 39880402--39880446 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
39880392 GTCTTAACCG
39880402 AATTAATTAG-GTTTTAG-TTT
1 AATTAATT-GTGTTTT-GTTTT
39880422 AATTAATTGTGTTTTGTTTT
1 AATTAATTGTGTTTTGTTTT
39880442 AATTA
1 AATTA
39880447 TAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AATTAATTGTGTTTTGTTTT
Found at i:39881388 original size:23 final size:23
Alignment explanation
Indices: 39881362--39881435 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
39881352 AATTTGGTTT
39881362 ATTTCGTACCAAAATCTC-ATACC
1 ATTTCGTACCAAAATC-CAATACC
* *
39881385 ATTTCGTACCAACATCCAATTCC
1 ATTTCGTACCAAAATCCAATACC
* *
39881408 ATTTCTTACCAAACA-CCAAAACC
1 ATTTCGTACCAAA-ATCCAATACC
39881431 ATTTC
1 ATTTC
39881436 CTAATTAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.02
23 41 0.95
24 1 0.02
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (23 bp):
ATTTCGTACCAAAATCCAATACC
Found at i:39883314 original size:29 final size:27
Alignment explanation
Indices: 39883283--39883337 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
39883273 TAAATGTGTT
*
39883283 TTTTATTATATGTTATTAATG-TGTCTAA
1 TTTTATTA-ATGCT-TTAATGATGTCTAA
39883311 TTTTATTAATGCTTTAATGATGTCTAA
1 TTTTATTAATGCTTTAATGATGTCTAA
39883338 GTCAAGCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 11 0.44
28 8 0.32
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (27 bp):
TTTTATTAATGCTTTAATGATGTCTAA
Found at i:39891779 original size:19 final size:18
Alignment explanation
Indices: 39891743--39891782 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39891733 TTTCCACTCG
*
39891743 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
39891761 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
39891780 TTT
1 TTT
39891783 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:39892930 original size:11 final size:12
Alignment explanation
Indices: 39892911--39892957 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
39892901 ATGGAAACCA
*
39892911 AATTTTTTTTTT
1 AATTTTTTTTTG
39892923 AATTTTTTTTTG
1 AATTTTTTTTTG
39892935 AATTTTTTTTTCG
1 AATTTTTTTTT-G
*
39892948 AGTTTTTTTT
1 AATTTTTTTT
39892958 CGAGAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:39892953 original size:13 final size:13
Alignment explanation
Indices: 39892925--39892961 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
39892915 TTTTTTTTAA
*
39892925 TTTTTTTTT-GAA
1 TTTTTTTTTCGAG
39892937 TTTTTTTTTCGAG
1 TTTTTTTTTCGAG
39892950 -TTTTTTTTCGAG
1 TTTTTTTTTCGAG
39892962 AAACTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 21 0.91
13 2 0.09
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTTTTTTTCGAG
Found at i:39896419 original size:12 final size:12
Alignment explanation
Indices: 39896370--39896419 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
39896360 ATAGGTGCGT
39896370 AAAAAAAAAGTTCG
1 AAAAAAAAA-TT-G
39896384 AAAAAAAAAATT-
1 -AAAAAAAAATTG
39896396 AAAAAAAAATTG
1 AAAAAAAAATTG
39896408 AAAAAAAAATTG
1 AAAAAAAAATTG
39896420 CATACGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.32
12 12 0.35
14 2 0.06
15 9 0.26
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:39900725 original size:27 final size:25
Alignment explanation
Indices: 39900669--39900726 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
39900659 TTGGAGTAAC
* **
39900669 AAAAAAAATAAAAAAAAAATTGATTG
1 AAAAAAAATAAAAAAAAAAGTGA-AA
*
39900695 AAAAAAATTCAAAAAAAAAAGTGAAA
1 AAAAAAAAT-AAAAAAAAAAGTGAAA
39900721 AAAAAA
1 AAAAAA
39900727 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAAAATAAAAAAAAAAGTGAAA
Found at i:39900736 original size:15 final size:15
Alignment explanation
Indices: 39900706--39900756 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
39900696 AAAAAATTCA
39900706 AAAAAAAAAGT--G-
1 AAAAAAAAAGTGAGC
39900718 AAAAAAAAA-TCGAGC
1 AAAAAAAAAGT-GAGC
39900733 AAAAAAAAAGGTGAGC
1 AAAAAAAAA-GTGAGC
39900749 AAAAAAAA
1 AAAAAAAA
39900757 TCAAGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
14 1 0.03
15 9 0.27
16 12 0.36
17 1 0.03
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
AAAAAAAAAGTGAGC
Found at i:39906423 original size:21 final size:23
Alignment explanation
Indices: 39906378--39906424 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39906368 TCACCTACAA
* *
39906378 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39906401 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39906422 TAA
1 TAA
39906425 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39909749 original size:26 final size:23
Alignment explanation
Indices: 39909697--39909741 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39909687 CAATTTTTTC
* *
39909697 TTTCTTTCTTTCTTTTTTTCATT
1 TTTCTTTCTCTCTCTTTTTCATT
39909720 TTTCTTGTCTCTCTCTTTTTCA
1 TTTCTT-TCTCTCTCTTTTTCA
39909742 ATCTTTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTCTTTCTCTCTCTTTTTCATT
Found at i:39911843 original size:11 final size:11
Alignment explanation
Indices: 39911827--39911868 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
39911817 ACCAAATTTT
39911827 TTTTTTTTGAA
1 TTTTTTTTGAA
39911838 TTTTTTTTGAA
1 TTTTTTTTGAA
*
39911849 TTTTTTTTCGAG
1 TTTTTTTT-GAA
39911861 TTTTTTTT
1 TTTTTTTT
39911869 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39911872 original size:12 final size:12
Alignment explanation
Indices: 39911826--39911871 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
39911816 AACCAAATTT
*
39911826 TTTTTTTTTGAA
1 TTTTTTTTCGAA
39911838 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
39911849 TTTTTTTTCGAG
1 TTTTTTTTCGAA
39911861 TTTTTTTTCGA
1 TTTTTTTTCGA
39911872 GAAACTACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.13, C:0.04, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:39912873 original size:23 final size:23
Alignment explanation
Indices: 39912843--39912892 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
39912833 GTCACCTGCA
39912843 AAAATGAGTTTATTAAACACATT
1 AAAATGAGTTTATTAAACACATT
39912866 AAAATGAGTTTATTAAACACATT
1 AAAATGAGTTTATTAAACACATT
39912889 AAAA
1 AAAA
39912893 CACTTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (23 bp):
AAAATGAGTTTATTAAACACATT
Found at i:39914525 original size:24 final size:23
Alignment explanation
Indices: 39914481--39914525 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
39914471 TTCTTAGGAC
* *
39914481 TTTCTTTATTTTATTGTTGTTCG
1 TTTCTTTAATTTATTGCTGTTCG
*
39914504 TTTCTTTTAATTTCTTGCTGTT
1 TTTC-TTTAATTTATTGCTGTT
39914526 TGCGTCAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (23 bp):
TTTCTTTAATTTATTGCTGTTCG
Found at i:39916670 original size:21 final size:22
Alignment explanation
Indices: 39916634--39916681 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
39916624 AACAAGTGAG
39916634 GAAAAAGAAAAGTGAAAAAGAA
1 GAAAAAGAAAAGTGAAAAAGAA
* *
39916656 GAAAATGAAAA-TGAAAAAGAC
1 GAAAAAGAAAAGTGAAAAAGAA
39916677 GAAAA
1 GAAAA
39916682 GGGAAGCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (22 bp):
GAAAAAGAAAAGTGAAAAAGAA
Found at i:39924561 original size:22 final size:23
Alignment explanation
Indices: 39924536--39924584 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
39924526 ATGAGCTTCT
39924536 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
39924558 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
39924580 TTAAT
1 TTAAT
39924585 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:39929049 original size:24 final size:23
Alignment explanation
Indices: 39929009--39929053 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39928999 TTTTTAGGAC
*
39929009 TTTCTTTATTTTATTGTTGTTCA
1 TTTCTTTAATTTATTGTTGTTCA
*
39929032 TTTCTTTTAATTTCTTGTTGTT
1 TTTC-TTTAATTTATTGTTGTT
39929054 TGCGTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (23 bp):
TTTCTTTAATTTATTGTTGTTCA
Done.