Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 49 of 135
Found at i:19854622 original size:24 final size:24
Alignment explanation
Indices: 19854595--19854666 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
19854585 TACTTGAGTA
* *
19854595 ATTTGCCGTCAATTTATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
19854619 ATTTACCGTCAATTCATTCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
*
19854643 ATTTACTGTCAATTCATCCTTTGC
1 ATTTACCGTCAATTCATCCTTTGC
19854667 CACAGAACGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCCTTTGC
Found at i:19863717 original size:19 final size:19
Alignment explanation
Indices: 19863682--19863719 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19863672 ACACATAAGC
*
19863682 ATTTAAATAAATTTTTTAA
1 ATTTAAATAAATATTTTAA
19863701 ATTTAAA-AAATAATTTTAA
1 ATTTAAATAAAT-ATTTTAA
19863720 TGATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAATATTTTAA
Found at i:19863728 original size:29 final size:30
Alignment explanation
Indices: 19863682--19863774 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 30
19863672 ACACATAAGC
*
19863682 ATTTAAATAAATTTTTTAAATTTAAAAAATA
1 ATTTTAAT-AATTTTTTAAATTTAAAAAATA
* * *
19863713 ATTTTAATGA-TTTTTAATTTTTAAAAATA
1 ATTTTAATAATTTTTTAAATTTAAAAAATA
* * *
19863742 GTTTTTATAATTTTTTGAAATTTTAAAATATA
1 ATTTTAATAATTTTTT-AAA-TTTAAAAAATA
19863774 A
1 A
19863775 AAATTAATTA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 24 0.50
30 6 0.12
31 9 0.19
32 9 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTAATAATTTTTTAAATTTAAAAAATA
Found at i:19870213 original size:23 final size:25
Alignment explanation
Indices: 19870175--19870361 Score: 180
Period size: 25 Copynumber: 7.8 Consensus size: 25
19870165 ATGAGGAACC
* *
19870175 TTAGCGCTATCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
19870200 TTAGTGCTC-C-GATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* * *
19870223 TCAGTGTTATCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* *
19870248 TCAGGGCTCTCTGATTATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
* *
19870273 TTAATGCTCTCTGATTATTAGCACG
1 TTAGTGCTCTCTGATTATTAGCACA
*
19870298 TTAGTGCTCTCCG---ATTAGCACA
1 TTAGTGCTCTCTGATTATTAGCACA
19870320 TCT-GTGCTCTCTG--TA-TAGCAC-
1 T-TAGTGCTCTCTGATTATTAGCACA
*
19870341 TTTGTGCTCTCTG-TTCATTAG
1 TTAGTGCTCTCTGATT-ATTAG
19870362 TGCATAATAA
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.01
21 11 0.08
22 25 0.18
23 22 0.16
24 5 0.04
25 74 0.54
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (25 bp):
TTAGTGCTCTCTGATTATTAGCACA
Found at i:19870317 original size:22 final size:20
Alignment explanation
Indices: 19870289--19870351 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 20
19870279 CTCTCTGATT
19870289 ATTAGCACGTTAGTGCTCTCCG
1 ATTAGCAC-TT-GTGCTCTCCG
*
19870311 ATTAGCACATCTGTGCTCTCTG
1 ATTAGCAC-T-TGTGCTCTCCG
19870333 -TATAGCACTTTGTGCTCTC
1 AT-TAGCAC-TTGTGCTCTC
19870352 TGTTCATTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 10 0.28
22 25 0.69
23 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTAGCACTTGTGCTCTCCG
Found at i:19877433 original size:17 final size:18
Alignment explanation
Indices: 19877411--19877444 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19877401 AATCCATACA
19877411 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
19877428 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
19877445 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:19879199 original size:16 final size:16
Alignment explanation
Indices: 19879178--19879259 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
19879168 ATTTTCCCTT
19879178 TTCTTTCTTTCTTTTC
1 TTCTTTCTTTCTTTTC
* * *
19879194 TTCTTTCCTTCCTTCC
1 TTCTTTCTTTCTTTTC
* *
19879210 TTCTCTGTTTCTTTT-
1 TTCTTTCTTTCTTTTC
* *
19879225 TGCTTTTGTTTC-TTTC
1 TTC-TTTCTTTCTTTTC
19879241 TT-TTTCATTTCTTTT-
1 TTCTTTC-TTTCTTTTC
19879256 TTCT
1 TTCT
19879260 AATAATATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
14 3 0.06
15 11 0.22
16 35 0.71
ACGTcount: A:0.01, C:0.24, G:0.04, T:0.71
Consensus pattern (16 bp):
TTCTTTCTTTCTTTTC
Found at i:19879368 original size:8 final size:8
Alignment explanation
Indices: 19879357--19879419 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
19879347 ATTTATTTAA
19879357 AATATAAT
1 AATATAAT
19879365 AATATAAT
1 AATATAAT
19879373 AATATAAT
1 AATATAAT
19879381 AATATAAT
1 AATATAAT
* *
19879389 -ATAATTTAC
1 AAT-A-TAAT
19879398 AATATAAT
1 AATATAAT
*
19879406 AAAATAAT
1 AATATAAT
19879414 AATATA
1 AATATA
19879420 CTTCAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 2 0.04
8 39 0.85
9 3 0.07
10 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:19879920 original size:15 final size:15
Alignment explanation
Indices: 19879900--19879928 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19879890 GATAATAGAC
19879900 TAACAATCTCTATAT
1 TAACAATCTCTATAT
19879915 TAACAATCTCTATA
1 TAACAATCTCTATA
19879929 CTCTAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (15 bp):
TAACAATCTCTATAT
Found at i:19895146 original size:28 final size:28
Alignment explanation
Indices: 19895106--19895162 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19895096 AGAAAGAATG
19895106 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
19895134 ATATCTAGCATTATACTATAATCCTTTT
1 ATATCTAGCATTATACTATAATCCTTTT
19895162 A
1 A
19895163 CTCCATTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATCTAGCATTATACTATAATCCTTTT
Found at i:19912928 original size:26 final size:26
Alignment explanation
Indices: 19912867--19912930 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
19912857 TTTGAAATTT
*
19912867 AAATAC-ATTTTTATAATTTTTTACA
1 AAATACAATTTTTAAAATTTTTTACA
*
19912892 AAA-AAATATTTTTAAAATTTTTTA-A
1 AAATACA-ATTTTTAAAATTTTTTACA
19912917 AAGATACAATTTTT
1 AA-ATACAATTTTT
19912931 TTATAGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 23 0.72
27 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (26 bp):
AAATACAATTTTTAAAATTTTTTACA
Found at i:19912983 original size:20 final size:19
Alignment explanation
Indices: 19912937--19912990 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
19912927 TTTTTTATAG
* *
19912937 TTTTATAATTTTTTCATTT
1 TTTTATAATTTATTAATTT
**
19912956 TTAAATAATATTATTAATTT
1 TTTTATAAT-TTATTAATTT
19912976 TTTTATAATCTTATT
1 TTTTATAAT-TTATT
19912991 GTATTTTTGT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTATTAATTT
Found at i:19913029 original size:16 final size:15
Alignment explanation
Indices: 19912992--19913028 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
19912982 AATCTTATTG
* *
19912992 TATTTTTGTAAACTT
1 TATTTTTATAAACTA
19913007 TATTTTTATAAACTA
1 TATTTTTATAAACTA
19913022 TATTTTT
1 TATTTTT
19913029 TTCTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTTTATAAACTA
Found at i:19921099 original size:14 final size:14
Alignment explanation
Indices: 19921080--19921106 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19921070 TCAAAGCAGA
19921080 TCACTTTTGCAAAG
1 TCACTTTTGCAAAG
19921094 TCACTTTTGCAAA
1 TCACTTTTGCAAA
19921107 CAATGTTGAA
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:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (14 bp):
TCACTTTTGCAAAG
Found at i:19937478 original size:22 final size:22
Alignment explanation
Indices: 19937452--19937496 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19937442 TGAGATAAAG
* * *
19937452 AAAAGCTCAAGTATCAATTTGA
1 AAAAGATCAAGTACCAAATTGA
19937474 AAAAGATCAAGTACCAAATTGA
1 AAAAGATCAAGTACCAAATTGA
19937496 A
1 A
19937497 CATTAAAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (22 bp):
AAAAGATCAAGTACCAAATTGA
Found at i:19945436 original size:3 final size:3
Alignment explanation
Indices: 19945430--19945458 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19945420 TAAGAAACCA
19945430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19945459 AAGTCTTGTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19954044 original size:23 final size:24
Alignment explanation
Indices: 19954018--19954069 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
19954008 AGAATTAGAA
19954018 AAATTT-TGTAAATGTTAAAAATT-
1 AAATTTAT-TAAATGTTAAAAATTC
* *
19954041 AAATTTATTAAATTTTTAAAATTC
1 AAATTTATTAAATGTTAAAAATTC
19954065 AAATT
1 AAATT
19954070 AAAATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTATTAAATGTTAAAAATTC
Found at i:19954090 original size:21 final size:23
Alignment explanation
Indices: 19954066--19954113 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
19954056 TTAAAATTCA
*
19954066 AATTAAAAT-GATAAAT-TTTAT
1 AATTAAAATAGATAAATATTTAG
*
19954087 AATTAAAATATATAAATATTTAG
1 AATTAAAATAGATAAATATTTAG
19954110 AATT
1 AATT
19954114 TATGATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 6 0.26
23 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AATTAAAATAGATAAATATTTAG
Found at i:19963069 original size:9 final size:9
Alignment explanation
Indices: 19963051--19963108 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
19963041 TTTGGTTAAA
19963051 AATTAACCG
1 AATTAACCG
*
19963060 AATTATCCG
1 AATTAACCG
19963069 AATTAACCG
1 AATTAACCG
* *
19963078 AATTACCCA
1 AATTAACCG
*
19963087 AATTACCCG
1 AATTAACCG
*
19963096 AATTAACCT
1 AATTAACCG
19963105 AATT
1 AATT
19963109 GAATCATACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:19963090 original size:27 final size:27
Alignment explanation
Indices: 19963051--19963108 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
19963041 TTTGGTTAAA
* *
19963051 AATTAACCGAATTATCCGAATTAACCG
1 AATTAACCAAATTACCCGAATTAACCG
* *
19963078 AATTACCCAAATTACCCGAATTAACCT
1 AATTAACCAAATTACCCGAATTAACCG
19963105 AATT
1 AATT
19963109 GAATCATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTACCCGAATTAACCG
Found at i:19963228 original size:13 final size:13
Alignment explanation
Indices: 19963210--19963244 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
19963200 TATGATTGGG
19963210 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
*
19963223 TTGGGTTTGGTAA
1 TTGGGTTGGGTAA
19963236 TTGGGTTGG
1 TTGGGTTGG
19963245 ATTGAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:19963240 original size:31 final size:29
Alignment explanation
Indices: 19963203--19963271 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
19963193 TAATTTTTAT
* **
19963203 GATTGGGTTGGGTTGGGTAATTGGGTTTG
1 GATTGGGTTGGATTGAATAATTGGGTTTG
*
19963232 GTAATTGGGTTGGATTGAATACTTGGGTTTG
1 G--ATTGGGTTGGATTGAATAATTGGGTTTG
19963263 GATTGGGTT
1 GATTGGGTT
19963272 TAGGTGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 9 0.26
31 25 0.74
ACGTcount: A:0.14, C:0.01, G:0.42, T:0.42
Consensus pattern (29 bp):
GATTGGGTTGGATTGAATAATTGGGTTTG
Found at i:19965581 original size:25 final size:25
Alignment explanation
Indices: 19965537--19965619 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
19965527 ATGTATGCTT
*
19965537 ATACGAGCATGTA-AACGGGAAGCTC
1 ATACGAGC-TGTATAAAGGGAAGCTC
*
19965562 -TTCTGAGCTGTATAAAGGGAAGCTC
1 ATAC-GAGCTGTATAAAGGGAAGCTC
**
19965587 ATACGAGCTGTATATTGGGAAGCTC
1 ATACGAGCTGTATAAAGGGAAGCTC
*
19965612 ATGCGAGC
1 ATACGAGC
19965620 CATTTATCGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 6 0.12
25 41 0.84
26 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (25 bp):
ATACGAGCTGTATAAAGGGAAGCTC
Found at i:19965631 original size:25 final size:25
Alignment explanation
Indices: 19965578--19965639 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
19965568 GCTGTATAAA
** *
19965578 GGGAAGCTCATACGAGCTGTATATT
1 GGGAAGCTCATACGAGCCATATATC
* *
19965603 GGGAAGCTCATGCGAGCCATTTATC
1 GGGAAGCTCATACGAGCCATATATC
19965628 GGGAAGCTCATA
1 GGGAAGCTCATA
19965640 AGAGTTGTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (25 bp):
GGGAAGCTCATACGAGCCATATATC
Found at i:19965678 original size:50 final size:50
Alignment explanation
Indices: 19965578--19965697 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
19965568 GCTGTATAAA
* * ** * * * **
19965578 GGGAAGCTCATACGAGCTGTATATTGGGAAGCTCATGCGAGCCATTTATC
1 GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
*
19965628 GGGAAGCTCATAAGAGTTGTAAATTAAGAAACTCATGCAACCCAAATATC
1 GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
*
19965678 GAGAAGCTCA-AGAGAGCTGT
1 GGGAAGCTCATA-AGAGCTGT
19965698 GGTGTGTCCA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.02
50 56 0.98
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
GGGAAGCTCATAAGAGCTGTAAATTAAGAAACTCATGCAACCCAAATATC
Found at i:19967938 original size:20 final size:20
Alignment explanation
Indices: 19967915--19967978 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
19967905 TAAAATTAGA
19967915 AAAAAATTGTAAAAAAATTT
1 AAAAAATTGTAAAAAAATTT
*
19967935 AAAAAATTGT--AAAATTTT
1 AAAAAATTGTAAAAAAATTT
*
19967953 ATAAAAATCGTAAAAAAATTAT
1 A-AAAAATTGTAAAAAAATT-T
19967975 AAAA
1 AAAA
19967979 TTTTATAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 10 0.27
21 9 0.24
22 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAAATTGTAAAAAAATTT
Found at i:19967938 original size:39 final size:39
Alignment explanation
Indices: 19967895--19968046 Score: 125
Period size: 39 Copynumber: 3.9 Consensus size: 39
19967885 TAAATTTTAA
* *
19967895 TAAAAAATATTAAAATTAGAAAAAAATTGTAAAAAAATT
1 TAAAAAATATTAAAATTATAAAAAAATTATAAAAAAATT
* * **
19967934 TAAAAAAT-TGTAAAATTTTATAAAAATCGTAAAAAAA-T
1 TAAAAAATAT-TAAAATTATAAAAAAATTATAAAAAAATT
* * * * *
19967972 TATAAAATTTTATAAAGCTATAAGAAAATTAT-AAAAAATG
1 TAAAAAATATTA-AAA-TTATAAAAAAATTATAAAAAAATT
19968012 TAAAGAAATA-TAAAATTCAT-AAAAAATTATAAAAA
1 TAAA-AAATATTAAAATT-ATAAAAAAATTATAAAAA
19968047 TTATCTTACC
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
38 21 0.24
39 50 0.56
40 14 0.16
41 4 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (39 bp):
TAAAAAATATTAAAATTATAAAAAAATTATAAAAAAATT
Found at i:19967958 original size:30 final size:30
Alignment explanation
Indices: 19967867--19967987 Score: 84
Period size: 30 Copynumber: 4.0 Consensus size: 30
19967857 GAAAATCAAT
* * *
19967867 AAAAGGTATAAAAATTATTAAATTTTA-ATA
1 AAAAAGTAAAAAAATTATAAAATTTTATA-A
** * ** *
19967897 AAAAA-TATTAAAATTAGAAAAAAATTGTAA
1 AAAAAGTAAAAAAATTA-TAAAATTTTATAA
* * *
19967927 AAAAATTTAAAAAATTGTAAAATTTTATAA
1 AAAAAGTAAAAAAATTATAAAATTTTATAA
**
19967957 AAATCGTAAAAAAATTATAAAATTTTATAA
1 AAAAAGTAAAAAAATTATAAAATTTTATAA
19967987 A
1 A
19967988 GCTATAAGAA
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
29 10 0.15
30 50 0.74
31 8 0.12
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAAGTAAAAAAATTATAAAATTTTATAA
Found at i:19968039 original size:11 final size:10
Alignment explanation
Indices: 19967894--19968050 Score: 68
Period size: 11 Copynumber: 16.2 Consensus size: 10
19967884 TTAAATTTTA
19967894 ATAAAAAA-T
1 ATAAAAAATT
*
19967903 AT-TAAAATT
1 ATAAAAAATT
*
19967912 AGAAAAAAATT
1 A-TAAAAAATT
*
19967923 GTAAAAAAATT
1 AT-AAAAAATT
19967934 -TAAAAAATT
1 ATAAAAAATT
* **
19967943 GTAAAATTTT
1 ATAAAAAATT
19967953 AT-AAAAATCGT
1 ATAAAAAAT--T
19967964 A-AAAAAATT
1 ATAAAAAATT
19967973 AT--AAAATT
1 ATAAAAAATT
* * **
19967981 TTATAAAGCT
1 ATAAAAAATT
19967991 ATAAGAAAATT
1 ATAA-AAAATT
19968002 ATAAAAAATGT
1 ATAAAAAAT-T
*
19968013 A-AAGAAA-T
1 ATAAAAAATT
19968021 AT--AAAATT
1 ATAAAAAATT
19968029 CATAAAAAATT
1 -ATAAAAAATT
19968040 AT-AAAAATT
1 ATAAAAAATT
19968049 AT
1 AT
19968051 CTTACCAAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
7 3 0.03
8 14 0.13
9 29 0.26
10 27 0.24
11 38 0.34
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:19968252 original size:19 final size:19
Alignment explanation
Indices: 19968230--19968301 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
19968220 TTTTGATACA
**
19968230 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTACAAT
**
19968249 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
*
19968268 TTCTTAT-ATATTTCTACAAT
1 TT-TTATAAT-TTTTTACAAT
19968288 TTTTATAATTTTTT
1 TTTTATAATTTTTT
19968302 TATATTTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:19968326 original size:30 final size:29
Alignment explanation
Indices: 19968229--19968330 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 29
19968219 TTTTTGATAC
19968229 ATTTTATAATTTTTTATGATTTTT-A-TAAA
1 ATTTTATAATTTTTTAT-ATTTTTCACT-AA
* * *
19968258 ATTTTACAATTTCTTATATATTTCTAC-AA
1 ATTTTATAATTTTTTATATTTTTC-ACTAA
*
19968287 TTTTTATAATTTTTTTATATTTTTCACTAA
1 ATTTTATAA-TTTTTTATATTTTTCACTAA
*
19968317 ATTTAATAATTTTT
1 ATTTTATAATTTTT
19968331 ATAACTTGTT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
28 5 0.08
29 31 0.53
30 23 0.39
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTATAATTTTTTATATTTTTCACTAA
Found at i:19974496 original size:25 final size:25
Alignment explanation
Indices: 19974463--19974510 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
19974453 TTTAAATTTT
*
19974463 ATATTAATATTTAATAAAAATAATG
1 ATATTAATATTAAATAAAAATAATG
*
19974488 ATATTAATATTAAATAATAATAA
1 ATATTAATATTAAATAAAAATAA
19974511 AACCCTCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATTAATATTAAATAAAAATAATG
Found at i:19975137 original size:10 final size:10
Alignment explanation
Indices: 19975122--19975187 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
19975112 TAATATTTCT
19975122 TATTTTTATA
1 TATTTTTATA
19975132 TATTTTTA-A
1 TATTTTTATA
*
19975141 AATTTATTATTA
1 TATTT-TTA-TA
*
19975153 TATCTTTTAAA
1 TAT-TTTTATA
* *
19975164 AATATTTATA
1 TATTTTTATA
*
19975174 TACTTTTATA
1 TATTTTTATA
19975184 TATT
1 TATT
19975188 GAATTGAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.62
11 3 0.07
12 6 0.14
13 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTTTATA
Found at i:19975147 original size:23 final size:23
Alignment explanation
Indices: 19975121--19975166 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19975111 ATAATATTTC
* *
19975121 TTATTTTTATATATTTTTAAAAT
1 TTATTATTATATATTTTAAAAAT
*
19975144 TTATTATTATATCTTTTAAAAAT
1 TTATTATTATATATTTTAAAAAT
19975167 ATTTATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTATTATATATTTTAAAAAT
Found at i:19975169 original size:21 final size:20
Alignment explanation
Indices: 19975130--19975181 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
19975120 CTTATTTTTA
*
19975130 TATAT-TTTTAAAATTTATTAT
1 TATATCTTTTAAAATATA-T-T
19975151 TATATCTTTTAAAA-ATATT
1 TATATCTTTTAAAATATATT
19975170 TATATACTTTTA
1 TATAT-CTTTTA
19975182 TATATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 7 0.25
21 7 0.25
22 8 0.29
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATCTTTTAAAATATATT
Found at i:19985949 original size:22 final size:22
Alignment explanation
Indices: 19985890--19985951 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
19985880 TATGAAATAT
*
19985890 GAAAATAAATATATAAAAATTCA
1 GAAAAAAAATATAT-AAAATTCA
* * *
19985913 GAAAACATATGTATAAAA-TCTA
1 GAAAAAAAATATATAAAATTC-A
19985935 GAAAAAAAATATATAAA
1 GAAAAAAAATATATAAA
19985952 TTATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.06
22 19 0.59
23 11 0.34
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (22 bp):
GAAAAAAAATATATAAAATTCA
Found at i:19992346 original size:17 final size:17
Alignment explanation
Indices: 19992305--19992346 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
19992295 ATTTGGTTCT
19992305 TATTTAT-AATATTAAA
1 TATTTATAAATATTAAA
19992321 TATTT-TAAATAATTAAA
1 TATTTATAAAT-ATTAAA
19992338 T-TTTATAAA
1 TATTTATAAA
19992347 AATATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 11 0.48
17 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTATAAATATTAAA
Found at i:20016473 original size:2 final size:2
Alignment explanation
Indices: 20016466--20016501 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20016456 ACAGTCATTC
20016466 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
20016502 CACATTATGG
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:20020515 original size:12 final size:12
Alignment explanation
Indices: 20020498--20020524 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20020488 TATGTGTATA
20020498 ATTATTATAATT
1 ATTATTATAATT
20020510 ATTATTATAATT
1 ATTATTATAATT
20020522 ATT
1 ATT
20020525 CATTCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTATAATT
Found at i:20020873 original size:20 final size:19
Alignment explanation
Indices: 20020840--20020891 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
20020830 TATTAAACAT
*
20020840 AAAGTAAAATAAAACAAAGCA
1 AAAG-AAAAGAAAACAAAG-A
*
20020861 AAAGAAAAGAAAAGAAAGA
1 AAAGAAAAGAAAACAAAGA
*
20020880 AACAGAATAGAA
1 AA-AGAAAAGAA
20020892 GGAGACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 20 0.74
21 4 0.15
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAGAAAAGAAAACAAAGA
Found at i:20021995 original size:39 final size:39
Alignment explanation
Indices: 20021933--20022047 Score: 151
Period size: 39 Copynumber: 3.0 Consensus size: 39
20021923 TTACTGATCA
* *
20021933 GGCAC-TTATGTGCCGACTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
* *
20021971 GGCACTTTGTGTGTCGAATACTGTTACTGTTACCAATTC
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
* * * *
20022010 GGCACTTGGTGTGGCGAATACTGTTACCGTTACTGATT
1 GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATT
20022048 ACTGCTACTG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
38 5 0.07
39 62 0.93
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (39 bp):
GGCACTTTGTGTGCCGAATACTGTTACTGTTACCGATTC
Found at i:20030842 original size:16 final size:17
Alignment explanation
Indices: 20030821--20030852 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20030811 TTCTTATAAT
20030821 TTTAAAAATTA-AAAAC
1 TTTAAAAATTAGAAAAC
20030837 TTTAAAAATTAGAAAA
1 TTTAAAAATTAGAAAA
20030853 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TTTAAAAATTAGAAAAC
Found at i:20030913 original size:21 final size:20
Alignment explanation
Indices: 20030869--20030919 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
20030859 AAATTTTATT
*
20030869 TTTATAAAAGTACATAAGAT
1 TTTATAAAAGTACATAAGAA
20030889 TTTATAAAAGTTACATACA-AA
1 TTTATAAAAG-TACATA-AGAA
20030910 TTTATCAAAA
1 TTTAT-AAAA
20030920 TATTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTATAAAAGTACATAAGAA
Found at i:20030998 original size:18 final size:18
Alignment explanation
Indices: 20030975--20031011 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20030965 TTTATTTATT
*
20030975 AAAATAATAATTTTATAA
1 AAAATAATAATCTTATAA
20030993 AAAATAATAATCTTATAA
1 AAAATAATAATCTTATAA
20031011 A
1 A
20031012 TAAAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATAATAATCTTATAA
Found at i:20031000 original size:15 final size:17
Alignment explanation
Indices: 20030969--20031008 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
20030959 ATAAAATTTA
20030969 TTTATTAAAATAATAAT
1 TTTATTAAAATAATAAT
*
20030986 TTTATAAAAAATAATAAT
1 TTTAT-TAAAATAATAAT
*
20031004 CTTAT
1 TTTAT
20031009 AAATAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATTAAAATAATAAT
Found at i:20033347 original size:70 final size:71
Alignment explanation
Indices: 20033229--20033372 Score: 245
Period size: 70 Copynumber: 2.0 Consensus size: 71
20033219 AAGCCAACTA
* *
20033229 ACTGCTGTCTTGTTTTGATATATATGTTGCTTGTTAAACATGATTTCATGTGCTGTAATGATGCT
1 ACTGCTGTCTTGTTTTGA-ATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCT
20033294 TAATCCT
65 TAATCCT
*
20033301 ACTGCTGTCTTGTTTTG-ATATATGTTGCTTGTTAAACATGACTTCATGTGTTGCAATGATGCTT
1 ACTGCTGTCTTGTTTTGAATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCTT
20033365 AATCCT
66 AATCCT
20033371 AC
1 AC
20033373 CTTTGAATCT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 52 0.75
72 17 0.25
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.44
Consensus pattern (71 bp):
ACTGCTGTCTTGTTTTGAATATATGTTGCTTGTTAAACATGACTTCATGTGCTGCAATGATGCTT
AATCCT
Found at i:20033822 original size:17 final size:17
Alignment explanation
Indices: 20033787--20033831 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
20033777 ATAAATTTAA
*
20033787 TTATTATTTAACATATT
1 TTATTATTTAAAATATT
20033804 TTATT-TTTAAAATATTT
1 TTATTATTTAAAATA-TT
20033821 TTAATTATTTA
1 TT-ATTATTTA
20033832 TTCTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 9 0.38
18 3 0.12
19 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATTTAAAATATT
Found at i:20035495 original size:46 final size:46
Alignment explanation
Indices: 20035365--20035503 Score: 199
Period size: 46 Copynumber: 3.0 Consensus size: 46
20035355 ACATTGTTAT
* * * *
20035365 AACTCAGTATGGTTTTCTTCACTGAAACACCATACTTAATTTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
20035411 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
20035457 AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
20035503 A
1 A
20035504 CTTTGCCATG
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 81 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:20036764 original size:16 final size:17
Alignment explanation
Indices: 20036718--20036765 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
20036708 AAATTCTTTT
20036718 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
20036735 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
20036752 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
20036766 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:20036956 original size:24 final size:24
Alignment explanation
Indices: 20036922--20036967 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20036912 TTGGCTTCGG
* **
20036922 TGAGATTGAAAATGTCAGTGGCGA
1 TGAGATCGAAAATCACAGTGGCGA
20036946 TGAGATCGAAAATCACAGTGGC
1 TGAGATCGAAAATCACAGTGGC
20036968 AGACTCAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (24 bp):
TGAGATCGAAAATCACAGTGGCGA
Found at i:20037119 original size:22 final size:23
Alignment explanation
Indices: 20037069--20037129 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 23
20037059 AGTTGTTAAA
20037069 AATAATTATCAATATATAATAATT
1 AATAATTA-CAATATATAATAATT
* *
20037093 -A-AATTA-AATTTATATTAATT
1 AATAATTACAATATATAATAATT
*
20037113 AATAATTATTAATATAT
1 AATAATTA-CAATATAT
20037130 GTTAACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 10 0.33
23 1 0.03
24 6 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATAATTACAATATATAATAATT
Found at i:20043342 original size:11 final size:11
Alignment explanation
Indices: 20043328--20043370 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
20043318 TTCTACGTTC
20043328 TTCTTTTCTTT
1 TTCTTTTCTTT
*
20043339 TTCTTTTGTTT
1 TTCTTTTCTTT
* *
20043350 TTTTTTTCATT
1 TTCTTTTCTTT
*
20043361 TTCCTTTCTT
1 TTCTTTTCTT
20043371 CACTATAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:20047406 original size:50 final size:51
Alignment explanation
Indices: 20047292--20047418 Score: 161
Period size: 50 Copynumber: 2.5 Consensus size: 51
20047282 CGGATATCCG
* ** *
20047292 GTGGCCTGCACATAGTACCACTTTTGTAGTCAAAGCTACCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAA
* *
20047343 GTGGCGC-TCACATAGTACCACACTTGT-GACCAAAGCTATC-TCTTCTCAAA
1 GTGGC-CTTCACATAGTACCACACTTGTAG-CCAAAGCTACCTTCTTCACAAA
20047393 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
20047419 AGTCACTAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
49 1 0.01
50 34 0.51
51 31 0.46
52 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTAGCCAAAGCTACCTTCTTCACAAA
Found at i:20049095 original size:53 final size:53
Alignment explanation
Indices: 20049015--20049121 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
20049005 ACTGAACCTG
20049015 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
*
20049068 TATAACCAAGATACACCCAAATATATTATTAATACAACCCGAATCAAATTAAC
1 TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
20049121 T
1 T
20049122 TACACTTCCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.49, C:0.23, G:0.04, T:0.24
Consensus pattern (53 bp):
TATAACCAAGATACACCCAAATATATTATCAATACAACCCGAATCAAATTAAC
Found at i:20050410 original size:35 final size:36
Alignment explanation
Indices: 20050331--20050410 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 36
20050321 TATACAATTC
20050331 ATACATTTTATTTCAACTTATAGAATTTAAAAAACATAT
1 ATACATTTTATTTCAACTTATAGAATTT---AAACATAT
* *
20050370 ATACATTTTATTTTAACTTATAGAATTT-CACATAT
1 ATACATTTTATTTCAACTTATAGAATTTAAACATAT
20050405 ATACAT
1 ATACAT
20050411 AATCGGCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 12 0.31
39 27 0.69
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
ATACATTTTATTTCAACTTATAGAATTTAAACATAT
Found at i:20059354 original size:23 final size:23
Alignment explanation
Indices: 20059324--20059372 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
20059314 TATTTGTAGA
20059324 TAAAAAGAAGAAGAAGATATGTT
1 TAAAAAGAAGAAGAAGATATGTT
20059347 TAAAAAGAAGAAGAAGATATGTT
1 TAAAAAGAAGAAGAAGATATGTT
20059370 TAA
1 TAA
20059373 GAATTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.22
Consensus pattern (23 bp):
TAAAAAGAAGAAGAAGATATGTT
Found at i:20073751 original size:28 final size:28
Alignment explanation
Indices: 20073719--20073773 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
20073709 TTTAAGTGTT
*
20073719 AAAGTTGTTATTCTGCTATTTTTAAAAA
1 AAAGTTGTTATTATGCTATTTTTAAAAA
20073747 AAAGTTGTTATTATGCTATTTTTAAAA
1 AAAGTTGTTATTATGCTATTTTTAAAA
20073774 GCTGACACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.47
Consensus pattern (28 bp):
AAAGTTGTTATTATGCTATTTTTAAAAA
Found at i:20079823 original size:2 final size:2
Alignment explanation
Indices: 20079818--20079850 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20079808 AGTCCCCTTT
20079818 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
20079851 TTGTTGTTAT
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:20080050 original size:21 final size:21
Alignment explanation
Indices: 20080009--20080050 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20079999 CATAGATTAC
* *
20080009 ATTGTTTATTATTTTTTTGCT
1 ATTGTTTACTATTTTTCTGCT
20080030 ATTGTTT-CTATTGTTTCTGCT
1 ATTGTTTACTATT-TTTCTGCT
20080051 TTCGTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (21 bp):
ATTGTTTACTATTTTTCTGCT
Found at i:20082270 original size:39 final size:39
Alignment explanation
Indices: 20082211--20082296 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
20082201 GAGCTCAACC
*
20082211 TTTTAGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
1 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
20082250 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
1 TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
20082289 TTTTTGAT
1 TTTTTGAT
20082297 GGGTAGCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (39 bp):
TTTTTGATTGTTTTGGCAGACAAAAGGGGAAAAAAATTG
Found at i:20086686 original size:21 final size:22
Alignment explanation
Indices: 20086642--20086690 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
20086632 ATTTTTAAAT
20086642 TTAATAAATTAAAAAATAGATAA
1 TTAA-AAATTAAAAAATAGATAA
20086665 TTAAAAATTAAAATAA-AG-TAA
1 TTAAAAATTAAAA-AATAGATAA
20086686 TTAAA
1 TTAAA
20086691 CCATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
TTAAAAATTAAAAAATAGATAA
Found at i:20086911 original size:21 final size:21
Alignment explanation
Indices: 20086873--20086913 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20086863 ACCGTTAATT
* **
20086873 TTATTTTTAAATTTAATGTAA
1 TTATTTATAAATAAAATGTAA
20086894 TTATTTATAAATAAAATGTA
1 TTATTTATAAATAAAATGTA
20086914 GAATATTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTTATAAATAAAATGTAA
Found at i:20087587 original size:21 final size:20
Alignment explanation
Indices: 20087562--20087601 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20087552 AAAATTACAA
20087562 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
* *
20087582 AAAAAATTCCAAATTTTTAT
1 AAAAAATTCAAAATATTTAT
20087602 TTTAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:20087641 original size:22 final size:23
Alignment explanation
Indices: 20087615--20087658 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20087605 AAGAAATTAT
*
20087615 ATATATTTAAA-AAATCTAAAAA
1 ATATATATAAAGAAATCTAAAAA
*
20087637 ATATATATAAAGAAATTTAAAA
1 ATATATATAAAGAAATCTAAAA
20087659 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
ATATATATAAAGAAATCTAAAAA
Found at i:20091013 original size:159 final size:159
Alignment explanation
Indices: 20090840--20091228 Score: 667
Period size: 159 Copynumber: 2.5 Consensus size: 159
20090830 CGGCACCCCA
* *
20090840 CATTTGTTCGTATTTTTCTTATTTTCGAATTTTATTACTTTCAAAAAATATACTATTTTTATATT
1 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTATT
*
20090905 TTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATA
66 TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATA
*
20090970 TAAATTTTGTAAAAAACCCTCATTTTGGC
131 TAAATTTAGTAAAAAACCCTCATTTTGGC
20090999 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTATT
1 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTATT
* *
20091064 TTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTTATA
66 TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATA
* *
20091129 TAAATTTAGTGAAAAACCCTTATTTTGGC
131 TAAATTTAGTAAAAAACCCTCATTTTGGC
**
20091158 CATTTGTTCGTATTTTTCTT-TTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTTGT-TT
1 CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTATT
20091221 TT-TTATTT
66 TTATTATTT
20091229 CTTTTCGTAT
Statistics
Matches: 220, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
156 6 0.03
157 4 0.02
158 39 0.18
159 171 0.78
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.56
Consensus pattern (159 bp):
CATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTTGTATT
TTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATA
TAAATTTAGTAAAAAACCCTCATTTTGGC
Found at i:20091870 original size:2 final size:2
Alignment explanation
Indices: 20091858--20091899 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20091848 TGTAAATATT
*
20091858 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20091900 TTACCAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20094355 original size:113 final size:114
Alignment explanation
Indices: 20094157--20094375 Score: 422
Period size: 113 Copynumber: 1.9 Consensus size: 114
20094147 CCATCAAGAA
*
20094157 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGTCCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
20094222 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCT-GTCATTAGAGGAGT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATTAGAGGAGT
20094270 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
1 ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
20094335 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATT
66 ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATT
20094376 CCCATGCTTC
Statistics
Matches: 104, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
113 98 0.94
114 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (114 bp):
ATCTATATTATAAGCTAAAATATTATAGAGGAGTATTTCAAGTCATGACCCGAGTGCCTACCTGA
ATGTGCTTAAAAAGAACATTGACTCTCAGAGGCTCGTCATTAGAGGAGT
Found at i:20097410 original size:22 final size:21
Alignment explanation
Indices: 20097384--20097444 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
20097374 ATCTAAATTC
*
20097384 AAATTAAATAATAAAATTATCT
1 AAATTAAAT-ATAAAATTATAT
* *
20097406 AAATTTAAGTATAAAAATATAT
1 AAA-TTAAATATAAAATTATAT
*
20097428 AAATATTAATATAAAAT
1 AAAT-TAAATATAAAAT
20097445 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.81
23 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTAAATATAAAATTATAT
Found at i:20102351 original size:21 final size:21
Alignment explanation
Indices: 20102327--20102376 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
20102317 CATTGTTTCT
* *
20102327 AATCTCACTGCTACAATATCC
1 AATCTCACAGCTACAATAACC
* *
20102348 AATCTCACAGCTACAGTAACT
1 AATCTCACAGCTACAATAACC
20102369 AATCTCAC
1 AATCTCAC
20102377 CACCACCGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.06, T:0.26
Consensus pattern (21 bp):
AATCTCACAGCTACAATAACC
Found at i:20102799 original size:25 final size:24
Alignment explanation
Indices: 20102765--20102812 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
20102755 ATGTATTAAA
* *
20102765 ATATTTTAATAGTTATATAATAAC
1 ATATTTTAATAATTAAATAATAAC
20102789 ATATATTTAATAATTAAATAATAA
1 ATAT-TTTAATAATTAAATAATAA
20102813 TTTGAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTTAATAATTAAATAATAAC
Found at i:20105494 original size:12 final size:12
Alignment explanation
Indices: 20105477--20105502 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20105467 AACATTGATA
20105477 TATAATATTACG
1 TATAATATTACG
20105489 TATAATATTACG
1 TATAATATTACG
20105501 TA
1 TA
20105503 AATTTCCTTA
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:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TATAATATTACG
Found at i:20106164 original size:20 final size:20
Alignment explanation
Indices: 20106139--20106198 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
20106129 GTAATCTTAT
20106139 AATCATAAATCATAACCATA
1 AATCATAAATCATAACCATA
*
20106159 AATCATTCAAAT--TAAACATA
1 AATCA-T-AAATCATAACCATA
20106179 AATCATATAATCATAACCAT
1 AATCATA-AATCATAACCAT
20106199 TTTAGTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 17 0.52
21 7 0.21
22 4 0.12
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.28
Consensus pattern (20 bp):
AATCATAAATCATAACCATA
Found at i:20106863 original size:23 final size:23
Alignment explanation
Indices: 20106832--20106876 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
20106822 TACAATCAAC
20106832 ATTACACATATC-AACAAGCCATA
1 ATTACACAT-TCAAACAAGCCATA
*
20106855 ATTAGACATTCAAAACAAGCCA
1 ATTACACATTC-AAACAAGCCA
20106877 AAATAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 8 0.42
24 9 0.47
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (23 bp):
ATTACACATTCAAACAAGCCATA
Found at i:20110056 original size:5 final size:5
Alignment explanation
Indices: 20110044--20110074 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
20110034 AAGGAAAATT
20110044 TCTT- TCTTC TCTTC TCTTC TCTTC TCTTC TC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TC
20110075 ACGTGGGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTTC
Found at i:20113848 original size:15 final size:17
Alignment explanation
Indices: 20113797--20113868 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 17
20113787 AAAACAAATA
*
20113797 AAAAAAAGAAAGAAAAG
1 AAAAAGAGAAAGAAAAG
** *
20113814 --AAAGCCAAACGAAAAC
1 AAAAAGAGAAA-GAAAAG
20113830 AAAAAG-GAAA-AAAAG
1 AAAAAGAGAAAGAAAAG
20113845 AAAAAAGAGAAAGAGAAAG
1 -AAAAAGAGAAAGA-AAAG
20113864 AAAAA
1 AAAAA
20113869 CGCAAGGCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
15 10 0.24
16 11 0.26
17 7 0.17
18 10 0.24
19 4 0.10
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAAAGAAAAG
Found at i:20114157 original size:25 final size:26
Alignment explanation
Indices: 20114124--20114180 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
20114114 TATATATATT
* * *
20114124 ATAATAATAAATTAATGTATAATAAA
1 ATAATAATAAATAAATGAATAAAAAA
*
20114150 ATAA-AATAAGTAAATGAATAAAAAA
1 ATAATAATAAATAAATGAATAAAAAA
20114175 ATAATA
1 ATAATA
20114181 GAAAGCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATAATAAATAAATGAATAAAAAA
Found at i:20114643 original size:19 final size:20
Alignment explanation
Indices: 20114619--20114659 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
20114609 GAATTTAGGA
*
20114619 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
20114638 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
20114658 AA
1 AA
20114660 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:20127630 original size:29 final size:29
Alignment explanation
Indices: 20127596--20127665 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 29
20127586 TAAATTTTGT
*
20127596 TTTGATCACTTAATTAAAAAAAGTTATAA
1 TTTGATCAATTAATTAAAAAAAGTTATAA
20127625 TTTGATCATTGAATTAATTAAAAAAAGTTATAA
1 TTTGATC----AATTAATTAAAAAAAGTTATAA
20127658 TTTGATCA
1 TTTGATCA
20127666 TTGAACTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 8 0.22
33 28 0.78
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTGATCAATTAATTAAAAAAAGTTATAA
Found at i:20127647 original size:33 final size:33
Alignment explanation
Indices: 20127605--20127670 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
20127595 TTTTGATCAC
20127605 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
1 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
20127638 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
1 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
20127671 CTATTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (33 bp):
TTAATTAAAAAAAGTTATAATTTGATCATTGAA
Found at i:20127697 original size:30 final size:31
Alignment explanation
Indices: 20127663--20127737 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
20127653 TATAATTTGA
*
20127663 TCATTGAACTATTTGAAAG-TTTTACTTAAG
1 TCATTGAACTATTTAAAAGTTTTTACTTAAG
* *
20127693 TCATTGAACTATTCAAAAGTTTTTATTTAAG
1 TCATTGAACTATTTAAAAGTTTTTACTTAAG
*
20127724 TCATTGGACTATTT
1 TCATTGAACTATTT
20127738 TTTTTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (31 bp):
TCATTGAACTATTTAAAAGTTTTTACTTAAG
Found at i:20129833 original size:3 final size:3
Alignment explanation
Indices: 20129825--20129854 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20129815 AAATAAGCCC
20129825 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20129855 TGAATGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20140964 original size:66 final size:66
Alignment explanation
Indices: 20140883--20141016 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
20140873 GACGAACATC
20140883 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
1 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
20140948 T
66 T
20140949 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
1 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
20141014 T
66 T
20141015 AT
1 AT
20141017 GATCTTATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (66 bp):
ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
T
Found at i:20148180 original size:22 final size:23
Alignment explanation
Indices: 20148127--20148182 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
20148117 TTTAATTAAA
* * *
20148127 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
20148150 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
20148172 ATTAAAATTAA
1 ATTAAAATTAA
20148183 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:20148195 original size:16 final size:16
Alignment explanation
Indices: 20148158--20148197 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
20148148 TTAATAAAAT
* *
20148158 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
20148174 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
20148190 TAAAATTA
1 TAAAATTA
20148198 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:20148303 original size:9 final size:9
Alignment explanation
Indices: 20148270--20148297 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148260 TTTATCAAAT
20148270 TATTAATTG
1 TATTAATTG
20148279 TATTAATTG
1 TATTAATTG
20148288 TATTAATTG
1 TATTAATTG
20148297 T
1 T
20148298 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148307 original size:68 final size:68
Alignment explanation
Indices: 20148186--20148827 Score: 1261
Period size: 68 Copynumber: 9.5 Consensus size: 68
20148176 AAATTAATTG
*
20148186 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148249 TGA
66 TGA
20148252 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148317 TGA
66 TGA
20148320 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148385 TGA
66 TGA
20148388 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148453 TGA
66 TGA
20148456 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148521 TGA
66 TGA
20148524 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148589 TGA
66 TGA
20148592 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148657 TGA
66 TGA
20148660 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148725 TGA
66 TGA
20148728 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
20148793 TGA
66 TGA
20148796 TTAGTAAATTTATCAAATTATTAATTGTATTA
1 TTAGTAAATTTATCAAATTATTAATTGTATTA
20148828 TAAATAATAT
Statistics
Matches: 573, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
66 26 0.05
68 547 0.95
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:20148371 original size:9 final size:9
Alignment explanation
Indices: 20148338--20148365 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148328 TTTATCAAAT
20148338 TATTAATTG
1 TATTAATTG
20148347 TATTAATTG
1 TATTAATTG
20148356 TATTAATTG
1 TATTAATTG
20148365 T
1 T
20148366 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148439 original size:9 final size:9
Alignment explanation
Indices: 20148406--20148433 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148396 TTTATCAAAT
20148406 TATTAATTG
1 TATTAATTG
20148415 TATTAATTG
1 TATTAATTG
20148424 TATTAATTG
1 TATTAATTG
20148433 T
1 T
20148434 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148507 original size:9 final size:9
Alignment explanation
Indices: 20148474--20148501 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148464 TTTATCAAAT
20148474 TATTAATTG
1 TATTAATTG
20148483 TATTAATTG
1 TATTAATTG
20148492 TATTAATTG
1 TATTAATTG
20148501 T
1 T
20148502 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148575 original size:9 final size:9
Alignment explanation
Indices: 20148542--20148569 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148532 TTTATCAAAT
20148542 TATTAATTG
1 TATTAATTG
20148551 TATTAATTG
1 TATTAATTG
20148560 TATTAATTG
1 TATTAATTG
20148569 T
1 T
20148570 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148643 original size:9 final size:9
Alignment explanation
Indices: 20148610--20148637 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148600 TTTATCAAAT
20148610 TATTAATTG
1 TATTAATTG
20148619 TATTAATTG
1 TATTAATTG
20148628 TATTAATTG
1 TATTAATTG
20148637 T
1 T
20148638 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148711 original size:9 final size:9
Alignment explanation
Indices: 20148678--20148705 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148668 TTTATCAAAT
20148678 TATTAATTG
1 TATTAATTG
20148687 TATTAATTG
1 TATTAATTG
20148696 TATTAATTG
1 TATTAATTG
20148705 T
1 T
20148706 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20148779 original size:9 final size:9
Alignment explanation
Indices: 20148746--20148773 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20148736 TTTATCAAAT
20148746 TATTAATTG
1 TATTAATTG
20148755 TATTAATTG
1 TATTAATTG
20148764 TATTAATTG
1 TATTAATTG
20148773 T
1 T
20148774 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:20151248 original size:16 final size:16
Alignment explanation
Indices: 20151227--20151260 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20151217 GTGATTTGAT
*
20151227 AAAAAATAAAAATTTA
1 AAAAAATAAAAAATTA
20151243 AAAAAATAAAAAATTA
1 AAAAAATAAAAAATTA
20151259 AA
1 AA
20151261 TGAATGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAAAATTA
Found at i:20151869 original size:34 final size:34
Alignment explanation
Indices: 20151831--20151902 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
20151821 ATCCTGGTAA
* *
20151831 ATTTTTT-TTAATGATTTTTTGTTTCTTCTTTTAG
1 ATTTTTTCTGAATGA-TTTTTGTTTCTTATTTTAG
20151865 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
1 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
20151899 ATTT
1 ATTT
20151903 ATGATCTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.68
Consensus pattern (34 bp):
ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
Found at i:20154521 original size:14 final size:15
Alignment explanation
Indices: 20154499--20154531 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20154489 AACTAATATT
*
20154499 TTATTTTTTA-AAAA
1 TTATGTTTTAGAAAA
20154513 TTATGTTTTAGAAAA
1 TTATGTTTTAGAAAA
20154528 TTAT
1 TTAT
20154532 ATTTCTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTATGTTTTAGAAAA
Found at i:20173444 original size:10 final size:10
Alignment explanation
Indices: 20173429--20173459 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
20173419 TATCAAATAG
20173429 ATAAAGTTTA
1 ATAAAGTTTA
20173439 ATAAAGTTTA
1 ATAAAGTTTA
20173449 ATAAAGTTTA
1 ATAAAGTTTA
20173459 A
1 A
20173460 AAAACCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (10 bp):
ATAAAGTTTA
Found at i:20175271 original size:8 final size:9
Alignment explanation
Indices: 20175257--20175289 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
20175247 CAGACGGTCT
20175257 TATATATACA
1 TATATAT-CA
20175267 TATATATCA
1 TATATATCA
20175276 TAT-TATCA
1 TATATATCA
20175284 TATATA
1 TATATA
20175290 CTTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 7 0.32
10 7 0.32
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATATCA
Found at i:20182264 original size:16 final size:16
Alignment explanation
Indices: 20182243--20182274 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20182233 TCATACAAAA
20182243 TGAGCTTCGACTACAC
1 TGAGCTTCGACTACAC
20182259 TGAGCTTCGACTACAC
1 TGAGCTTCGACTACAC
20182275 GTGTTGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (16 bp):
TGAGCTTCGACTACAC
Found at i:20188456 original size:23 final size:23
Alignment explanation
Indices: 20188424--20188485 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
20188414 ATATGTATAC
* * *
20188424 TAAAATAAATATATACATATAGA
1 TAAAAAAAATATATACAAATAAA
* *
20188447 TAAAAAAAATACATATAAATAAA
1 TAAAAAAAATATATACAAATAAA
20188470 TAAAAAATAATTATAT
1 TAAAAAA-AA-TATAT
20188486 TATACTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 25 0.81
24 2 0.06
25 4 0.13
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAAAAAATATATACAAATAAA
Found at i:20188460 original size:19 final size:20
Alignment explanation
Indices: 20188426--20188475 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
20188416 ATGTATACTA
*
20188426 AAATAAATATATACATATAGAT
1 AAATAAA-A-ATACATATAAAT
20188448 AAA-AAAAATACATATAAAT
1 AAATAAAAATACATATAAAT
20188467 AAATAAAAA
1 AAATAAAAA
20188476 ATAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 14 0.54
20 6 0.23
21 3 0.12
22 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATAAAAATACATATAAAT
Found at i:20188534 original size:21 final size:21
Alignment explanation
Indices: 20188495--20188535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20188485 TTATACTACA
* *
20188495 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
20188516 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
20188536 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:20188574 original size:27 final size:28
Alignment explanation
Indices: 20188544--20188603 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
20188534 ATATATTTTT
20188544 TAAAAATAACTAAAT-ATAAAAAAAGAA
1 TAAAAATAACTAAATAATAAAAAAAGAA
* *
20188571 TAAAAA-AACTAATTAATAAAAAAATAA
1 TAAAAATAACTAAATAATAAAAAAAGAA
20188598 -AAAAAT
1 TAAAAAT
20188604 GAAAAAAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAAAATAACTAAATAATAAAAAAAGAA
Found at i:20188582 original size:26 final size:24
Alignment explanation
Indices: 20188544--20188602 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 24
20188534 ATATATTTTT
20188544 TAAAAATAACTAAATATAA-AAAAAGAA
1 TAAAAA-AACT-AAT-TAATAAAAA-AA
20188571 TAAAAAAACTAATTAATAAAAAAA
1 TAAAAAAACTAATTAATAAAAAAA
20188595 TAAAAAAA
1 TAAAAAAA
20188603 TGAAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 13 0.42
25 8 0.26
26 4 0.13
27 6 0.19
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (24 bp):
TAAAAAAACTAATTAATAAAAAAA
Found at i:20189127 original size:19 final size:19
Alignment explanation
Indices: 20189103--20189178 Score: 125
Period size: 19 Copynumber: 4.0 Consensus size: 19
20189093 NNNNNNNNNN
20189103 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
** *
20189122 ATATCTAAGATTATATATT
1 ATATCTAAGATTGCATATC
20189141 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
20189160 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
20189179 CCTGAAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCTAAGATTGCATATC
Found at i:20190434 original size:3 final size:3
Alignment explanation
Indices: 20190426--20190453 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20190416 CTTTCTCCAG
20190426 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
20190454 CTTTGTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:20192733 original size:29 final size:30
Alignment explanation
Indices: 20192669--20192737 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
20192659 TATTAATTTA
20192669 TAATTTTATCATTTTTGAAGGAATTAAATAG
1 TAATTTTATCATTTTT-AAGGAATTAAATAG
*
20192700 AAATTATT-TCATTTTT-AGGAAGTTAAAT-G
1 TAATT-TTATCATTTTTAAGGAA-TTAAATAG
20192729 TAATTTTAT
1 TAATTTTAT
20192738 TATATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
28 2 0.06
29 11 0.33
30 6 0.18
31 12 0.36
32 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (30 bp):
TAATTTTATCATTTTTAAGGAATTAAATAG
Found at i:20196035 original size:46 final size:45
Alignment explanation
Indices: 20195968--20196106 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
20195958 CATGGAAAAG
20195968 TGTGAAACA-TAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGGTATGGTATTCC-GTGAAGAAAACCATACTGAGT
* * *
20196014 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAAACATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTCCGTGAAGAAAACCATACTGAGT
20196060 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTCCGTGAAGAAAACCATACTGAGT
20196106 T
1 T
20196107 ATAGCCTTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
45 1 0.01
46 81 0.95
47 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (45 bp):
TGTGAAAAGTAGGTATGGTATTCCGTGAAGAAAACCATACTGAGT
Found at i:20200238 original size:23 final size:25
Alignment explanation
Indices: 20200208--20200264 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
20200198 AAATTTTATT
20200208 ATTATAAATATTATACATTC-AT-A
1 ATTATAAATATTATACATTCAATCA
*
20200231 ATTATAAATA-TATATATTCAATCA
1 ATTATAAATATTATACATTCAATCA
20200255 ATTA-AAATAT
1 ATTATAAATAT
20200265 AAAGTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.27
23 17 0.57
24 5 0.17
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATAAATATTATACATTCAATCA
Found at i:20200272 original size:21 final size:24
Alignment explanation
Indices: 20200208--20200272 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 24
20200198 AAATTTTATT
* *
20200208 ATTATAAATATTATACATTC-AT-A
1 ATTATAAATA-TATATAGTCAATCA
*
20200231 ATTATAAATATATATATTCAATCA
1 ATTATAAATATATATAGTCAATCA
20200255 ATTA-AAATATA-A-AGTCAA
1 ATTATAAATATATATAGTCAA
20200273 AACAGTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.13
22 9 0.24
23 19 0.50
24 5 0.13
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTATAAATATATATAGTCAATCA
Found at i:20211799 original size:51 final size:50
Alignment explanation
Indices: 20211672--20211809 Score: 179
Period size: 50 Copynumber: 2.7 Consensus size: 50
20211662 AAAGTAATGG
*
20211672 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGA
* * * * * * *
20211722 TCGCATGTGTAGTACTATGTGCAGGCTATTATGTGTACTGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATAGA
20211773 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
20211810 TCAGATGGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
49 2 0.03
50 37 0.50
51 35 0.47
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGA
Found at i:20211833 original size:51 final size:48
Alignment explanation
Indices: 20211669--20211854 Score: 183
Period size: 51 Copynumber: 3.7 Consensus size: 48
20211659 GTGAAAGTAA
* *
20211669 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGG-ATGGT
* * * * *
20211719 AGGTCGCATGTGTAGTACTATGTGCAGGCTATTATGTGTACTGGATAGTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GGAT-GGT
* * *
20211769 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGGT
* * *
20211819 CGTGGTCATATGTGTAGTACTATATGTAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
20211855 TGTGAACCGA
Statistics
Matches: 111, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
49 3 0.03
50 41 0.37
51 65 0.59
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (48 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATGGT
Found at i:20213826 original size:45 final size:45
Alignment explanation
Indices: 20213761--20213909 Score: 196
Period size: 45 Copynumber: 3.4 Consensus size: 45
20213751 GGGTGTTACA
* *
20213761 GATTCCACCAGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCT
1 GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
*
20213806 GATTCCACCGGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCT
1 GATTCCACCGGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCT
* * * *
20213851 GATTCCACTGAGTATCATTGACTATAAGGGTGG-TGCTATGTGCT
1 GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
*
20213895 GA-TCCACCGTGTATC
1 GATTCCACCGGGTATC
20213910 TGTTATTATT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
43 11 0.12
44 14 0.15
45 66 0.72
46 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (45 bp):
GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
Found at i:20216410 original size:41 final size:41
Alignment explanation
Indices: 20216353--20216485 Score: 212
Period size: 41 Copynumber: 3.2 Consensus size: 41
20216343 NNNNNNNNNN
20216353 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
*
20216394 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGACA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
** * * *
20216435 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
20216476 AGCCTGCTAG
1 AGCCTGCTAG
20216486 GCACCGAGCT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:20218091 original size:28 final size:26
Alignment explanation
Indices: 20218060--20218111 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
20218050 TTTTTAATGT
20218060 TTATTATAACATAATAATATATTATACC
1 TTATTATAACAT-AT-ATATATTATACC
20218088 TTATTATAACATATATATATTATA
1 TTATTATAACATATATATATTATA
20218112 TTAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 2 0.08
28 12 0.50
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATTATAACATATATATATTATACC
Found at i:20219994 original size:21 final size:23
Alignment explanation
Indices: 20219969--20220020 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
20219959 AAAAATAAAC
20219969 GCATGTAA-AAAA-TTTAATGTT
1 GCATGTAATAAAATTTTAATGTT
20219990 GCATGTATAATAAAATTTTAATGTT
1 GCATG--TAATAAAATTTTAATGTT
20220015 GCATGT
1 GCATGT
20220021 GTAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.19
23 4 0.15
24 4 0.15
25 14 0.52
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (23 bp):
GCATGTAATAAAATTTTAATGTT
Found at i:20220010 original size:25 final size:25
Alignment explanation
Indices: 20219976--20220027 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
20219966 AACGCATGTA
20219976 AAAAATTTAATGTTGCATGTATAAT
1 AAAAATTTAATGTTGCATGTATAAT
* *
20220001 AAAATTTTAATGTTGCATGTGTAAT
1 AAAAATTTAATGTTGCATGTATAAT
20220026 AA
1 AA
20220028 TAACACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (25 bp):
AAAAATTTAATGTTGCATGTATAAT
Found at i:20239132 original size:24 final size:24
Alignment explanation
Indices: 20239098--20239149 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20239088 TTTTTAGAAG
* **
20239098 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
20239122 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
20239146 ATTT
1 ATTT
20239150 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:20277449 original size:30 final size:30
Alignment explanation
Indices: 20277409--20277465 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
20277399 ATATATATAT
*
20277409 ATATATATAACCCTTTTCCGGATAGTCAAA
1 ATATACATAACCCTTTTCCGGATAGTCAAA
*
20277439 ATATACATAACCCTTTTCTGGATAGTC
1 ATATACATAACCCTTTTCCGGATAGTC
20277466 GGAAGCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (30 bp):
ATATACATAACCCTTTTCCGGATAGTCAAA
Found at i:20281908 original size:21 final size:19
Alignment explanation
Indices: 20281882--20281923 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
20281872 TAAAAAATCC
20281882 AAAAATATCATAAAATTATTT
1 AAAAATATCAT-AAATT-TTT
*
20281903 AAAAATTTCATAAATTTTT
1 AAAAATATCATAAATTTTT
20281922 AA
1 AA
20281924 GATTTTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATATCATAAATTTTT
Done.