Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003370.1 Hibiscus syriacus cultivar Beakdansim tig00007084_pilon, whole genome shotgun sequence
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: 109560
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:238 original size:43 final size:43
Alignment explanation
Indices: 190--279 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
180 ATAAATGATT
* * *
190 AATTAGGAGAC-TCAATTATAAATGTA-AAATGTGAGATTAAAAA
1 AATTAGGAG-CTTCAATTATAAATATAGAAA-GTAAAATTAAAAA
*
233 AATTAGGTGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
1 AATTAGGAGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
276 AATT
1 AATT
280 GATATTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 37 0.90
44 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (43 bp):
AATTAGGAGCTTCAATTATAAATATAGAAAGTAAAATTAAAAA
Found at i:6271 original size:2 final size:2
Alignment explanation
Indices: 6264--6290 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6254 TTTTATTTAT
6264 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
6291 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6896 original size:24 final size:23
Alignment explanation
Indices: 6869--6923 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
6859 CTATGATACA
* *
6869 AAATAATATTATTTTTATAATCAT
1 AAATAATATTAATTGTAT-ATCAT
* *
6893 AAATAAAATTAATTGTATATTAT
1 AAATAATATTAATTGTATATCAT
6916 AAATAATA
1 AAATAATA
6924 AATCTTCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
AAATAATATTAATTGTATATCAT
Found at i:8546 original size:32 final size:32
Alignment explanation
Indices: 8510--8580 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
8500 ATAGTGACCG
8510 TTATATAACGATAATAATATTGTCGGAAACCA
1 TTATATAACGATAATAATATTGTCGGAAACCA
**
8542 TTATATAACGATAATAATATTGTCGGAAACTG
1 TTATATAACGATAATAATATTGTCGGAAACCA
8574 TTATATA
1 TTATATA
8581 TATACTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
TTATATAACGATAATAATATTGTCGGAAACCA
Found at i:12184 original size:60 final size:60
Alignment explanation
Indices: 12050--12188 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
12040 AATATAATGA
* * *
12050 ATAGTCG-GGTGATCATTTTGTAACGTTTAATAGTCGAGAGACTTAATAAAGCAACATTCT
1 ATAGTCGAGG-GACCATTTTGTAACGTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
* ** * * * * **
12110 ATAGTCAAAAGACCATTTTGTAACTTTTAATGGT-GAAGGGACTTAATAAAATAGTATCCT
1 ATAGTCGAGGGACCATTTTGTAACGTTTAATAGTCG-AGAGACTTAATAAAACAACATCCT
12170 ATAGTCGAGGGACCATTTT
1 ATAGTCGAGGGACCATTTT
12189 TTTACTTTAC
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
59 1 0.02
60 61 0.98
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (60 bp):
ATAGTCGAGGGACCATTTTGTAACGTTTAATAGTCGAGAGACTTAATAAAACAACATCCT
Found at i:15281 original size:29 final size:29
Alignment explanation
Indices: 15248--15315 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
15238 AACATAGGTT
*
15248 TTCATGGAGAATCTAATTTTATTTTGTGG
1 TTCATGGAGAATCTAATTTTATTTTGTGA
15277 TTCATGGAGAATCTAATTTTATTTTGTGA
1 TTCATGGAGAATCTAATTTTATTTTGTGA
*
15306 TTAATGGAGA
1 TTCATGGAGA
15316 TATCACGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (29 bp):
TTCATGGAGAATCTAATTTTATTTTGTGA
Found at i:17095 original size:2 final size:2
Alignment explanation
Indices: 17090--17118 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17080 ATAGATTTAA
17090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17119 AAGAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18139 original size:11 final size:11
Alignment explanation
Indices: 18123--18150 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
18113 TGTATTCTAT
18123 TAATTTTATCA
1 TAATTTTATCA
18134 TAATTTTATCA
1 TAATTTTATCA
18145 TAATTT
1 TAATTT
18151 AATATTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTTTATCA
Found at i:18445 original size:24 final size:26
Alignment explanation
Indices: 18412--18472 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
18402 GAATACATTT
* *
18412 TATATATATTTAAAAT-TGT-AATCAA
1 TATA-ATATTTAAAATAAGTAAATAAA
18437 TATAATATTTAAAATAAGTAAATAAA
1 TATAATATTTAAAATAAGTAAATAAA
18463 TATAATATTT
1 TATAATATTT
18473 TTAAACTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 6 0.19
26 15 0.47
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAATATTTAAAATAAGTAAATAAA
Found at i:22660 original size:24 final size:25
Alignment explanation
Indices: 22610--22661 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
22600 GCTTTTATCC
* *
22610 TCTAAAATTTTATAAATTTATTCTT
1 TCTAAAATTATATAAATTTAATCTT
*
22635 TCTAAAATTATATAATTTTAAT-TT
1 TCTAAAATTATATAAATTTAATCTT
22659 TCT
1 TCT
22662 TAATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (25 bp):
TCTAAAATTATATAAATTTAATCTT
Found at i:25444 original size:11 final size:11
Alignment explanation
Indices: 25427--25497 Score: 79
Period size: 11 Copynumber: 6.5 Consensus size: 11
25417 GAAAATATTC
25427 GTTTAATGTTT
1 GTTTAATGTTT
*
25438 CTTTAATGTTT
1 GTTTAATGTTT
**
25449 GTTTAGCGTTT
1 GTTTAATGTTT
* *
25460 GTTTAACGTTC
1 GTTTAATGTTT
25471 GTTTAATGTTT
1 GTTTAATGTTT
* *
25482 GTTTAGTGTTC
1 GTTTAATGTTT
25493 GTTTA
1 GTTTA
25498 TACATTCAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 50 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.58
Consensus pattern (11 bp):
GTTTAATGTTT
Found at i:25464 original size:33 final size:33
Alignment explanation
Indices: 25424--25497 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
25414 CACGAAAATA
* **
25424 TTCGTTTAATGTTTCTTTAATGTTTGTTTAGCG
1 TTCGTTTAACGTTCGTTTAATGTTTGTTTAGCG
* *
25457 TTTGTTTAACGTTCGTTTAATGTTTGTTTAGTG
1 TTCGTTTAACGTTCGTTTAATGTTTGTTTAGCG
25490 TTCGTTTA
1 TTCGTTTA
25498 TACATTCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (33 bp):
TTCGTTTAACGTTCGTTTAATGTTTGTTTAGCG
Found at i:25481 original size:22 final size:22
Alignment explanation
Indices: 25424--25497 Score: 94
Period size: 22 Copynumber: 3.4 Consensus size: 22
25414 CACGAAAATA
*
25424 TTCGTTTAATGTTTCTTTAATG
1 TTCGTTTAATGTTTGTTTAATG
* ** *
25446 TTTGTTTAGCGTTTGTTTAACG
1 TTCGTTTAATGTTTGTTTAATG
*
25468 TTCGTTTAATGTTTGTTTAGTG
1 TTCGTTTAATGTTTGTTTAATG
25490 TTCGTTTA
1 TTCGTTTA
25498 TACATTCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.15, C:0.08, G:0.19, T:0.58
Consensus pattern (22 bp):
TTCGTTTAATGTTTGTTTAATG
Found at i:40919 original size:174 final size:174
Alignment explanation
Indices: 40604--40920 Score: 437
Period size: 174 Copynumber: 1.8 Consensus size: 174
40594 ATTAATCACA
* * * *
40604 AGGTTGCTCAGGTAACCGCTCAGGATCGACACGATGGTCGAAAGTTTCATGAAGCATTCAATGAA
1 AGGTTGCTCAGGTAACCACTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCAAAGAA
* *
40669 TGCCTTCCACTGTATCCAAAACATCATCATTGCAAACCCAATGGTCAAAATAACATTCAATAACA
66 TGCCTTCCACTGTATCCAAAACATCATCACTGCAAACCCAACGGTCAAAATAACATTCAATAACA
* *
40734 CGAATAAAATAAAGATGAATAGGTAGCACAACAATTAAGTCAAT
131 CAAACAAAATAAAGATGAATAGGTAGCACAACAATTAAGTCAAT
*
40778 AGGTTGGTCAGGTAACCACTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCAACAG-
1 AGGTTGCTCAGGTAACCACTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCAA-AGA
* * *
40842 ATGCCTTCCACTG-ATTCCAAAA-ATTCATCACTG-TAACCCAACGGTC-GAATAACATTGAATA
65 ATGCCTTCCACTGTA-TCCAAAACA-TCATCACTGCAAACCCAACGGTCAAAATAACATTCAAT-
*
40903 AAACATAAACAAAATAAA
127 -AACACAAACAAAATAAA
40921 ATAAAATAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
172 12 0.10
173 13 0.10
174 99 0.79
175 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (174 bp):
AGGTTGCTCAGGTAACCACTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCAAAGAA
TGCCTTCCACTGTATCCAAAACATCATCACTGCAAACCCAACGGTCAAAATAACATTCAATAACA
CAAACAAAATAAAGATGAATAGGTAGCACAACAATTAAGTCAAT
Found at i:42261 original size:30 final size:31
Alignment explanation
Indices: 42203--42265 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
42193 ATTTAAATTT
*
42203 TAATTTGACTCCTAAATTTTAAATAAAATAC
1 TAATTTGACTCCTAAACTTTAAATAAAATAC
* *
42234 TAATTTGAC-CTTAAACTTTAGATAAAATAC
1 TAATTTGACTCCTAAACTTTAAATAAAATAC
42264 TA
1 TA
42266 TCGATCGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (31 bp):
TAATTTGACTCCTAAACTTTAAATAAAATAC
Found at i:45673 original size:27 final size:26
Alignment explanation
Indices: 45640--45726 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 26
45630 TTAAATTCAT
45640 AATATTTTATATATATTAACTTAAAAA
1 AATATTTT-TATATATTAACTTAAAAA
* **
45667 AATA-TTTT-TATATTAAATT-ATTA
1 AATATTTTTATATATTAACTTAAAAA
45690 AATATATTTTAT-TATTAACTTAATCTAAA
1 AATAT-TTTTATATATTAACTTAA---AAA
45719 AATATTTT
1 AATATTTT
45727 ATTTTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
23 6 0.13
24 10 0.21
25 13 0.28
26 5 0.11
27 4 0.09
28 3 0.06
29 6 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTTTTATATATTAACTTAAAAA
Found at i:45682 original size:24 final size:24
Alignment explanation
Indices: 45651--45726 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
45641 ATATTTTATA
45651 TATATTAACTTAAAAAAATATTTT
1 TATATTAACTTAAAAAAATATTTT
* **
45675 TATATTAAATT-ATTAAATATATTT
1 TATATTAACTTAAAAAAATAT-TTT
45699 TATTATTAACTTAATCTAAAAATATTTT
1 TA-TATTAACTTAA---AAAAATATTTT
45727 ATTTTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 7 0.17
24 15 0.38
25 8 0.20
26 1 0.03
28 3 0.08
29 6 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATTAACTTAAAAAAATATTTT
Found at i:45727 original size:27 final size:26
Alignment explanation
Indices: 45653--45729 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 26
45643 ATTTTATATA
45653 TATTAACTTAA--AAAAATATTTT-T
1 TATTAACTTAATTAAAAATATTTTAT
* *
45676 ATATTAAATT-ATTAAATATATTTTAT
1 -TATTAACTTAATTAAAAATATTTTAT
45702 TATTAACTTAATCTAAAAATATTTTAT
1 TATTAACTTAAT-TAAAAATATTTTAT
45729 T
1 T
45730 TTTATTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 1 0.02
24 8 0.18
25 18 0.41
26 3 0.07
27 14 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTAACTTAATTAAAAATATTTTAT
Found at i:45745 original size:27 final size:27
Alignment explanation
Indices: 45653--45750 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 27
45643 ATTTTATATA
45653 TATTAACTTAA---AAAAATATTTT-T
1 TATTAACTTAATTTAAAAATATTTTAT
* *
45676 ATATTAAATT-A-TTAAATATATTTTAT
1 -TATTAACTTAATTTAAAAATATTTTAT
*
45702 TATTAACTTAATCTAAAAATATTTTAT
1 TATTAACTTAATTTAAAAATATTTTAT
* ** *
45729 TTTTATTTTCATTTAAAAATAT
1 TATTAACTTAATTTAAAAATAT
45751 ATATTTTATG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 8 0.14
25 18 0.31
26 2 0.03
27 30 0.51
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TATTAACTTAATTTAAAAATATTTTAT
Found at i:45926 original size:31 final size:31
Alignment explanation
Indices: 45883--45955 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
45873 ACCCATGATG
* *
45883 ATCACATCTTAATTAAATAAAAACGAAAGTA
1 ATCATATCTTAATTAAATAAAAACAAAAGTA
* *
45914 ATCATATCTTAATTAAATAAAAATAAAAGTG
1 ATCATATCTTAATTAAATAAAAACAAAAGTA
45945 ATCATATCTTA
1 ATCATATCTTA
45956 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACAAAAGTA
Found at i:62239 original size:15 final size:16
Alignment explanation
Indices: 62215--62251 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
62205 TAGGTGTGGT
*
62215 TTTAAAAAAAATAAAG
1 TTTAAAAAAAATAAAA
62231 TTTAAAAAAAATAAAA
1 TTTAAAAAAAATAAAA
62247 TTTAA
1 TTTAA
62252 GTAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TTTAAAAAAAATAAAA
Found at i:64487 original size:2 final size:2
Alignment explanation
Indices: 64480--64531 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
64470 TAAAGGATGC
* *
64480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
64522 AT TT AT AT AT
1 AT AT AT AT AT
64532 TTTTAATCGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66459 original size:153 final size:153
Alignment explanation
Indices: 66179--66483 Score: 495
Period size: 153 Copynumber: 2.0 Consensus size: 153
66169 TTACGTTGAT
* * * *
66179 AATTAAATTAGGAAGGGGTTCTGATTGGTACACTGAAGAAATAGACTTTGCGGATCAATTGGTTG
1 AATTAAACTAGGAAGAGGTTCTGATTGGTACACTGAAGAAATAGACTGTGCAGATCAATTGGTTG
66244 ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
66 ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
66309 GATTTAGACAAACCCCATTTTTC
131 GATTTAGACAAACCCCATTTTTC
*
66332 AATTAAACTAGGAAGAGGTTTTGATTGGTACACTG-AGTAAATAGACTGTGCAGATCAATTGGTT
1 AATTAAACTAGGAAGAGGTTCTGATTGGTACACTGAAG-AAATAGACTGTGCAGATCAATTGGTT
* * *
66396 GATCATTGACGTCCTGTGACCATACTCCGTGAATCATAAAAATATTATCATATGGTTGTGGGAGA
65 GATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGA
* * *
66461 GGATTTAGATAAATCTCATTTTT
130 GGATTTAGACAAACCCCATTTTT
66484 AGAATTACAA
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 2 0.01
153 138 0.99
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (153 bp):
AATTAAACTAGGAAGAGGTTCTGATTGGTACACTGAAGAAATAGACTGTGCAGATCAATTGGTTG
ATCATTGACGTCCTGTGACCATACTACGTGAATCATAAAAATATTATCATATGATTGCGGGAGAG
GATTTAGACAAACCCCATTTTTC
Found at i:67419 original size:18 final size:19
Alignment explanation
Indices: 67398--67438 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
67388 AATATTGTAA
67398 ATAAAT-AGA-ATAAAAAAT
1 ATAAATAAGATAT-AAAAAT
*
67416 ATAATTAAGATATAAAAAT
1 ATAAATAAGATATAAAAAT
67435 ATAA
1 ATAA
67439 TTATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 5 0.25
19 13 0.65
20 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
ATAAATAAGATATAAAAAT
Found at i:67642 original size:2 final size:2
Alignment explanation
Indices: 67635--67664 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
67625 AACTAAATTA
67635 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
67665 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67669 original size:4 final size:4
Alignment explanation
Indices: 67662--67687 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
67652 TATATATATA
67662 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
67688 AATAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:69288 original size:152 final size:152
Alignment explanation
Indices: 69012--69315 Score: 527
Period size: 152 Copynumber: 2.0 Consensus size: 152
69002 ATCAACTCAT
* * *
69012 ATCCATCGTCTTCAATATGAATTTGATGGACACGTATTATACGTTCCACGTACTCTGATCTTCCA
1 ATCCATCGTCTTCAATATGAATTTAATGGACACGTATTATACGTTCCACATACGCTGATCTTCCA
*
69077 TTGAATTGAAACAAGCTCTCAACATAAGTAATAATTTGTATTGTTCTTTCATAAGCATGGATATC
66 TTGAATGGAAACAAGCTCTCAACATAAGTAATAATTTGTATTGTTCTTTCATAAGCATGGATATC
69142 CAAATTTTTAAGCTCTCGTGTG
131 CAAATTTTTAAGCTCTCGTGTG
* * *
69164 ATCCATCGTCTTCAATATGAATTTAATGGGCATGTATTATACGTTCCTCATACGCTGATCTTCCA
1 ATCCATCGTCTTCAATATGAATTTAATGGACACGTATTATACGTTCCACATACGCTGATCTTCCA
69229 TTGAATGGAAACAAGCTCTCAACATAAGTAATAATTTGTATTGTTCTTTCATAAGCATGGATATC
66 TTGAATGGAAACAAGCTCTCAACATAAGTAATAATTTGTATTGTTCTTTCATAAGCATGGATATC
**
69294 CATTTTTTTAAGCTCTCGTGTG
131 CAAATTTTTAAGCTCTCGTGTG
69316 GAGGGGTCAA
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 143 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (152 bp):
ATCCATCGTCTTCAATATGAATTTAATGGACACGTATTATACGTTCCACATACGCTGATCTTCCA
TTGAATGGAAACAAGCTCTCAACATAAGTAATAATTTGTATTGTTCTTTCATAAGCATGGATATC
CAAATTTTTAAGCTCTCGTGTG
Found at i:78113 original size:20 final size:19
Alignment explanation
Indices: 78073--78114 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
78063 AGTAATCTTA
**
78073 TTCCCTGATAATCTTTTAT
1 TTCCCTGATAATCTTACAT
78092 TTCCACTGATAATCTTACAT
1 TTCC-CTGATAATCTTACAT
78112 TTC
1 TTC
78115 GTGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (19 bp):
TTCCCTGATAATCTTACAT
Found at i:78267 original size:52 final size:52
Alignment explanation
Indices: 78205--78307 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
78195 GATAGATAAA
78205 AACATATATGACTATATCGGTAAATAAACCACAATAGAAAATAAAACTATTG
1 AACATATATGACTATATCGGTAAATAAACCACAATAGAAAATAAAACTATTG
* * *
78257 AACATATATGACTATATCGGTAGATGAACCACAATAGAAAATTAAACTATT
1 AACATATATGACTATATCGGTAAATAAACCACAATAGAAAATAAAACTATT
78308 AAAGGGTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.26
Consensus pattern (52 bp):
AACATATATGACTATATCGGTAAATAAACCACAATAGAAAATAAAACTATTG
Found at i:80148 original size:5 final size:5
Alignment explanation
Indices: 80138--80163 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
80128 AGTCATATAT
80138 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
80164 GAAATCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:81185 original size:33 final size:33
Alignment explanation
Indices: 81107--81218 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 33
81097 CCAACACGCT
* * * * *
81107 GGGCATCTGAGGCCATCCGACCAAGGCCATCCGA
1 GGGCATCCGAGGCCATCCGAAC-GGGCTATGCGA
*
81141 GAGCATCCGAGGCCATCCGAACGGGCTATGCGA
1 GGGCATCCGAGGCCATCCGAACGGGCTATGCGA
* * * *
81174 GGGCATCCGAGGGCAACCGAGCGAGCTATGCGA
1 GGGCATCCGAGGCCATCCGAACGGGCTATGCGA
*
81207 GGGAATCCGAGG
1 GGGCATCCGAGG
81219 GAAGCCGAGC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 47 0.71
34 19 0.29
ACGTcount: A:0.24, C:0.29, G:0.36, T:0.11
Consensus pattern (33 bp):
GGGCATCCGAGGCCATCCGAACGGGCTATGCGA
Found at i:81186 original size:10 final size:10
Alignment explanation
Indices: 81134--81219 Score: 64
Period size: 10 Copynumber: 8.0 Consensus size: 10
81124 CGACCAAGGC
*
81134 CATCCGAGAG
1 CATCCGAGGG
*
81144 CATCCGAGGC
1 CATCCGAGGG
81154 CATCCGAACGGG
1 CATCCG-A-GGG
*
81166 CTATGCGAGGG
1 C-ATCCGAGGG
81177 CATCCGAGGG
1 CATCCGAGGG
*
81187 CAACCGAGCGAG
1 CATCCGAG-G-G
*
81199 CTATGCGAGGG
1 C-ATCCGAGGG
*
81210 AATCCGAGGG
1 CATCCGAGGG
81220 AAGCCGAGCG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
10 37 0.62
11 7 0.12
12 7 0.12
13 9 0.15
ACGTcount: A:0.24, C:0.28, G:0.37, T:0.10
Consensus pattern (10 bp):
CATCCGAGGG
Found at i:81219 original size:33 final size:33
Alignment explanation
Indices: 81145--81231 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
81135 ATCCGAGAGC
* * * * *
81145 ATCCGAGGCCATCCGAACGGGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
81178 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
81211 ATCCGAGGG-AAGCCGAGCGAG
1 ATCCGAGGGCAA-CCGAGCGAG
81232 GATAGGTCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.25, C:0.26, G:0.39, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:81268 original size:29 final size:29
Alignment explanation
Indices: 81235--81319 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
81225 GAGCGAGGAT
*
81235 AGGTCGCCCGAAGGGCATGTCGACCTACA
1 AGGTCGCCCGAAGGGCATGGCGACCTACA
* *
81264 AGGTCTCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGAAGGGCATGGCGACCTACA
81293 AGGTCGCCC-AGAGGGCATGGCGACCTA
1 AGGTCGCCCGA-AGGGCATGGCGACCTA
81320 TGTGTTGGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGAAGGGCATGGCGACCTACA
Found at i:82468 original size:33 final size:33
Alignment explanation
Indices: 82429--82499 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82419 TTCACTTAGA
*
82429 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
82462 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
82495 TTTCA
1 TTTCA
82500 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:82639 original size:14 final size:14
Alignment explanation
Indices: 82620--82674 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
82610 AGAATGACTG
82620 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
82634 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
82653 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
82667 TCGCAACG
1 TCGCAACG
82675 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:82687 original size:33 final size:33
Alignment explanation
Indices: 82620--82690 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82610 AGAATGACTG
***
82620 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82653 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82686 TCGCA
1 TCGCA
82691 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:82708 original size:19 final size:19
Alignment explanation
Indices: 82686--82787 Score: 91
Period size: 19 Copynumber: 5.9 Consensus size: 19
82676 GAAACCAAAA
* *
82686 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
82705 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
82721 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATC
*
82737 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATC
82756 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
82772 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
82788 TTCAACCAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
14 16 0.23
15 3 0.04
16 10 0.14
17 6 0.09
18 8 0.12
19 26 0.38
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:82727 original size:14 final size:15
Alignment explanation
Indices: 82708--82782 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 15
82698 TTTCATTTCG
82708 CGTTGCGATTC-TCT
1 CGTTGCGATTCATCT
*
82722 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTCA--TCT
82740 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TCATCT
82757 CGCGTTGCGATTC-TCT
1 --CGTTGCGATTCATCT
82773 CGTTGCGATT
1 CGTTGCGATT
82783 TTCATTTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
14 18 0.35
15 3 0.06
16 3 0.06
17 4 0.08
18 13 0.25
19 11 0.21
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.41
Consensus pattern (15 bp):
CGTTGCGATTCATCT
Found at i:82767 original size:51 final size:52
Alignment explanation
Indices: 82686--82790 Score: 176
Period size: 51 Copynumber: 2.0 Consensus size: 52
82676 GAAACCAAAA
* *
82686 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
82737 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
82789 TC
1 TC
82791 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
51 41 0.82
52 9 0.18
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:84797 original size:184 final size:186
Alignment explanation
Indices: 84488--84959 Score: 930
Period size: 184 Copynumber: 2.5 Consensus size: 186
84478 TAGATTGCTT
84488 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84553 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
84618 GTGTATTCTTTAACACTGTGAAATA-TA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
84672 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84737 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
84802 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
84858 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84923 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
84960 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 155 0.54
185 2 0.01
186 129 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:84804 original size:93 final size:93
Alignment explanation
Indices: 84488--84959 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
84478 TAGATTGCTT
84488 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84553 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84581 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84645 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84672 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84737 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84765 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84830 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84858 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84923 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84951 AGTAAATTT
1 AGTAAATTT
84960 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.24
92 4 0.01
93 284 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:85043 original size:19 final size:19
Alignment explanation
Indices: 85003--85131 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
84993 TAGTTTACTT
* *
85003 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
85023 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
85042 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
85061 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
85075 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
85094 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
85108 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
85127 TCGCA
1 TCGCA
85132 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:85082 original size:33 final size:32
Alignment explanation
Indices: 85039--85131 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
85029 CGCGAAACCA
**
85039 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
85071 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
85104 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
85132 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:85129 original size:52 final size:52
Alignment explanation
Indices: 85003--85131 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
84993 TAGTTTACTT
**
85003 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
85055 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
85108 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
85132 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:85149 original size:19 final size:19
Alignment explanation
Indices: 85127--85247 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
85117 GAAACCAAAA
*
85127 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
85146 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
85165 TCGCATTGCGA--TT-ATG
1 TCGCGTTGCGATTTTCATT
85181 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
85198 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
85217 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
85237 TCGTGTTGCGA
1 TCGCGTTGCGA
85248 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:87169 original size:14 final size:14
Alignment explanation
Indices: 87150--87185 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
87140 ATTGTTTAAT
87150 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
87164 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
87178 TGATTTGT
1 TGATTTGT
87186 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:87307 original size:19 final size:19
Alignment explanation
Indices: 87291--87392 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
87281 AAAAATGACT
87291 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87310 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
87329 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
87343 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87362 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
87382 ATCGCAATGCG
1 ATCGCAATGCG
87393 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:87445 original size:19 final size:19
Alignment explanation
Indices: 87421--87798 Score: 474
Period size: 19 Copynumber: 21.4 Consensus size: 19
87411 GATTATCTCG
87421 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87440 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87459 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
87473 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87530 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
87544 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87563 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87582 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
87601 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87620 TTGCGA--TT-ATGTCG--
1 TTGCGATTTTCATTTCGCA
87634 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87653 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87672 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
87686 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87705 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87724 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
87738 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
87758 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
87772 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
87791 TTGCGATT
1 TTGCGATT
87799 GTATTTTCCG
Statistics
Matches: 317, Mismatches: 11, Indels: 62
0.81 0.03 0.16
Matches are distributed among these distances:
14 41 0.13
16 39 0.12
17 36 0.11
18 3 0.01
19 186 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:87461 original size:52 final size:52
Alignment explanation
Indices: 87399--87770 Score: 529
Period size: 52 Copynumber: 7.0 Consensus size: 52
87389 TGCGTTTATA
87399 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
87451 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
87503 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* * *
87555 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
87612 ATTTCGCATTGCGATTATGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
87664 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
87716 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
87769 AT
1 AT
87771 GTTGGGATTT
Statistics
Matches: 300, Mismatches: 9, Indels: 21
0.91 0.03 0.06
Matches are distributed among these distances:
52 223 0.74
53 17 0.06
54 15 0.05
55 15 0.05
57 30 0.10
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:87496 original size:71 final size:71
Alignment explanation
Indices: 87421--87731 Score: 506
Period size: 71 Copynumber: 4.4 Consensus size: 71
87411 GATTATCTCG
87421 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
87486 TTCGCA
66 TTCGCA
87492 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
87557 TTCGCA
66 TTCGCA
* *
87563 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
87626 TT-ATGTCG--
61 TTCATTTCGCA
*
87634 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
87699 TTCGCA
66 TTCGCA
87705 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
87732 CTCTCGTTGC
Statistics
Matches: 223, Mismatches: 7, Indels: 20
0.89 0.03 0.08
Matches are distributed among these distances:
66 6 0.03
68 6 0.03
69 7 0.03
71 184 0.83
73 7 0.03
74 7 0.03
76 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:90119 original size:12 final size:12
Alignment explanation
Indices: 90102--90126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90092 TCTTCGGGGA
90102 CTTTTTCTTCTT
1 CTTTTTCTTCTT
90114 CTTTTTCTTCTT
1 CTTTTTCTTCTT
90126 C
1 C
90127 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:90335 original size:24 final size:24
Alignment explanation
Indices: 90301--90347 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
90291 CTGAAACATC
90301 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
90325 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
90348 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:91057 original size:20 final size:20
Alignment explanation
Indices: 91029--91397 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
91019 AAATTTCAGT
* * * *
91029 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
91049 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
91069 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
91089 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
91109 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91129 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
91149 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
91169 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91189 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91209 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
91229 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
91249 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91269 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
91289 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
91309 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
91329 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
91349 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
91369 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
91389 GTTGCGATT
1 GTTGCGATT
91398 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:92273 original size:18 final size:18
Alignment explanation
Indices: 92250--92285 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
92240 TTTGATAGTC
92250 GTAATTAATTTTTATAAT
1 GTAATTAATTTTTATAAT
* *
92268 GTAATTCATTTTTCTAAT
1 GTAATTAATTTTTATAAT
92286 TCTTTTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
GTAATTAATTTTTATAAT
Found at i:92498 original size:19 final size:19
Alignment explanation
Indices: 92455--92500 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
92445 TATTTAATAT
*
92455 TATTATAATATAATTTTAA
1 TATTATATTATAATTTTAA
*
92474 TA--ATATTATATTTTTAA
1 TATTATATTATAATTTTAA
92491 TATTATATTA
1 TATTATATTA
92501 ATATGTAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATATTATAATTTTAA
Found at i:92503 original size:11 final size:10
Alignment explanation
Indices: 92445--92504 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 10
92435 ATTATAAACA
92445 TATTTAATAT
1 TATTTAATAT
92455 TATTATAATAT
1 TATT-TAATAT
* *
92466 AATTTTAATAA
1 TA-TTTAATAT
92477 TA-TT-ATAT
1 TATTTAATAT
92485 T-TTTAATAT
1 TATTTAATAT
92494 TATATTAATAT
1 TAT-TTAATAT
92505 GTAGTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.15
9 7 0.17
10 5 0.12
11 20 0.50
12 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTAATAT
Found at i:95677 original size:43 final size:42
Alignment explanation
Indices: 95630--95827 Score: 123
Period size: 43 Copynumber: 4.6 Consensus size: 42
95620 TGATCTTATG
* * * *
95630 TTTTTCAATCCCACTTTGTACATTTATAATT-AAGCTCGTGAT
1 TTTTTCAATCCCATTTTTTAC-TTTATAATTGAAGCTCATAAT
* * * *
95672 CTTTTTTAATCTCATTTTTTACTTTTATAGTTGAGGCTCATAAT
1 -TTTTTCAATCCCATTTTTTAC-TTTATAATTGAAGCTCATAAT
* * **
95716 TTTTTCAATCCCATTTTTTACTTATATAATTTAGGC-CACTGCTT
1 TTTTTCAATCCCATTTTTTACTT-TATAATTGAAGCTCA-T-AAT
* * * * *
95760 TTTTTTAATCTCACTTTTTACTTTAATAATTG-AGGTCCCTAAT
1 TTTTTCAATCCCATTTTTTACTTT-ATAATTGAAGCT-CATAAT
**
95803 TTTTTCAATCATACTTTTTTACTTT
1 TTTTTCAATCCCA-TTTTTTACTTT
95828 TATAGTTTAA
Statistics
Matches: 119, Mismatches: 28, Indels: 15
0.73 0.17 0.09
Matches are distributed among these distances:
42 4 0.03
43 68 0.57
44 46 0.39
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (42 bp):
TTTTTCAATCCCATTTTTTACTTTATAATTGAAGCTCATAAT
Found at i:95779 original size:44 final size:42
Alignment explanation
Indices: 95673--95827 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 42
95663 GCTCGTGATC
*
95673 TTTTTTAATCTCATTTTTTACTTTTATAGTTGAGGCTCATAAT
1 TTTTTTAATCTCATTTTTTAC-TTTATAATTGAGGCTCATAAT
* * * **
95716 TTTTTCAATCCCATTTTTTACTTATATAATTTAGGC-CACTGCTT
1 TTTTTTAATCTCATTTTTTACTT-TATAATTGAGGCTCA-T-AAT
* *
95760 TTTTTTAATCTCACTTTTTACTTTAATAATTGAGG-TCCCTAAT
1 TTTTTTAATCTCATTTTTTACTTT-ATAATTGAGGCT-CATAAT
*
95803 TTTTTCAATCAT-ACTTTTTTACTTT
1 TTTTTTAATC-TCA-TTTTTTACTTT
95828 TATAGTTTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 15
0.75 0.13 0.13
Matches are distributed among these distances:
42 4 0.04
43 42 0.47
44 42 0.47
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.54
Consensus pattern (42 bp):
TTTTTTAATCTCATTTTTTACTTTATAATTGAGGCTCATAAT
Found at i:95793 original size:87 final size:88
Alignment explanation
Indices: 95673--95836 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 88
95663 GCTCGTGATC
* * * *
95673 TTTTTTAATCTCATTTTTTACTTTTATAGTTGAGG-CTCATAATTTTTTCAATCCCA-TTTTTTA
1 TTTTTTAATCTCACTTTTTACTTTAATAATTGAGGTC-CATAATTTTTTCAATCACACTTTTTTA
95736 CTTATATAATTTAGGCCACTGCTT
65 CTTATATAATTTAGGCCACTGCTT
* *
95760 TTTTTTAATCTCACTTTTTACTTTAATAATTGAGGTCCCTAATTTTTTCAATCATACTTTTTTAC
1 TTTTTTAATCTCACTTTTTACTTTAATAATTGAGGTCCATAATTTTTTCAATCACACTTTTTTAC
* *
95825 TTTTATAGTTTA
66 TTATATAATTTA
95837 AGCCCCTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
87 48 0.72
88 19 0.28
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (88 bp):
TTTTTTAATCTCACTTTTTACTTTAATAATTGAGGTCCATAATTTTTTCAATCACACTTTTTTAC
TTATATAATTTAGGCCACTGCTT
Found at i:95844 original size:44 final size:43
Alignment explanation
Indices: 95673--95848 Score: 144
Period size: 44 Copynumber: 4.1 Consensus size: 43
95663 GCTCGTGATC
* * *
95673 TTTTTT-AATCT-CATTTTTTACTTTTATAGTTGAGGCTCATAA
1 TTTTTTCAATCTAC-TTTTTTACTTTTATAATTGAGGCCCCTAA
* * * * **
95715 TTTTTTCAATC-CCATTTTTTACTTATATAATTTAGGCCACTGCT
1 TTTTTTCAATCTAC-TTTTTTACTTTTATAATTGAGGCCCCT-AA
* * *
95759 TTTTTTTAATCTCAC-TTTTTACTTTAATAATTGAGGTCCCTAA
1 TTTTTTCAATCT-ACTTTTTTACTTTTATAATTGAGGCCCCTAA
* * *
95802 TTTTTTCAATCATACTTTTTTACTTTTATAGTTTAAGCCCCTAA
1 TTTTTTCAATC-TACTTTTTTACTTTTATAATTGAGGCCCCTAA
95846 TTT
1 TTT
95849 AATCATTTTT
Statistics
Matches: 104, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
42 6 0.06
43 39 0.38
44 58 0.56
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (43 bp):
TTTTTTCAATCTACTTTTTTACTTTTATAATTGAGGCCCCTAA
Found at i:98839 original size:17 final size:18
Alignment explanation
Indices: 98807--98840 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
98797 CCATACTTGA
*
98807 TTAAATATTTAATATTTT
1 TTAAATATTAAATATTTT
98825 TTAAAT-TTAAATATTT
1 TTAAATATTAAATATTT
98841 ATTTTTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATATTAAATATTTT
Found at i:101823 original size:31 final size:31
Alignment explanation
Indices: 101776--101837 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
101766 TTTCTACTTC
* * * *
101776 TTAATGTGGTCTTCTAACTCATAAAATAAAT
1 TTAACGTGGTCCTCTAACTCAGAAAACAAAT
*
101807 TTAACGTGGTCCTCTAATTCAGAAAACAAAT
1 TTAACGTGGTCCTCTAACTCAGAAAACAAAT
101838 CTAATATGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (31 bp):
TTAACGTGGTCCTCTAACTCAGAAAACAAAT
Found at i:102981 original size:10 final size:10
Alignment explanation
Indices: 102966--102992 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
102956 TTAAATTAAT
102966 GATGCTCATC
1 GATGCTCATC
102976 GATGCTCATC
1 GATGCTCATC
102986 GATGCTC
1 GATGCTC
102993 GTCAAGCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.30
Consensus pattern (10 bp):
GATGCTCATC
Found at i:104366 original size:60 final size:60
Alignment explanation
Indices: 104295--104413 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
104285 TAAGTGGCCA
* * * *
104295 TTTTATAACTTTTGATAGTC-GAGGGACTCAACAAAATAACATGTCATAGTTGAGAGACCG
1 TTTTATAACTTTTAATAGTCGGA-AGACTCAACAAAATAACATCTCATAGTCGAGAGACCG
* * * *
104355 TTTTGTAACTTTTAATAGTCGGAAGACTTAACAAAATAATATCTTATAGTCGAGAGACC
1 TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACC
104414 ATTCGTGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
60 48 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGGAAGACTCAACAAAATAACATCTCATAGTCGAGAGACCG
Done.