Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007088.1 Corchorus capsularis cultivar CVL-1 contig07109, 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: 119806
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2337 original size:30 final size:29
Alignment explanation
Indices: 2275--2344 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2265 ACCGAACCGT
****
2275 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
2304 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
2334 CAAATAAGCCC
1 CAAATAAGCCC
2345 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:7394 original size:31 final size:31
Alignment explanation
Indices: 7356--7557 Score: 291
Period size: 31 Copynumber: 6.6 Consensus size: 31
7346 ATAGTGTATC
* *
7356 TGACAACTTCTTGTGTCAACTGTAAGAACAT
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
* *
7387 TGACAACTTTTGGTGTTAATTGTAAGAACAT
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
* *
7418 TGACAACTTCTAGTGTCAATTGTAAGAATAT
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
*
7449 TGACAACTTCTGGTGTCAATTGTAAGAAAAT
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
* * *
7480 TGACAGCTTTTGGTGTCAATTGTAAGATCA-
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
*
7510 TGACAACTTCTGGTGTCAATTGTAAGATCA-
1 TGACAACTTCTGGTGTCAATTGTAAGAACAT
7540 TGACAACTTCTGGTGTCA
1 TGACAACTTCTGGTGTCA
7558 TTTGGAGATT
Statistics
Matches: 155, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 46 0.30
31 109 0.70
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (31 bp):
TGACAACTTCTGGTGTCAATTGTAAGAACAT
Found at i:7578 original size:33 final size:31
Alignment explanation
Indices: 7356--7599 Score: 151
Period size: 31 Copynumber: 7.9 Consensus size: 31
7346 ATAGTGTATC
* ** * *
7356 TGACAACTTCTTGTGTCAACTGTA-AGAACA
1 TGACAACTTCTGGTGTCATTTGGAGAGATCA
* * * * *
7386 TTGACAACTTTTGGTGTTAATTGTA-AGAACA
1 -TGACAACTTCTGGTGTCATTTGGAGAGATCA
* * *
7417 TTGACAACTTCTAGTGTCAATTGTA-AGAAT-A
1 -TGACAACTTCTGGTGTCATTTGGAGAG-ATCA
* * **
7448 TTGACAACTTCTGGTGTCAATTGTA-AGAAAA
1 -TGACAACTTCTGGTGTCATTTGGAGAGATCA
* * * *
7479 TTGACAGCTTTTGGTGTCAATTGTA-AGATCA
1 -TGACAACTTCTGGTGTCATTTGGAGAGATCA
* *
7510 TGACAACTTCTGGTGTCAATTGTA-AGATCA
1 TGACAACTTCTGGTGTCATTTGGAGAGATCA
*
7540 TGACAACTTCTGGTGTCATTTGGAGATTTATCA
1 TGACAACTTCTGGTGTCATTTGGAGA--GATCA
*
7573 TGACAACTTTTGGTGTCATTTGGAGAG
1 TGACAACTTCTGGTGTCATTTGGAGAG
7600 TAAAATAAAT
Statistics
Matches: 187, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
30 51 0.27
31 106 0.57
32 1 0.01
33 29 0.16
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
TGACAACTTCTGGTGTCATTTGGAGAGATCA
Found at i:7629 original size:39 final size:39
Alignment explanation
Indices: 7573--7666 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
7563 AGATTTATCA
* *
7573 TGACAACTTTTGGTGTCATTTGGAGAGTAAAATAAATTG
1 TGACAACTTCTGCTGTCATTTGGAGAGTAAAATAAATTG
7612 TGACAACTTCTGCTGTCATTTGGAGAGTAAAATAAATTG
1 TGACAACTTCTGCTGTCATTTGGAGAGTAAAATAAATTG
7651 TGACAACTTCTGCTGT
1 TGACAACTTCTGCTGT
7667 GACAATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (39 bp):
TGACAACTTCTGCTGTCATTTGGAGAGTAAAATAAATTG
Found at i:10790 original size:32 final size:32
Alignment explanation
Indices: 10745--10808 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
10735 ATCTNGGCGC
*
10745 GGAGGCGTCCCAGGGGGCG-CCCACCATGGTG
1 GGAGGCGTCCCAGGGGGCGCCCCACCACGGTG
*
10776 GGAGGCTTCCCCAGGGGGCGCCCCACCACGGTG
1 GGAGGCGT-CCCAGGGGGCGCCCCACCACGGTG
10809 ACGCCTCCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 7 0.24
32 11 0.38
33 11 0.38
ACGTcount: A:0.12, C:0.36, G:0.42, T:0.09
Consensus pattern (32 bp):
GGAGGCGTCCCAGGGGGCGCCCCACCACGGTG
Found at i:11842 original size:13 final size:13
Alignment explanation
Indices: 11826--11851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11816 TAAATCAATG
11826 TTATAAATATTAT
1 TTATAAATATTAT
11839 TTATAAATATTAT
1 TTATAAATATTAT
11852 CTTTGGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATAAATATTAT
Found at i:13171 original size:27 final size:27
Alignment explanation
Indices: 13120--13171 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13110 TACTCAACTT
* **
13120 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAACACCAAACGA
*
13147 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
13172 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACGA
Found at i:14255 original size:47 final size:48
Alignment explanation
Indices: 14198--14290 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 48
14188 TTTTCTTGGA
14198 CATTTATCCCAGGAAGCAG-TTTTTTTAAATGAAGGTTTCTGGGTTAG
1 CATTTATCCCAGGAAGCAGTTTTTTTTAAATGAAGGTTTCTGGGTTAG
14245 CATTTATCCCAGGAAGCAGTTTTTTTTTAAATGAAGGTTTCTGGGT
1 CATTTATCCCAGGAAGCAG-TTTTTTTTAAATGAAGGTTTCTGGGT
14291 CAGTTATGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 19 0.43
49 25 0.57
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
CATTTATCCCAGGAAGCAGTTTTTTTTAAATGAAGGTTTCTGGGTTAG
Found at i:17310 original size:11 final size:10
Alignment explanation
Indices: 17292--17325 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
17282 AATTGTCTTC
17292 AAATCTTCAA
1 AAATCTTCAA
17302 AATATCTTCAA
1 AA-ATCTTCAA
17313 GAAATCTTCAA
1 -AAATCTTCAA
17324 AA
1 AA
17326 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:18226 original size:14 final size:14
Alignment explanation
Indices: 18207--18234 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18197 TTAAACTACC
18207 CTTCTAATATAGAT
1 CTTCTAATATAGAT
18221 CTTCTAATATAGAT
1 CTTCTAATATAGAT
18235 AGTCCCCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTCTAATATAGAT
Found at i:19472 original size:11 final size:11
Alignment explanation
Indices: 19456--19488 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19446 GGTGATTCGG
19456 GTGGCCGGGCT
1 GTGGCCGGGCT
19467 GTGGCCGGGCT
1 GTGGCCGGGCT
*
19478 GTGGCAGGGCT
1 GTGGCCGGGCT
19489 AGGCGCACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.24, G:0.55, T:0.18
Consensus pattern (11 bp):
GTGGCCGGGCT
Found at i:22913 original size:71 final size:72
Alignment explanation
Indices: 22830--23085 Score: 372
Period size: 71 Copynumber: 3.5 Consensus size: 72
22820 TAAGGAAGTA
22830 AAGGTAATAG-TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATT
1 AAGGTAATAGTTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATT
22894 AAGAGTC
66 AAGAGTC
* *
22901 AAGGTAATAG-TAATCAGTAAATCAGTAATTTAGTAAAAACAGATTAATCAGTAAATTGATAATT
1 AAGGTAATAGTTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATT
22965 AAGAGTC
66 AAGAGTC
* *
22972 AAGGTAATAGTAATAAGTTAATCAGTTAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAATTT
1 AA-G-----GTAAT-AGTTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATT
23037 GATAATTAAGAGTC
59 GATAATTAAGAGTC
*
23051 AAGGTAAGAGATTAATCAGTAAAGTCAGTAATTAA
1 AAGGTAATAG-TTAATCAGTAAA-TCAGTAATTAA
23086 AGAGTCAAAG
Statistics
Matches: 167, Mismatches: 8, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
71 71 0.43
72 3 0.02
73 15 0.09
74 11 0.07
77 5 0.03
78 3 0.02
79 59 0.35
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (72 bp):
AAGGTAATAGTTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATT
AAGAGTC
Found at i:22919 original size:37 final size:37
Alignment explanation
Indices: 22874--22985 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 37
22864 AAAAAGAGAT
22874 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
* * * *
22911 TAATCAGTAAA-TCAGTAATT--TAGT-AA--AAACAG
1 TAATCAGTAAATTGA-TAATTAAGAGTCAAGGTAATAG
22943 ATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 --TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
22982 TAAT
1 TAAT
22986 AAGTTAATCA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
32 4 0.07
34 18 0.31
35 5 0.09
36 5 0.09
37 22 0.38
39 4 0.07
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.30
Consensus pattern (37 bp):
TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
Found at i:22964 original size:34 final size:34
Alignment explanation
Indices: 22840--22956 Score: 114
Period size: 34 Copynumber: 3.4 Consensus size: 34
22830 AAGGTAATAG
*
22840 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGAT
1 TAATCAGTAAATCAGTAATTAAGTAAAAACAGAT
* * *
22874 TAATCAGTAAAT-TGATAATTAAGAGTCAAGGTAATAG--
1 TAATCAGTAAATCAG-TAATT-A-AGT-AA--AAACAGAT
*
22911 TAATCAGTAAATCAGTAATTTAGTAAAAACAGAT
1 TAATCAGTAAATCAGTAATTAAGTAAAAACAGAT
22945 TAATCAGTAAAT
1 TAATCAGTAAAT
22957 TGATAATTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
32 4 0.06
33 1 0.01
34 31 0.46
35 4 0.06
36 3 0.04
37 19 0.28
38 1 0.01
39 4 0.06
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.29
Consensus pattern (34 bp):
TAATCAGTAAATCAGTAATTAAGTAAAAACAGAT
Found at i:23027 original size:34 final size:36
Alignment explanation
Indices: 22989--23085 Score: 92
Period size: 39 Copynumber: 2.6 Consensus size: 36
22979 TAGTAATAAG
22989 TTAATCAGTTAATCAGTAATTAAGT-AA-AAAGAGA
1 TTAATCAGTTAATCAGTAATTAAGTCAAGAAAGAGA
** *
23023 TTAATCAG-TAATTTGATAATTAAGAGTCAAGGTAAGAGA
1 TTAATCAGTTAATCAG-TAATT-A-AGTCAA-GAAAGAGA
*
23062 TTAATCAGTAAAGTCAGTAATTAA
1 TTAATCAGTTAA-TCAGTAATTAA
23086 AGAGTCAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
33 5 0.10
34 13 0.27
35 1 0.02
36 3 0.06
37 2 0.04
38 1 0.02
39 15 0.31
40 7 0.14
41 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.31
Consensus pattern (36 bp):
TTAATCAGTTAATCAGTAATTAAGTCAAGAAAGAGA
Found at i:23173 original size:16 final size:16
Alignment explanation
Indices: 23134--23278 Score: 77
Period size: 16 Copynumber: 9.1 Consensus size: 16
23124 GGTAATCAAG
* *
23134 AGAAGCAATCAGTAGA
1 AGAAGTAATCAGTAAA
*
23150 TGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
** *
23166 AGGGGTAA-AAGTAAA
1 AGAAGTAATCAGTAAA
23181 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* ** *
23197 AGTAAAAGAACAAAAGTAAC
1 AG---AAGTA-ATCAGTAAA
23217 AGAAGTAATCAG-AAA
1 AGAAGTAATCAGTAAA
* *
23232 A-ATGGTAAT---TAAG
1 AGA-AGTAATCAGTAAA
*
23245 AGAAGTAATCAGTAGA
1 AGAAGTAATCAGTAAA
*
23261 GGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
23277 AG
1 AG
23279 GGAGTAAAAG
Statistics
Matches: 92, Mismatches: 26, Indels: 22
0.66 0.19 0.16
Matches are distributed among these distances:
13 8 0.09
14 2 0.02
15 20 0.22
16 46 0.50
17 4 0.04
19 4 0.04
20 8 0.09
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:23424 original size:14 final size:14
Alignment explanation
Indices: 23405--23431 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23395 CAATCAGTAC
23405 TAATCAGTAAAGAG
1 TAATCAGTAAAGAG
23419 TAATCAGTAAAGA
1 TAATCAGTAAAGA
23432 AAATGGTAAA
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:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAATCAGTAAAGAG
Found at i:23490 original size:36 final size:35
Alignment explanation
Indices: 23413--23531 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 35
23403 ACTAATCAGT
*
23413 AAAGAGTAATCAGT-AAAG-AAAATGGTAAAGAGTA
1 AAAG-GTAATCAGTAAAAGAAAAATGGTAAAGAATA
* *
23447 AAAGGTAATCATTAAAAGAAAAGATGGTAAAGAATG
1 AAAGGTAATCAGTAAAAGAAAA-ATGGTAAAGAATA
*
23483 AATGGTAATCAGTAAAA-AAAAATGGTAAA-AAGTA
1 AAAGGTAATCAGTAAAAGAAAAATGGTAAAGAA-TA
* *
23517 AAAAGTAATTAGTAA
1 AAAGGTAATCAGTAA
23532 GAAGGTAAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
33 10 0.14
34 29 0.40
35 7 0.10
36 26 0.36
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (35 bp):
AAAGGTAATCAGTAAAAGAAAAATGGTAAAGAATA
Found at i:23508 original size:20 final size:20
Alignment explanation
Indices: 23483--23520 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23473 GTAAAGAATG
**
23483 AATGGTAATCAGTAAAAAAA
1 AATGGTAAAAAGTAAAAAAA
23503 AATGGTAAAAAGTAAAAA
1 AATGGTAAAAAGTAAAAA
23521 GTAATTAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (20 bp):
AATGGTAAAAAGTAAAAAAA
Found at i:23545 original size:29 final size:28
Alignment explanation
Indices: 23506--23570 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
23496 AAAAAAAAAT
*
23506 GGTAAAAAGTAAAAAGTAATTAGTAAGAA
1 GGTAAAAAGTAAAAAGTAATCAGT-AGAA
* *
23535 GGTAAAGAGTAAAGAGTAATCAGTAGAA
1 GGTAAAAAGTAAAAAGTAATCAGTAGAA
*
23563 AGTAAAAA
1 GGTAAAAA
23571 TGATAAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.18
Consensus pattern (28 bp):
GGTAAAAAGTAAAAAGTAATCAGTAGAA
Found at i:23581 original size:29 final size:28
Alignment explanation
Indices: 23507--23582 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
23497 AAAAAAAATG
* *
23507 GTAAAAAGTAAAAAGTAATTAGTAAGAAG
1 GTAAAAAGT-AAAAGTAATCAGTAAGAAA
*
23536 GTAAAGAGTAAAGAGTAATCAGT-AGAAA
1 GTAAAAAGTAAA-AGTAATCAGTAAGAAA
23564 GTAAAAATGATAAAAGTAA
1 GTAAAAA-G-TAAAAGTAA
23583 CAAAAGTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 13 0.32
29 23 0.57
30 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.21, T:0.20
Consensus pattern (28 bp):
GTAAAAAGTAAAAGTAATCAGTAAGAAA
Found at i:27557 original size:15 final size:15
Alignment explanation
Indices: 27522--27561 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
27512 TAATCCCCTA
27522 AAAAC-AATT-AAAC
1 AAAACAAATTAAAAC
*
27535 TAAA-AAATTAAAAC
1 AAAACAAATTAAAAC
27549 AAAACAAATTAAA
1 AAAACAAATTAAA
27562 TCTAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.32
14 7 0.32
15 8 0.36
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAACAAATTAAAAC
Found at i:28943 original size:11 final size:10
Alignment explanation
Indices: 28925--28958 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
28915 AATTGTCTTC
28925 AAATCTTCAA
1 AAATCTTCAA
28935 AATATCTTCAA
1 AA-ATCTTCAA
28946 GAAATCTTCAA
1 -AAATCTTCAA
28957 AA
1 AA
28959 CACGAACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:29907 original size:13 final size:13
Alignment explanation
Indices: 29889--29913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29879 TTTCCTTCTT
29889 CAGTCCATTTTTC
1 CAGTCCATTTTTC
29902 CAGTCCATTTTT
1 CAGTCCATTTTT
29914 GTTGGGTCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:32231 original size:13 final size:13
Alignment explanation
Indices: 32213--32237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32203 TAATTTTTTA
32213 ATTAATATTAATC
1 ATTAATATTAATC
32226 ATTAATATTAAT
1 ATTAATATTAAT
32238 GGTGTCATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAATATTAATC
Found at i:35122 original size:110 final size:110
Alignment explanation
Indices: 34924--35124 Score: 262
Period size: 110 Copynumber: 1.8 Consensus size: 110
34914 TCAGGTTCTT
* * * * *
34924 CATGAAAGTCGTAGATCATATAGTAACCTTTTAACCGACACTTTAATAACTTTAATCGGACATAT
1 CATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATAT
* * * *
34989 GGATCGAAAATTATATGGCATTAAATAGACCAACAATCGAAACGA
66 GGAACAAAAATTATACGACATTAAATAGACCAACAATCGAAACGA
* *
35034 CATGAAAGTCGTAAATCATGCAATAACCTTTT-ACCTGACACTTCAATAACTTCAATCGGACATG
1 CATGAAAGTCGTAAATCATACAATAACCTTTTAACC-GACACTTCAATAACTTCAATCGGACATA
*
35098 T-GAACAAAAAATTATACGATATTAAAT
65 TGGAAC-AAAAATTATACGACATTAAAT
35125 TGATCGGCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
109 6 0.08
110 71 0.92
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (110 bp):
CATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATAT
GGAACAAAAATTATACGACATTAAATAGACCAACAATCGAAACGA
Found at i:41533 original size:14 final size:15
Alignment explanation
Indices: 41509--41538 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41499 GTAGGGAAAG
41509 CTGTAATGATTCAAT
1 CTGTAATGATTCAAT
41524 CTGT-ATGATTCAAT
1 CTGTAATGATTCAAT
41538 C
1 C
41539 CGTGGCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (15 bp):
CTGTAATGATTCAAT
Found at i:42894 original size:14 final size:14
Alignment explanation
Indices: 42875--42901 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42865 TTTGAGCGCA
42875 TTATCATTGAGGGC
1 TTATCATTGAGGGC
42889 TTATCATTGAGGG
1 TTATCATTGAGGG
42902 AATGATGCGC
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:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (14 bp):
TTATCATTGAGGGC
Found at i:44791 original size:983 final size:983
Alignment explanation
Indices: 42887--44835 Score: 3461
Period size: 983 Copynumber: 2.0 Consensus size: 983
42877 ATCATTGAGG
* * *
42887 GCTTATCATTGAGGGAATGATGCGCCAAGGACTTATCATGGAGTTGAAGACAAGCATGGAGAGCA
1 GCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGACAAGCATGGAGAACA
* * *
42952 TGGAAAGGGTGTGCATGGGCTGCAAGGAAGCATGAAGATGCATGGAGACCATGGAGATATCGATA
66 TGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGAAGATGCATGGAAACCATGCAGATATCGATA
*
43017 ATCATGTTCCAAGCACTAAAAAGATGCCATTCGATCCATTGAAGATGCTTATTGGTCCGATGACA
131 ATCATGTTCCAAGCACTAAAAAGATGCCATTCGATCCATTGAAGATGCCTATTGGTCCGATGACA
* *
43082 AGAGCAAGAGCTAAAAAATTCAAGGATGCACTCATGGGCCTTGTTCGATCTCATCTTGATGACAT
196 AGAGCAAAAGCTAAAAAATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGATGACAT
43147 GAAGACTATTCAAGTTCAATTGAAGAGCTTTGATGATGAGTTGAGCAAGAAAACACCAACAAATT
261 GAAGACTATTCAAGTTCAATTGAAGAGCTTTGATGATGAGTTGAGCAAGAAAACACCAACAAATT
*
43212 ACAAGTTCATCACTTTGCTTGCTATTGATTCTAAATGGCCGGATTGACATCGTGGCATGAGTCCA
326 ACAAGTTCATCACTTCGCTTGCTATTGATTCTAAATGGCCGGATTGACATCGTGGCATGAGTCCA
*
43277 TTGGCATTAGTTTGCTTTGTTTGGACTTAATTCTATCTTAGATTAGCTTATTTTTAACTTTGGAT
391 TTAGCATTAGTTTGCTTTGTTTGGACTTAATTCTATCTTAGATTAGCTTATTTTTAACTTTGGAT
*
43342 GTTATTTGGGTTGTGCCTTGTTTGACTAAGTCCAATCCTTAGCTATTTTTCTATTGGTTGTATTT
456 GTTATTTGCGTTGTGCCTTGTTTGACTAAGTCCAATCCTTAGCTATTTTTCTATTGGTTGTATTT
* *
43407 TTGGATAGTTTCTAGAAGGATCTTTTGTATAGCCTTTATATTTGGACGAAAATTAGGGTTTAAAG
521 TTGGATAGTATCTAGAAGGATCTTTTGTATAACCTTTATATTTGGACGAAAATTAGGGTTTAAAG
* *
43472 TAGGTTACGCGTTATCTTTGTGCCTATATAAGGGCACCAATCTCTCTTGTAAACATAAGTTGAGT
586 TAGGTTACGCATTATCTTTGTGCCTATATAAGGGCACCAATATCTCTTGTAAACATAAGTTGAGT
*
43537 TGATTAATAAAGTTGAGGTTTTATTCCTAATTGATTATCTTAACTTCATTATTCTAGTTTGAGCA
651 TGATTAATAAAGTTGAGGTTTTATTCCCAATTGATTATCTTAACTTCATTATTCTAGTTTGAGCA
* *
43602 AACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTCTTGTGAGCTTAATTGTTT
716 AACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTCTTATGAACTTAATTGTTT
* *
43667 GTGAATCTTGTGATCCTAGGTGTTCAATTGTAGGTCAAATTGAAGACTTAGGGCGACGAACGAAG
781 GTGAATCTTATGATCCTAGGTGTTCAATTGCAGGTCAAATTGAAGACTTAGGGCGACGAACGAAG
*
43732 AGATTAAGCATTGTGAAGATTATTGATCTACTCATCAAGGTGTGGAGGATATTCAAGTCGACTTT
846 AGACTAAGCATTGTGAAGATTATTGATCTACTCATCAAGGTGTGGAGGATATTCAAGTCGACTTT
43797 GATAGATATTCAAGGGTAGATTTGAATCTAAAGCAACTAGATTCGTATCAATTGGTCAACTGATG
911 GATAGATATTCAAGGGTAGATTTGAATCTAAAGCAACTAGATTCGTATCAATTGGTCAACTGATG
43862 CGCCCAAA
976 CGCCCAAA
*
43870 GCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCCTGGACTTGAAGACAAGCATGGAGAACA
1 GCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGACAAGCATGGAGAACA
43935 TGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGAAGATGCATGGAAACCATGCAGATATCGATA
66 TGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGAAGATGCATGGAAACCATGCAGATATCGATA
*
44000 ATCATGTTCCAAGTACTAAAAAGATGCCATTCGATCCATTGAAGATGCCTATTGGTCCGATGACA
131 ATCATGTTCCAAGCACTAAAAAGATGCCATTCGATCCATTGAAGATGCCTATTGGTCCGATGACA
* *
44065 AGAGCAAAAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGATGACAT
196 AGAGCAAAAGCTAAAAAATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGATGACAT
* *
44130 GAAGACTATTCAAGTTCAATTGAAGAGCTTTGATGATGATTTGAGCAAGAAAACATCAACAAATT
261 GAAGACTATTCAAGTTCAATTGAAGAGCTTTGATGATGAGTTGAGCAAGAAAACACCAACAAATT
* *
44195 ACAAGTTTATCACTTCGCTTGCTATTGATTCTAAATGGCCGGATTGACATCGTGTCATGAGTCCA
326 ACAAGTTCATCACTTCGCTTGCTATTGATTCTAAATGGCCGGATTGACATCGTGGCATGAGTCCA
* *
44260 TTAGCATTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTATTTTTAAGTTTGGAT
391 TTAGCATTAGTTTGCTTTGTTTGGACTTAATTCTATCTTAGATTAGCTTATTTTTAACTTTGGAT
44325 GTTATTTGCGTTG-GACCTTGTTTGACTAAGTCCAATCCTTAGCTATTTTTCTATTGGTTGTATT
456 GTTATTTGCGTTGTG-CCTTGTTTGACTAAGTCCAATCCTTAGCTATTTTTCTATTGGTTGTATT
* * *
44389 TTTGGATAGTATCTAGAAGGATCTTTTGTGTAACCTTTATATTTGGATGAAAATTAGGGTTTAGA
520 TTTGGATAGTATCTAGAAGGATCTTTTGTATAACCTTTATATTTGGACGAAAATTAGGGTTTAAA
* *
44454 GTAGGTTATGCATTATCTTTGTGCCTATATAAGGGCACCAATATCTCTTGTAAAGATAAGTTGAG
585 GTAGGTTACGCATTATCTTTGTGCCTATATAAGGGCACCAATATCTCTTGTAAACATAAGTTGAG
* *
44519 TTGATTAATAAAGTTGAGGTTTTATTCCCAATTGATTATCTTAGCTTCATTGTTCTAGTTTGAGC
650 TTGATTAATAAAGTTGAGGTTTTATTCCCAATTGATTATCTTAACTTCATTATTCTAGTTTGAGC
*
44584 AAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCGAACAATTAGGTCTTATGAACTTAATTGTT
715 AAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTCTTATGAACTTAATTGTT
*
44649 TGTGAATCTTATGATCTTAGGTGTTCAATTGCAGGTCAAATTGAAGACTTAGGGCGACGAACGAA
780 TGTGAATCTTATGATCCTAGGTGTTCAATTGCAGGTCAAATTGAAGACTTAGGGCGACGAACGAA
* * *
44714 GAGGCTAAGCTTTGTGAAGATTATTGATCTACTCATCAAGGTGTGGCGGA-AGTTCAAGTCGACT
845 GAGACTAAGCATTGTGAAGATTATTGATCTACTCATCAAGGTGTGGAGGATA-TTCAAGTCGACT
*
44778 TTGATAGATATTCAAGGGTAGATTTGATTCTAAAGCAACTAGATTCGTATCAATTGGT
909 TTGATAGATATTCAAGGGTAGATTTGAATCTAAAGCAACTAGATTCGTATCAATTGGT
44836 ATCAGAGCAT
Statistics
Matches: 919, Mismatches: 45, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
982 2 0.00
983 917 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (983 bp):
GCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGACAAGCATGGAGAACA
TGGAAAGGATGTGCATGGGCTGCAAGGAAGCATGAAGATGCATGGAAACCATGCAGATATCGATA
ATCATGTTCCAAGCACTAAAAAGATGCCATTCGATCCATTGAAGATGCCTATTGGTCCGATGACA
AGAGCAAAAGCTAAAAAATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGATGACAT
GAAGACTATTCAAGTTCAATTGAAGAGCTTTGATGATGAGTTGAGCAAGAAAACACCAACAAATT
ACAAGTTCATCACTTCGCTTGCTATTGATTCTAAATGGCCGGATTGACATCGTGGCATGAGTCCA
TTAGCATTAGTTTGCTTTGTTTGGACTTAATTCTATCTTAGATTAGCTTATTTTTAACTTTGGAT
GTTATTTGCGTTGTGCCTTGTTTGACTAAGTCCAATCCTTAGCTATTTTTCTATTGGTTGTATTT
TTGGATAGTATCTAGAAGGATCTTTTGTATAACCTTTATATTTGGACGAAAATTAGGGTTTAAAG
TAGGTTACGCATTATCTTTGTGCCTATATAAGGGCACCAATATCTCTTGTAAACATAAGTTGAGT
TGATTAATAAAGTTGAGGTTTTATTCCCAATTGATTATCTTAACTTCATTATTCTAGTTTGAGCA
AACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTCTTATGAACTTAATTGTTT
GTGAATCTTATGATCCTAGGTGTTCAATTGCAGGTCAAATTGAAGACTTAGGGCGACGAACGAAG
AGACTAAGCATTGTGAAGATTATTGATCTACTCATCAAGGTGTGGAGGATATTCAAGTCGACTTT
GATAGATATTCAAGGGTAGATTTGAATCTAAAGCAACTAGATTCGTATCAATTGGTCAACTGATG
CGCCCAAA
Found at i:47846 original size:2 final size:2
Alignment explanation
Indices: 47839--47868 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
47829 ATTCTTCTTC
*
47839 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47869 ACAATCTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:49683 original size:22 final size:21
Alignment explanation
Indices: 49621--49686 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
49611 TTTCAACAGA
*
49621 CCAAGTTCTAGGCAAAAGTTAT
1 CCAAGTTCT-GGCAAAAGTTGT
* * **
49643 CAAAGTTTTGGGCTGAAGTTGT
1 CCAAGTTCT-GGCAAAAGTTGT
49665 CCAAGTTCTGGACAAAAGTTGT
1 CCAAGTTCTGG-CAAAAGTTGT
49687 ATAAGTTCGG
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (21 bp):
CCAAGTTCTGGCAAAAGTTGT
Found at i:51479 original size:2 final size:2
Alignment explanation
Indices: 51467--51496 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
51457 CTTAATTAGC
51467 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51497 CACGTGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58494 original size:310 final size:310
Alignment explanation
Indices: 57932--59160 Score: 2404
Period size: 310 Copynumber: 4.0 Consensus size: 310
57922 CAGGTTAAAA
57932 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
57997 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58062 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
58127 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
58192 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
261 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
58242 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
58307 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58372 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
58437 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
58502 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
261 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
58552 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
58617 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58682 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
58747 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
* *
58812 TGTACCTAACTCCAGGTTGCCAACGAGCCCCATTTACAAATACAAAGTTAGC
261 TGTA-CTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTT-GC
58864 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
* *
58929 AAGTCCAAGTAACAAAATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58994 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
59059 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
59124 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACA
261 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACA
59161 TTCGTATTCT
Statistics
Matches: 911, Mismatches: 6, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
310 574 0.63
311 73 0.08
312 264 0.29
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (310 bp):
TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
Found at i:59128 original size:622 final size:620
Alignment explanation
Indices: 57932--59160 Score: 2404
Period size: 622 Copynumber: 2.0 Consensus size: 620
57922 CAGGTTAAAA
57932 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
57997 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58062 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
58127 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
* *
58192 TGTACTAACTCCAGGTTGCCGACGAGCCCTATTTACAAATACAAAGTTGCTACATTTCGAAATAC
261 TGTACTAACTCCAGGTTGCCAACGAGCCCCATTTACAAATACAAAGTTGCTACATTTCGAAATAC
58257 CAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAAAAGCCCAAGTAACAA
326 CAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAAAAGCCCAAGTAACAA
*
58322 CATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACAAGATTTAAGGAATAT
391 AATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACAAGATTTAAGGAATAT
58387 AAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCTTGCAAAAGTAAATCA
456 AAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCTTGCAAAAGTAAATCA
58452 CGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAATGTACTAACTCCAGG
521 CGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAATGTACTAACTCCAGG
58517 TTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
586 TTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
58552 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
1 TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
58617 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
66 AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
58682 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
131 AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
58747 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
196 TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
58812 TGTACCTAACTCCAGGTTGCCAACGAGCCCCATTTACAAATACAAAGTTAGCTACATTTCGAAAT
261 TGTA-CTAACTCCAGGTTGCCAACGAGCCCCATTTACAAATACAAAGTT-GCTACATTTCGAAAT
*
58877 ACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAAAAGTCCAAGTAAC
324 ACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAAAAGCCCAAGTAAC
58942 AAAATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACAAGATTTAAGGAAT
389 AAAATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACAAGATTTAAGGAAT
59007 ATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCTTGCAAAAGTAAAT
454 ATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCTTGCAAAAGTAAAT
59072 CACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAATGTACTAACTCCA
519 CACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAATGTACTAACTCCA
59137 GGTTGCCGACGAGCCCTATTTACA
584 GGTTGCCGACGAGCCCTATTTACA
59161 TTCGTATTCT
Statistics
Matches: 603, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
620 264 0.44
621 42 0.07
622 297 0.49
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (620 bp):
TACATTTCGAAATACCAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAA
AAGCCCAAGTAACAACATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACA
AGATTTAAGGAATATAAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCT
TGCAAAAGTAAATCACGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAA
TGTACTAACTCCAGGTTGCCAACGAGCCCCATTTACAAATACAAAGTTGCTACATTTCGAAATAC
CAAAGCGTTGTGCCTCTTCCAAATACACCACAAAGTTGCTACAAATTTAAAAGCCCAAGTAACAA
AATTTACGTTTTTCTTATTATTGGCACAACTATCTCGTAGCCAATCAACAAGATTTAAGGAATAT
AAACCATTCGGTGACCCTCCAAGGGCAAACGAGCAACTCCAAACTTCTCTTGCAAAAGTAAATCA
CGAAACAAATACAAAGAAGACTCCATGGAAGCTTGATAATTAGGGCACAATGTACTAACTCCAGG
TTGCCGACGAGCCCTATTTACAAATACAAAGTTGC
Found at i:59377 original size:18 final size:18
Alignment explanation
Indices: 59336--59377 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
59326 ATATCCATGA
*
59336 ATAATACTCCATATGAAC
1 ATAATTCTCCATATGAAC
59354 ATAATTCTCCATATGAAC
1 ATAATTCTCCATATGAAC
59372 ATAATT
1 ATAATT
59378 TGTACTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
ATAATTCTCCATATGAAC
Found at i:59896 original size:23 final size:22
Alignment explanation
Indices: 59844--59898 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
59834 CCCGCCCAAC
59844 TAAAAAAAAGAAAAAAAATAAA
1 TAAAAAAAAGAAAAAAAATAAA
**
59866 TTGGAAAAAAGAAAAGAAAATTAAA
1 -TAAAAAAAAGAAAA-AAAA-TAAA
59891 -AAAAAAAA
1 TAAAAAAAA
59899 CACCGCACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 18 0.69
24 4 0.15
25 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (22 bp):
TAAAAAAAAGAAAAAAAATAAA
Found at i:59955 original size:13 final size:15
Alignment explanation
Indices: 59927--59982 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
59917 CTTTAATTTA
59927 TTTTTCTCCTTTTTC
1 TTTTTCTCCTTTTTC
59942 TTTTTC-CCTTTTCTC
1 TTTTTCTCCTTTT-TC
*
59957 TATTTTCCTCCCCTTCTTC
1 T-TTTT-CT--CCTTTTTC
59976 TTTTTCT
1 TTTTTCT
59983 AAACCAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 6 0.18
15 9 0.26
16 4 0.12
17 3 0.09
18 4 0.12
19 3 0.09
20 5 0.15
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTCTCCTTTTTC
Found at i:62377 original size:1 final size:1
Alignment explanation
Indices: 62371--62401 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
62361 TTCTTGTTTT
62371 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
62402 CTCTACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:62477 original size:6 final size:6
Alignment explanation
Indices: 62437--62475 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
62427 AATTACGATT
*
62437 GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG GAGAGG GAG
1 GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG GAGTGG GAG
62476 AGAGATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.21, C:0.00, G:0.67, T:0.13
Consensus pattern (6 bp):
GAGTGG
Found at i:62736 original size:21 final size:21
Alignment explanation
Indices: 62712--62753 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
62702 GATAATTATT
62712 GGGGAAAAAAA-AAAGAAAAAA
1 GGGGAAAAAAAGAAA-AAAAAA
62733 GGGGAAAAAAAGAAAAAAAAA
1 GGGGAAAAAAAGAAAAAAAAA
62754 CACTCACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GGGGAAAAAAAGAAAAAAAAA
Found at i:62742 original size:20 final size:21
Alignment explanation
Indices: 62712--62752 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
62702 GATAATTATT
62712 GGGGAAAAAAAA-AAGAAAAAA
1 GGGGAAAAAAAAGAA-AAAAAA
62733 GGGG-AAAAAAAGAAAAAAAA
1 GGGGAAAAAAAAGAAAAAAAA
62753 ACACTCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GGGGAAAAAAAAGAAAAAAAA
Found at i:64809 original size:6 final size:6
Alignment explanation
Indices: 64798--64830 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
64788 CTAATTCACT
64798 TTTTTC TTTTTC -TTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
64831 TTTGGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:64815 original size:11 final size:11
Alignment explanation
Indices: 64799--64833 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
64789 TAATTCACTT
64799 TTTTCTTTTTC
1 TTTTCTTTTTC
64810 TTTTCTTTTTC
1 TTTTCTTTTTC
64821 TTTT-TTTTT-
1 TTTTCTTTTTC
64830 TTTT
1 TTTT
64834 GGGTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 5 0.21
11 15 0.62
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:65189 original size:15 final size:15
Alignment explanation
Indices: 65169--65200 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
65159 CAAATGGCCG
65169 TAACCATTTTGCTTT
1 TAACCATTTTGCTTT
*
65184 TAACCATTTTGTTTT
1 TAACCATTTTGCTTT
65199 TA
1 TA
65201 GCAGACCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (15 bp):
TAACCATTTTGCTTT
Found at i:65318 original size:11 final size:10
Alignment explanation
Indices: 65298--65330 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
65288 CGGAAGAAAT
65298 AAAATAAAAA
1 AAAATAAAAA
65308 AAAATTAAAAA
1 AAAA-TAAAAA
65319 AAAATAAAAA
1 AAAATAAAAA
65329 AA
1 AA
65331 CCTAGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:67841 original size:72 final size:72
Alignment explanation
Indices: 67753--67896 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
67743 CTTTGGTTTC
* *
67753 GGCTTTGATTTGTTAGGAGATTTTGTAGAACTAGTTCTCTTTTCTGGCTTTTTTATGGCTTTTTT
1 GGCTTTGATCTATTAGGAGATTTTGTAGAACTAGTTCTCTTTTCTGGCTTTTTTATGGCTTTTTT
67818 CCTGTCT
66 CCTGTCT
* *
67825 GGCTTTGATCTATTAGGAGATTTTGTAGAACTAGTTTTCTTTTCTGGCTTTTTTATTGCTTTTTT
1 GGCTTTGATCTATTAGGAGATTTTGTAGAACTAGTTCTCTTTTCTGGCTTTTTTATGGCTTTTTT
67890 CCTGTCT
66 CCTGTCT
67897 TTGACAACGC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.13, C:0.14, G:0.19, T:0.53
Consensus pattern (72 bp):
GGCTTTGATCTATTAGGAGATTTTGTAGAACTAGTTCTCTTTTCTGGCTTTTTTATGGCTTTTTT
CCTGTCT
Found at i:71787 original size:49 final size:49
Alignment explanation
Indices: 71676--72061 Score: 412
Period size: 49 Copynumber: 7.9 Consensus size: 49
71666 GGAAATTAGC
* * *
71676 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAATTG-A-GTAAAAAATTAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAA--GCAGGT-AAAAATAAGT
* * * * *
71726 GCCTTCCTTCCGGGAAAGGCACTTTTGGGAAAAAGTAAGTGAAAAT-AGT
1 GCCTTCCGTCCGGGAAGGGCA-TTTTGGGAAAAAGCAGGTAAAAATAAGT
* * * *
71775 GCCTTGCGTCCGGAAAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAGGTAAAAATAAGT
* *
71824 GCCTTCCGTCTC-GGAAGGGCGTTTTGGG-AAAAGCAAGT-AAAATAAGT
1 GCCTTCCGTC-CGGGAAGGGCATTTTGGGAAAAAGCAGGTAAAAATAAGT
* * *
71871 ACCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAGGTAAAAATAAGT
* * * *
71920 GTCTTCCGTACGGGAAGGGCGTTTT-GGAAAATAGCAGGTAAAAATAAAT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAGGTAAAAATAAGT
71969 GCCTTCCGTCCGGGAAGGGCATTTT-GGAAAATAGCAGGTAAAAA-AGAGT
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAA-AGCAGGTAAAAATA-AGT
* * * *
72018 GCCTTCCGTCCGGGAATGACATTTTGGGAAATAGCGGGTAAAAA
1 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAGGTAAAAA
72062 CTGAAAAATT
Statistics
Matches: 287, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
46 1 0.00
47 33 0.11
48 41 0.14
49 169 0.59
50 30 0.10
51 13 0.05
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
GCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAAGCAGGTAAAAATAAGT
Found at i:73961 original size:28 final size:28
Alignment explanation
Indices: 73929--74024 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 28
73919 TGTAACCAAG
*
73929 GAAGACCTGTCCGAGGTCTGAAACTTGA
1 GAAGACCTGTCCGAGGTCTGAAACTTAA
* * *
73957 GAAGACCAGTCCGTGGTCGACTTTAAAAC-TAA
1 GAAGACCTGTCCGAGGT---C--TGAAACTTAA
*
73989 GGAAGACCTGTCTGAGGTCTGAAACTTAA
1 -GAAGACCTGTCCGAGGTCTGAAACTTAA
74018 GAAGACC
1 GAAGACC
74025 AGTCTGTGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
28 27 0.51
29 3 0.06
30 1 0.02
31 1 0.02
32 2 0.04
33 19 0.36
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (28 bp):
GAAGACCTGTCCGAGGTCTGAAACTTAA
Found at i:73992 original size:61 final size:61
Alignment explanation
Indices: 73926--74072 Score: 208
Period size: 61 Copynumber: 2.4 Consensus size: 61
73916 TTCTGTAACC
* *
73926 AAGGAAGACCTGTCCGAGGTCTGAAACTTGAGAAGACCAGTCCGTGGTCGACT-TT-AAAACT
1 AAGGAAGACCTGTCTGAGGTCTGAAACTTAAGAAGACCAGTCCGTGGTCGA-TATTGAAAA-T
*
73987 AAGGAAGACCTGTCTGAGGTCTGAAACTTAAGAAGACCAGTCTGTGGTCGATATTGAAAAT
1 AAGGAAGACCTGTCTGAGGTCTGAAACTTAAGAAGACCAGTCCGTGGTCGATATTGAAAAT
* * *
74048 GAGAAAGACCTGTCTGAGGTATGAA
1 AAGGAAGACCTGTCTGAGGTCTGAA
74073 GTTGACATTG
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
60 1 0.01
61 73 0.94
62 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (61 bp):
AAGGAAGACCTGTCTGAGGTCTGAAACTTAAGAAGACCAGTCCGTGGTCGATATTGAAAAT
Found at i:74045 original size:33 final size:32
Alignment explanation
Indices: 73947--74045 Score: 91
Period size: 33 Copynumber: 3.2 Consensus size: 32
73937 GTCCGAGGTC
* *
73947 TGAAACTTGAGAAGACCAGTCCGTGGTCGACTT
1 TGAAACTTAAGAAGACCAGTCTGTGGTCGA-TT
* * *
73980 TAAAAC-TAAGGAAGACCTGTCTGAGGTC----
1 TGAAACTTAA-GAAGACCAGTCTGTGGTCGATT
74008 TGAAACTTAAGAAGACCAGTCTGTGGTCGATAT
1 TGAAACTTAAGAAGACCAGTCTGTGGTCGAT-T
74041 TGAAA
1 TGAAA
74046 ATGAGAAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
28 21 0.41
29 3 0.06
32 2 0.04
33 25 0.49
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (32 bp):
TGAAACTTAAGAAGACCAGTCTGTGGTCGATT
Found at i:74181 original size:61 final size:62
Alignment explanation
Indices: 74096--74328 Score: 280
Period size: 62 Copynumber: 3.8 Consensus size: 62
74086 TTGTAAATGG
74096 AGACCAGTCCGTGGTCGATATTGAAATC-GAGAAAGACCTGTCTGAGGTCTGAAATTGAAGA
1 AGACCAGTCCGTGGTCGATATTGAAATCTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGA
** * * * * *
74157 AGACCAAACCGTGGTCGACT-TTGAAAGCTTAGAAAGACCTGTCTAAGGTCTGAAACTGGAGA
1 AGACCAGTCCGTGGTCGA-TATTGAAATCTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGA
* * * *
74219 AGACCAGTCCGTGGTCGA-ATTTGAAAACTGAGAAAGACTTGTTTGAGGTC--AACTTTGAAGA
1 AGACCAGTCCGTGGTCGATA-TTGAAATCTGAGAAAGACCTGTCTGAGGTCTGAA-ATTGAAGA
* *
74280 AGACCAGTCTGTGGTCGATATTGAAAT-TGAGAAAGACCTGTTTGAGGTC
1 AGACCAGTCCGTGGTCGATATTGAAATCTGAGAAAGACCTGTCTGAGGTC
74329 AACTTTGAAA
Statistics
Matches: 146, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
60 23 0.16
61 51 0.35
62 72 0.49
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (62 bp):
AGACCAGTCCGTGGTCGATATTGAAATCTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGA
Found at i:74336 original size:27 final size:27
Alignment explanation
Indices: 74247--74336 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 27
74237 ATTTGAAAAC
*
74247 TGAGAAAGACTTGTTTGAGGTCAACTT
1 TGAGAAAGACCTGTTTGAGGTCAACTT
* * * *
74274 TGA-AGAAGACCAGTCTGTGGTCGATATTGAAAT
1 TGAGA-AAGACCTGTTTGAGGTC-A-ACT----T
74307 TGAGAAAGACCTGTTTGAGGTCAACTT
1 TGAGAAAGACCTGTTTGAGGTCAACTT
74334 TGA
1 TGA
74337 AAACTAAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 16
0.65 0.13 0.23
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 1 0.02
29 2 0.04
31 2 0.04
32 1 0.02
33 18 0.39
34 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (27 bp):
TGAGAAAGACCTGTTTGAGGTCAACTT
Found at i:74337 original size:33 final size:32
Alignment explanation
Indices: 74238--74338 Score: 79
Period size: 33 Copynumber: 3.2 Consensus size: 32
74228 CGTGGTCGAA
*
74238 TTTGAAAACTGAGAAAGACTTGTTTGAGGTCAAC
1 TTTG-AAA-TGAGAAAGACCTGTTTGAGGTCAAC
* * * *
74272 TTTG--A--AG-AAGACCAGTCTGTGGTCGA-
1 TTTGAAATGAGAAAGACCTGTTTGAGGTCAAC
74298 TATTGAAATTGAGAAAGACCTGTTTGAGGTCAAC
1 T-TTGAAA-TGAGAAAGACCTGTTTGAGGTCAAC
74332 TTTGAAA
1 TTTGAAA
74339 ACTAAGAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 17
0.66 0.12 0.22
Matches are distributed among these distances:
26 1 0.02
27 17 0.34
28 2 0.04
29 1 0.02
31 1 0.02
32 2 0.04
33 21 0.42
34 5 0.10
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (32 bp):
TTTGAAATGAGAAAGACCTGTTTGAGGTCAAC
Found at i:74455 original size:33 final size:33
Alignment explanation
Indices: 74417--74752 Score: 150
Period size: 33 Copynumber: 11.1 Consensus size: 33
74407 TGAGGTCTGG
74417 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
* * *
74450 AATTG-AGAAAGAGCTGTCTGAGGTC------GA
1 AATTGAAG-AAGACCAGTCTGTGGTCGATATTGA
* *
74477 AATTGAAGGAGACCAGTCTGTGGTCTATATTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
* * * *
74510 AATT-AAGAAAGACCTGCCTGAGGTC-A-ACT--
1 AATTGAAG-AAGACCAGTCTGTGGTCGATATTGA
74539 --TTGAAGAAGACCAGTCTGTGGTCGAT-TTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
* * *
74569 AACTG-AGAAAGACCTA-TCTGAGGTC-----CGA
1 AATTGAAG-AAGACC-AGTCTGTGGTCGATATTGA
* * *
74597 AATTGAGGACGACCGGTCTGTGGTCGATATTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
* * *
74630 AACTG-AGAAAGACCTA-TCTG-AG--G-T-TCGA
1 AATTGAAG-AAGACC-AGTCTGTGGTCGATATTGA
*
74658 AATTAAAGAAGACCAGTCTGTGGTCGATATTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
* * *
74691 AACTG-AGAAAGACCTGTCTGAGGTC------GA
1 AATTGAAG-AAGACCAGTCTGTGGTCGATATTGA
*
74718 AATTGAAGGAGACCAGTCTGTGGTCGATATTGA
1 AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
74751 AA
1 AA
74753 CTGAGAAAGA
Statistics
Matches: 218, Mismatches: 43, Indels: 84
0.63 0.12 0.24
Matches are distributed among these distances:
27 57 0.26
28 44 0.20
29 5 0.02
30 1 0.00
31 5 0.02
32 27 0.12
33 79 0.36
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (33 bp):
AATTGAAGAAGACCAGTCTGTGGTCGATATTGA
Found at i:74501 original size:60 final size:60
Alignment explanation
Indices: 74354--74776 Score: 571
Period size: 60 Copynumber: 7.0 Consensus size: 60
74344 GAAATACCTG
* * * * * * * *
74354 GAAACTGAAAAAGACTAGTCTGTGGTTGATATTGAAAATGACACAGACCTGTTTGAGGTC
1 GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
* * *
74414 TGGAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAATTGAGAAAGAGCTGTCTGAGGTC
1 -GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
* * * * *
74475 GAAATTGAAGGAGACCAGTCTGTGGTCTATATTGAAATTAAGAAAGACCTGCCTGAGGTC
1 GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
* *
74535 -AACTTTGAAGAAGACCAGTCTGTGGTCGAT-TTGAAACTGAGAAAGACCTATCTGAGGTCC
1 GAA-ATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGT-C
* * * *
74595 GAAATTGAGGACGACCGGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTTC
1 GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGG-TC
*
74656 GAAATTAAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
1 GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
* *
74716 GAAATTGAAGGAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTC
1 GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
74776 G
1 G
74777 GAAACTAAAG
Statistics
Matches: 322, Mismatches: 35, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
59 26 0.08
60 162 0.50
61 133 0.41
62 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (60 bp):
GAAATTGAAGAAGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTC
Found at i:74786 original size:121 final size:119
Alignment explanation
Indices: 74365--74786 Score: 553
Period size: 121 Copynumber: 3.5 Consensus size: 119
74355 AAACTGAAAA
* * * * * * * * *
74365 AGACTAGTCTGTGGTTGATATTGAAAATGACACAGACCTGTTTGAGGTCTGGAATTGAAGAAGAC
1 AGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTC--GAACTAAAGAAGAC
* *
74430 CAGTCTGTGGTCGATATTGAAATTGAGAAAGAGCTGTCTGAGGTCGAAATTGAAGG
64 CAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTCGAAATTGAAGG
* * * ** *
74486 AGACCAGTCTGTGGTCTATATTGAAATTAAGAAAGACCTGCCTGAGGTC-AACTTTGAAGAAGAC
1 AGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTCGAAC--TAAAGAAGAC
*
74550 CAGTCTGTGGTCGAT-TTGAAACTGAGAAAGACCTATCTGAGGTCCGAAATTG-AGG
64 CAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGT-CGAAATTGAAGG
* *
74605 ACGACCGGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTTCGAAATTAAAGAAGA
1 A-GACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGG-TCG-AACTAAAGAAGA
74670 CCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTCGAAATTGAAGG
63 CCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTCGAAATTGAAGG
74727 AGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTCGGAAACTAAAG
1 AGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTC-G-AACTAAAG
74787 GGAAACTGAC
Statistics
Matches: 267, Mismatches: 24, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
118 2 0.01
119 29 0.11
120 75 0.28
121 128 0.48
122 31 0.12
123 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (119 bp):
AGACCAGTCTGTGGTCGATATTGAAACTGAGAAAGACCTATCTGAGGTCGAACTAAAGAAGACCA
GTCTGTGGTCGATATTGAAACTGAGAAAGACCTGTCTGAGGTCGAAATTGAAGG
Found at i:74900 original size:47 final size:46
Alignment explanation
Indices: 74814--74906 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 46
74804 AAGGAAACCA
*
74814 ACTGTGGTCACCAAATTGTAGACTCATATGGAAGCGAGAAAAGACCG
1 ACTGTGATCACCAAATTGTAGACTCATA-GGAAGCGAGAAAAGACCG
*
74861 ACTGTGATCACCAAATTGTA-ACTTTGCATA-GAAGTGAGAAAAGACC
1 ACTGTGATCACCAAATTGTAGAC--T-CATAGGAAGCGAGAAAAGACC
74907 AACTTTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
46 2 0.05
47 34 0.83
48 1 0.02
49 4 0.10
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (46 bp):
ACTGTGATCACCAAATTGTAGACTCATAGGAAGCGAGAAAAGACCG
Found at i:74983 original size:48 final size:48
Alignment explanation
Indices: 74891--75439 Score: 757
Period size: 48 Copynumber: 11.5 Consensus size: 48
74881 ACTTTGCATA
* *** ***
74891 GAAGTGAGAAAAGACCAACTTTAATC-GAAGGACCACTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* *
74938 GAAGTGAGGAAACACCAACTTGGGTGGGAAGGATTTCTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* *
74986 GAAGTGAGGAAAGATCAACTTGGGTCGGAAGGATTACTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * *
75034 GAAGTGAGGAAAGACCAACTTGGGTCGAAATGATTTCTGACTCGCATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * *
75082 GAAGTGAGGAAAGACCAACTTGGGTCGGCATGATTACTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * *
75130 GAAGCGAGGAAAGACCAACTAGGGTCGGAAGGATTACTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * *
75178 GAAGCGAGGAAAGACCAACTGGGGTCAGAAGGATTTCTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * *
75226 AAAGTGAGGAAAGACCAACTTGGGTC-GAACGATTTTTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* * * * *
75273 GAAGTGGGGAAAAAACAACTTAGGTC-GAACGATTTCTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
* *
75320 GAAGTGAGGAAAGACCCACTTGGGTC-GAAGGGATTACTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAA-GGATTTCTGACTCACATG
75368 GAAGTGAGGAAAGACCAACTTGGGTC-GAAGGATTTCTGACTCACATG
1 GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
75415 GAAGTGAGGAAAGACCAACTTGGGT
1 GAAGTGAGGAAAGACCAACTTGGGT
75440 TGAAACGAAT
Statistics
Matches: 451, Mismatches: 49, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
47 146 0.32
48 305 0.68
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (48 bp):
GAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTCTGACTCACATG
Found at i:75586 original size:68 final size:67
Alignment explanation
Indices: 75497--75674 Score: 212
Period size: 68 Copynumber: 2.6 Consensus size: 67
75487 CTAAGGCTTT
* * *
75497 AACTGACTCGTATGGAAACGAGTTTGGCTTGTAGGAAAGCCCCTGCTGCTTGGATCGAACCAAGG
1 AACTAACTCGTATGGAAACGAGTTTGGCTTGT-GGAAAACCCCTGATGCTTGGATCGAACCAAGG
75562 CTA
65 CTA
* * *** * *
75565 AACTAACTCGCATTGAAACGAGTTTGGAACGTGGAAAAACCTCTGATGCTTGGATGGAACCAAGG
1 AACTAACTCGTATGGAAACGAGTTTGGCTTGTGG-AAAACCCCTGATGCTTGGATCGAACCAAGG
75630 CTA
65 CTA
75633 AACTAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
1 AACT-A---ACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
75675 GCCAAAGCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
67 2 0.02
68 59 0.66
69 1 0.01
71 4 0.04
72 24 0.27
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (67 bp):
AACTAACTCGTATGGAAACGAGTTTGGCTTGTGGAAAACCCCTGATGCTTGGATCGAACCAAGGC
TA
Found at i:76828 original size:10 final size:10
Alignment explanation
Indices: 76813--76852 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
76803 TCTTTGCTTA
76813 TTTTTTTTTC
1 TTTTTTTTTC
76823 TTTTTTTTTC
1 TTTTTTTTTC
**
76833 GATTTTTTTC
1 TTTTTTTTTC
76843 TTTTTCTTTT
1 TTTTT-TTTT
76853 TACCATGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 21 0.84
11 4 0.16
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:80431 original size:49 final size:49
Alignment explanation
Indices: 80246--80650 Score: 388
Period size: 49 Copynumber: 8.2 Consensus size: 49
80236 TTTGTCCGAA
* * * * *
80246 AAGGGTATTTTAGGAAAAAAGC-GAGTAGAAATTAGCGCCTTCCGTCCGGG
1 AAGGGCATTTTAGG-AAATAGCAG-GTAAAAATAAGTGCCTTCCGTCCGGG
* * * * *
80296 AAGGGCGTTTTAGGAAAAAGCAAGTAAAAAATTAGTGTCTTCCGTCCGGG
1 AAGGGCATTTTAGGAAATAGCAGGT-AAAAATAAGTGCCTTCCGTCCGGG
* * * * * ** * *
80346 AAAGGCACTTTTGGGAAAAAGTAAGTGGAAAT-AGTGCCTTCCGTCTGCG
1 AAGGGCA-TTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGG
* *
80395 AAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCTGTG
1 AAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGG
* * * * **
80444 AAGGGCGTTTTGGGAAA-ACGCAAGT-AAAATAAGTACCTTCCGTCCAAG
1 AAGGGCATTTTAGGAAATA-GCAGGTAAAAATAAGTGCCTTCCGTCCGGG
* * * * *
80492 AAGGGCATTTTGGGAAATAGCAGGTAAAGATAAATGTCTTCCGTACGGG
1 AAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGG
* * *
80541 AAGGGCATTTTTGGAAATAGCATGTAAAAATAAATGCCTTCCGTCCGGG
1 AAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGG
* *
80590 AAGGGCATTTTGGGAAATAGCAGGTAAAAA-AGAGTGCCTTCCGTCCGAG
1 AAGGGCATTTTAGGAAATAGCAGGTAAAAATA-AGTGCCTTCCGTCCGGG
80639 AAGGGCATTTTA
1 AAGGGCATTTTA
80651 TCAGCCTTTT
Statistics
Matches: 298, Mismatches: 49, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
48 60 0.20
49 180 0.60
50 42 0.14
51 16 0.05
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (49 bp):
AAGGGCATTTTAGGAAATAGCAGGTAAAAATAAGTGCCTTCCGTCCGGG
Found at i:80557 original size:146 final size:144
Alignment explanation
Indices: 80282--80649 Score: 434
Period size: 146 Copynumber: 2.5 Consensus size: 144
80272 AGAAATTAGC
* * * *
80282 GCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAAATTAGTGTCTTCCGTCCGGGA
1 GCCTTCCGTCCGGGAAGGGCGTTTT-GGGAAAAGCAAGT--AAAATAAGTGCCTTCCGTCCGAGA
* * * *
80347 AAGGCACTTTTGGGAAAAAGTAAGTGGAAATAGTGCCTTCCGTCTGCGAAGGGCATTTTAGGAAA
63 AGGGCA-TTTTGGGAAAAAGCAAGTGAAAATAATGCCTTCCGTCTGCGAAGGGCATTTTAGGAAA
*
80412 TAGCAGGTAAAAATAAGT
127 TAGCAGGTAAAAATAAAT
* * * *
80430 GCCTTCCGTCTGTGAAGGGCGTTTTGGGAAAACGCAAGTAAAATAAGTACCTTCCGTCCAAGAAG
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-GCAAGTAAAATAAGTGCCTTCCGTCCGAGAAG
* * * * *
80495 GGCATTTTGGGAAATAGCAGGT-AAAGATAAATGTCTTCCGTAC-GGGAAGGGCATTTTTGGAAA
65 GGCATTTTGGGAAAAAGCAAGTGAAA-AT-AATGCCTTCCGT-CTGCGAAGGGCATTTTAGGAAA
*
80558 TAGCATGTAAAAATAAAT
127 TAGCAGGTAAAAATAAAT
* * *
80576 GCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAGCAGGTAAAAAAGAGTGCCTTCCGTCCGAGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AGCAAGTAAAATA-AGTGCCTTCCGTCCGAGAA
80641 GGGCATTTT
64 GGGCATTTT
80650 ATCAGCCTTT
Statistics
Matches: 188, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
144 2 0.01
145 17 0.09
146 106 0.56
147 34 0.18
148 29 0.15
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (144 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAGCAAGTAAAATAAGTGCCTTCCGTCCGAGAAGG
GCATTTTGGGAAAAAGCAAGTGAAAATAATGCCTTCCGTCTGCGAAGGGCATTTTAGGAAATAGC
AGGTAAAAATAAAT
Found at i:81299 original size:30 final size:28
Alignment explanation
Indices: 81228--81305 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
81218 GAACTTACAC
*
81228 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
81256 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
81287 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
81306 TTTTTTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:87651 original size:19 final size:20
Alignment explanation
Indices: 87608--87644 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
87598 ATCCAATGTG
*
87608 ATTAAGAGAAAGTAAGGAAA
1 ATTAAGAGAAAGTAAGCAAA
87628 ATTAAG-GAAAGTAAGCA
1 ATTAAGAGAAAGTAAGCA
87645 TAGTTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.57, C:0.03, G:0.24, T:0.16
Consensus pattern (20 bp):
ATTAAGAGAAAGTAAGCAAA
Found at i:87853 original size:36 final size:36
Alignment explanation
Indices: 87781--87866 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
87771 ATTGGCTTCG
* * *
87781 TTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAA
1 TTTCAAGGAAATTAAGTAAAGAAAAGACTGACTTAA
* *
87817 TTTCAAGGAAATTAAGTAAA-TATAGACTGACTTTAA
1 TTTCAAGGAAATTAAGTAAAGAAAAGACTGAC-TTAA
87853 TTTCAAGGAAATTA
1 TTTCAAGGAAATTA
87867 GACTGGTAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 8 0.18
36 36 0.82
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (36 bp):
TTTCAAGGAAATTAAGTAAAGAAAAGACTGACTTAA
Found at i:87885 original size:22 final size:22
Alignment explanation
Indices: 87860--88307 Score: 304
Period size: 22 Copynumber: 21.0 Consensus size: 22
87850 TAATTTCAAG
*
87860 GAAATTAGACTGGTAGAAGACT
1 GAAATTAGACTGATAGAAGACT
87882 GAAATTAGA---AT-G-AGACT
1 GAAATTAGACTGATAGAAGACT
** **
87899 GAAAAAAGACTGATATTAGACT
1 GAAATTAGACTGATAGAAGACT
*
87921 GAAATTAGACTGATATAAGACT
1 GAAATTAGACTGATAGAAGACT
* * *
87943 GATATTAAACTGA-AAATAGACT
1 GAAATTAGACTGATAGA-AGACT
** **
87965 GAAAAAAGACTGATACCAGACT
1 GAAATTAGACTGATAGAAGACT
87987 GAAATTAGACTGATAGAAGACT
1 GAAATTAGACTGATAGAAGACT
88009 GAAATTAGA---AT-G-AGACT
1 GAAATTAGACTGATAGAAGACT
* **
88026 GAGAA-AAGACTGATATTAGACT
1 GA-AATTAGACTGATAGAAGACT
*
88048 GAAATTAGACTGATATTAA-ACT
1 GAAATTAGACTGATA-GAAGACT
* * * *
88070 GAAAATAGACTGAAAAAAAACT
1 GAAATTAGACTGATAGAAGACT
* * * *
88092 GATATCAGACTGAAAAAAGACT
1 GAAATTAGACTGATAGAAGACT
* * **
88114 GATATTAGACTGAAATTAGACT
1 GAAATTAGACTGATAGAAGACT
* * *
88136 GATATAAGACTGATATTAA-ACT
1 GAAATTAGACTGATA-GAAGACT
* * *
88158 GAAAATAGACTGAAAAAAGACT
1 GAAATTAGACTGATAGAAGACT
*
88180 GATATTAGACTGATAGAAGACT
1 GAAATTAGACTGATAGAAGACT
88202 GAAATTAGA---AT-G-AGACT
1 GAAATTAGACTGATAGAAGACT
** **
88219 GAAAAAAGACTGATATTAGACT
1 GAAATTAGACTGATAGAAGACT
*
88241 GAAATTAGACTGATATAAGACT
1 GAAATTAGACTGATAGAAGACT
* * * **
88263 GATATTAAACTGAAATCAGACT
1 GAAATTAGACTGATAGAAGACT
*
88285 GAAATTAGACTGATAAAAGACT
1 GAAATTAGACTGATAGAAGACT
88307 G
1 G
88308 GCTTAGTTTC
Statistics
Matches: 341, Mismatches: 62, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
17 34 0.10
18 5 0.01
19 5 0.01
20 6 0.02
21 8 0.02
22 278 0.82
23 5 0.01
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (22 bp):
GAAATTAGACTGATAGAAGACT
Found at i:87910 original size:11 final size:11
Alignment explanation
Indices: 87894--88307 Score: 218
Period size: 11 Copynumber: 38.5 Consensus size: 11
87884 AATTAGAATG
*
87894 AGACTGAAAAA
1 AGACTGAAATA
* *
87905 AGACTGATATT
1 AGACTGAAATA
*
87916 AGACTGAAATT
1 AGACTGAAATA
*
87927 AGACTGATATA
1 AGACTGAAATA
*
87938 AGACTGATATTA
1 AGACTGA-AATA
87950 A-ACTGAAA-A
1 AGACTGAAATA
*
87959 TAGACTGAAAAA
1 -AGACTGAAATA
* **
87971 AGACTGATACC
1 AGACTGAAATA
*
87982 AGACTGAAATT
1 AGACTGAAATA
* *
87993 AGACTGATAGA
1 AGACTGAAATA
88004 AGACTGAAAT-
1 AGACTGAAATA
* *
88014 -TA--G-AATG
1 AGACTGAAATA
88021 AGACTGAGAA-A
1 AGACTGA-AATA
* *
88032 AGACTGATATT
1 AGACTGAAATA
*
88043 AGACTGAAATT
1 AGACTGAAATA
*
88054 AGACTGATATTA
1 AGACTGA-AATA
88066 A-ACTGAAA-A
1 AGACTGAAATA
*
88075 TAGACTGAAAAA
1 -AGACTGAAATA
* * *
88087 AAACTGATATC
1 AGACTGAAATA
*
88098 AGACTGAAAAA
1 AGACTGAAATA
* *
88109 AGACTGATATT
1 AGACTGAAATA
*
88120 AGACTGAAATT
1 AGACTGAAATA
*
88131 AGACTGATATA
1 AGACTGAAATA
*
88142 AGACTGATATTA
1 AGACTGA-AATA
88154 A-ACTGAAA-A
1 AGACTGAAATA
*
88163 TAGACTGAAAAA
1 -AGACTGAAATA
* *
88175 AGACTGATATT
1 AGACTGAAATA
* *
88186 AGACTGATAGA
1 AGACTGAAATA
88197 AGACTGAAAT-
1 AGACTGAAATA
* *
88207 -TA--G-AATG
1 AGACTGAAATA
*
88214 AGACTGAAAAA
1 AGACTGAAATA
* *
88225 AGACTGATATT
1 AGACTGAAATA
*
88236 AGACTGAAATT
1 AGACTGAAATA
*
88247 AGACTGATATA
1 AGACTGAAATA
*
88258 AGACTGATATTA
1 AGACTGA-AATA
*
88270 A-ACTGAAATC
1 AGACTGAAATA
*
88280 AGACTGAAATT
1 AGACTGAAATA
88291 AGACTGATAA-A
1 AGACTGA-AATA
88302 AGACTG
1 AGACTG
88308 GCTTAGTTTC
Statistics
Matches: 307, Mismatches: 69, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
6 6 0.02
7 2 0.01
8 2 0.01
9 5 0.02
10 12 0.04
11 261 0.85
12 19 0.06
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (11 bp):
AGACTGAAATA
Found at i:87941 original size:33 final size:33
Alignment explanation
Indices: 87894--88299 Score: 332
Period size: 33 Copynumber: 12.6 Consensus size: 33
87884 AATTAGAATG
* *
87894 AGACTGAAAAAAGACTGATATTAGACTGAAATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* *
87927 AGACTGATATAAGACTGATATTAAACTGAAAAT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* * **
87960 AGACTGAAAAAAGACTGATACCAGACTGAAATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* * *
87993 AGACTGATAGAAGACTGAAATT--A--G-AATG
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* *
88021 AGACTGAGAAAAGACTGATATTAGACTGAAATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* * **
88054 AGACTGATATTAA-ACTGAAAATAGACTGAAAAA
1 AGACTGATA-TAAGACTGATATTAGACTGAAATT
* * * ** *
88087 AAACTGATATCAGACTGAAAAAAGACTGATATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* * * *
88120 AGACTGAAATTAGACTGATATAAGACTGATATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* * * ** *
88153 AAACTGA-AAATAGACTGAAAAAAGACTGATATT
1 AGACTGATATA-AGACTGATATTAGACTGAAATT
* * *
88186 AGACTGATAGAAGACTGAAATTAGAATG-----
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* *
88214 AGACTGAAAAAAGACTGATATTAGACTGAAATT
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* *
88247 AGACTGATATAAGACTGATATTAAACTGAAATC
1 AGACTGATATAAGACTGATATTAGACTGAAATT
* *
88280 AGACTGAAATTAGACTGATA
1 AGACTGATATAAGACTGATA
88300 AAAGACTGGC
Statistics
Matches: 302, Mismatches: 57, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
28 46 0.15
29 1 0.00
30 1 0.00
31 1 0.00
32 4 0.01
33 245 0.81
34 4 0.01
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (33 bp):
AGACTGATATAAGACTGATATTAGACTGAAATT
Found at i:88036 original size:116 final size:116
Alignment explanation
Indices: 87916--88249 Score: 360
Period size: 116 Copynumber: 2.9 Consensus size: 116
87906 GACTGATATT
* *
87916 AGACTGAAATTAGACTGATATAAGACTGATATTAAACTGAAAATAGACTGAAAAAAGACTGATAC
1 AGACTGAAATTAGACTGAAATAAGACTGATATTAAACTGAAAATAGACTGAAAAAAAACTGATAC
**
87981 CAGACTGAAATTAGACTGATAGAAGACTGAAATTAGAATGAGACTGAGAAA
66 CAGACTGAAAAAAGACTGATAGAAGACTGAAATTAGAATGAGACTGAGAAA
* * *
88032 AGACTGATATTAGACTGAAATTAGACTGATATTAAACTGAAAATAGACTGAAAAAAAACTGATAT
1 AGACTGAAATTAGACTGAAATAAGACTGATATTAAACTGAAAATAGACTGAAAAAAAACTGATAC
** * * *
88097 CAGACTGAAAAAAGACTGATATTAGACTGAAATTAGACTGATATAAGACTGATATTA
66 CAGACTGAAAAAAGACTGATAGAAGACTGAAATT--A--GA-ATGAGACTGAGA-AA
* * * * * *
88154 A-ACTGAAAATAGACTGAAAAAAGACTGATATTAGACTGATAGA-AGACTGAAATTAGAA-TG--
1 AGACTGAAATTAGACTGAAATAAGACTGATATTAAACTGA-AAATAGACTGAAA-AAAAACTGAT
**
88214 ---AGACTGAAAAAAGACTGATATTAGACTGAAATTAGA
64 ACCAGACTGAAAAAAGACTGATAGAAGACTGAAATTAGA
88250 CTGATATAAG
Statistics
Matches: 190, Mismatches: 20, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
112 2 0.01
114 1 0.01
116 123 0.65
118 1 0.01
120 2 0.01
121 54 0.28
122 7 0.04
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.23
Consensus pattern (116 bp):
AGACTGAAATTAGACTGAAATAAGACTGATATTAAACTGAAAATAGACTGAAAAAAAACTGATAC
CAGACTGAAAAAAGACTGATAGAAGACTGAAATTAGAATGAGACTGAGAAA
Found at i:88346 original size:36 final size:36
Alignment explanation
Indices: 88299--88618 Score: 477
Period size: 36 Copynumber: 9.0 Consensus size: 36
88289 TTAGACTGAT
88299 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
88335 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
88371 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAT
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
88407 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * *
88443 --AAGACTAGCTTAATTTCAAGGAAATTAAGTAAA-
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
*
88476 ACAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
88512 -AAAGAACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAG-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
88548 AAAGGACTGGCTTAGTTTCAAGGAAACTAGGTGAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
88584 AAAAGACTGGCTTAATTTCAAGGAAATTAAGTAAA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA
88619 AAGACACATG
Statistics
Matches: 261, Mismatches: 18, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
34 32 0.12
35 32 0.12
36 194 0.74
37 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.24
Consensus pattern (36 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
Found at i:88503 original size:177 final size:177
Alignment explanation
Indices: 88301--88643 Score: 602
Period size: 177 Copynumber: 1.9 Consensus size: 177
88291 AGACTGATAA
88301 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAA-AGACTGGCTTAGTTTCAAGGAAACTAG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGA-ACTGGCTTAGTTTCAAGGAAACTAG
*
88365 GTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAATAAAAGACTGGCTTAATTTCAAGG
65 GTAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGG
*
88430 AAATTAAGTAAAGAAGAC-TA-GCTTAATTTCAAGGAAATTAAGTAAAAC
130 AAATTAAGTAAA-AAGACACATGCTTAATTT-AAGGAAATTAAGTAAAAC
88478 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGAACTGGCTTAGTTTCAAGGAAACTAGG
1 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGAACTGGCTTAGTTTCAAGGAAACTAGG
* *
88543 TAAAGAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTGAAGAAAAGACTGGCTTAATTTCAAGGA
66 TAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGA
88608 AATTAAGTAAAAAGACACATGCTTAATTTAAGGAAA
131 AATTAAGTAAAAAGACACATGCTTAATTTAAGGAAA
88644 GGAAATTAAG
Statistics
Matches: 159, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
176 5 0.03
177 144 0.91
178 10 0.06
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (177 bp):
AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAGAACTGGCTTAGTTTCAAGGAAACTAGG
TAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAATTTCAAGGA
AATTAAGTAAAAAGACACATGCTTAATTTAAGGAAATTAAGTAAAAC
Found at i:88738 original size:32 final size:34
Alignment explanation
Indices: 88642--88775 Score: 129
Period size: 36 Copynumber: 3.9 Consensus size: 34
88632 AATTTAAGGA
*
88642 AAGGA-AATTAAGTA-AAATAAAGAACTTAATT-
1 AAGGATAATTAAGTAGCAATAAAGAACTTAATTC
* *
88673 TAGGATAATTAAGTGAAGTCAATAAA-AGGCTTAATTC
1 AAGGATAATTAAGT--AG-CAATAAAGA-ACTTAATTC
88710 AAGGA-AATTAAGTAG-AATAAAGAACTTAATTC
1 AAGGATAATTAAGTAGCAATAAAGAACTTAATTC
88742 -AGGATAATTAAGTGTAGTCAATAAAGAACTTAAT
1 AAGGATAATTAA--GTAG-CAATAAAGAACTTAAT
88776 CTAAAAAGAG
Statistics
Matches: 85, Mismatches: 5, Indels: 21
0.77 0.05 0.19
Matches are distributed among these distances:
31 8 0.09
32 28 0.33
33 1 0.01
34 7 0.08
35 1 0.01
36 36 0.42
37 4 0.05
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (34 bp):
AAGGATAATTAAGTAGCAATAAAGAACTTAATTC
Found at i:88774 original size:68 final size:68
Alignment explanation
Indices: 88642--88775 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
88632 AATTTAAGGA
* *
88642 AAGGAAATTAAGTAAAATAAAGAACTTAATTTAGGATAATTAAGTGAAGTCAATAAAAGGCTTAA
1 AAGGAAATTAAGTAAAATAAAGAACTTAATTCAGGATAATTAAGTGAAGTCAATAAAAGACTTAA
88707 TTC
66 TTC
* *
88710 AAGGAAATTAAGTAGAATAAAGAACTTAATTCAGGATAATTAAGTGTAGTCAAT-AAAGAACTTA
1 AAGGAAATTAAGTAAAATAAAGAACTTAATTCAGGATAATTAAGTGAAGTCAATAAAAG-ACTTA
88774 AT
65 AT
88776 CTAAAAAGAG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 4 0.07
68 57 0.93
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (68 bp):
AAGGAAATTAAGTAAAATAAAGAACTTAATTCAGGATAATTAAGTGAAGTCAATAAAAGACTTAA
TTC
Found at i:92500 original size:21 final size:22
Alignment explanation
Indices: 92474--92517 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
92464 ATTGTGCATA
92474 TTCA-TTTTCTTTAATA-GAAAT
1 TTCATTTTTCTTTAA-AGGAAAT
92495 TTCATTTTTCTTTAAAGGAAAT
1 TTCATTTTTCTTTAAAGGAAAT
92517 T
1 T
92518 GCAGCATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (22 bp):
TTCATTTTTCTTTAAAGGAAAT
Found at i:96413 original size:52 final size:52
Alignment explanation
Indices: 96352--96474 Score: 156
Period size: 52 Copynumber: 2.4 Consensus size: 52
96342 ATTTCATTCA
* *
96352 AAGTTTTCAAAGCATTCAATTTAGCCCTCTTCAAAGTGGGAAAGTTCCCATT
1 AAGTTTTCAAAACATTCAATTTAGCCCTCTTCAAAGTGGGAAAGTTCCCATC
** ** * *
96404 AAGTTTTCAAAATGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCCCATC
1 AAGTTTTCAAAACATTCAATTTAGCCCTCTTCAAAGTGGGAAAGTTCCCATC
**
96456 ATCTTTTCAAAACATTCAA
1 AAGTTTTCAAAACATTCAA
96475 ACAGCATTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (52 bp):
AAGTTTTCAAAACATTCAATTTAGCCCTCTTCAAAGTGGGAAAGTTCCCATC
Found at i:101692 original size:16 final size:16
Alignment explanation
Indices: 101649--101694 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
101639 AAAAACAGAG
101649 GAGAAGAAG-AGAAAAA
1 GAGAA-AAGAAGAAAAA
*
101665 GA-ATAAAAAAGAAAAA
1 GAGA-AAAGAAGAAAAA
101681 GAGAAAAGAAGAAA
1 GAGAAAAGAAGAAA
101695 TTGAATGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 21 0.84
17 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
GAGAAAAGAAGAAAAA
Found at i:103112 original size:36 final size:36
Alignment explanation
Indices: 103072--103142 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
103062 GTCACCTTTC
*
103072 AGCAATCATCAAAGTTTATCAA-AGTTGACTGGAAAT
1 AGCAATCATCAAAGTTTATCAAGA-TCGACTGGAAAT
* *
103108 AGCAATCATCGAGGTTTATCAAGATCGACTGGAAA
1 AGCAATCATCAAAGTTTATCAAGATCGACTGGAAA
103143 CAGGTCATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (36 bp):
AGCAATCATCAAAGTTTATCAAGATCGACTGGAAAT
Found at i:103175 original size:38 final size:38
Alignment explanation
Indices: 103123--103347 Score: 326
Period size: 38 Copynumber: 5.9 Consensus size: 38
103113 TCATCGAGGT
*
103123 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAC
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAC
*
103161 TTATCAAG-TCCGACTGGAAACAGGTCATCTTTCAACAA
1 TTATCAAGAT-CGACTGGAAACAGGTCATCTTTCAACAC
* * *
103199 TTATCAAGATTGACTGGAAACAGGTCATCTTTCAATAG
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAC
*
103237 TTATCAAGATTGACTGGAAACAGGTCATCTTTCAACAC
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAC
* * * *
103275 TTATCAAGACCGACTAGAAACAAGTCATCTTTCAACAG
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAC
* *
103313 TTATCAAGATCGATTAGAAACAGGTCATCTTTCAA
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAA
103348 TTTTCAGCTG
Statistics
Matches: 170, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
37 1 0.01
38 168 0.99
39 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (38 bp):
TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAC
Found at i:103288 original size:114 final size:114
Alignment explanation
Indices: 103123--103348 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
103113 TCATCGAGGT
* * * *
103123 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCACTTATCAAGTCCGACTGGAAACAGGTCA
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACACTTATCAAGACCGACTAGAAACAAGTCA
* *
103188 TCTTTCAACAATTATCAAGATTGACTGGAAACAGGTCATCTTTCAATAG
66 TCTTTCAACAATTATCAAGATCGACTAGAAACAGGTCATCTTTCAATAG
*
103237 TTATCAAGATTGACTGGAAACAGGTCATCTTTCAACACTTATCAAGACCGACTAGAAACAAGTCA
1 TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACACTTATCAAGACCGACTAGAAACAAGTCA
* *
103302 TCTTTCAACAGTTATCAAGATCGATTAGAAACAGGTCATCTTTCAAT
66 TCTTTCAACAATTATCAAGATCGACTAGAAACAGGTCATCTTTCAAT
103349 TTTCAGCTGC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (114 bp):
TTATCAAGATCGACTGGAAACAGGTCATCTTTCAACACTTATCAAGACCGACTAGAAACAAGTCA
TCTTTCAACAATTATCAAGATCGACTAGAAACAGGTCATCTTTCAATAG
Found at i:103475 original size:61 final size:62
Alignment explanation
Indices: 103341--103478 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 62
103331 AACAGGTCAT
** * * *
103341 CTTTCAATTTTCAGCTGCTCCACAAGGGAGTCCATGCCAACAACTTTTCAACACTCCAACAG
1 CTTTCAATTTTCAGCTAATCCACAAGGGAGGCCATGACAACAACTTTTCAACACTCCAACAA
* * * * * * *
103403 CTTTCAGTTTTCAGTTAATCC-CAA-GGAGGCCATTACAACAATTTTTCAGCATTCCAGCAA
1 CTTTCAATTTTCAGCTAATCCACAAGGGAGGCCATGACAACAACTTTTCAACACTCCAACAA
103463 CTTTTCAATTTTCAGC
1 C-TTTCAATTTTCAGC
103479 AGTTTTCAAC
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
60 29 0.48
61 15 0.25
62 17 0.28
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (62 bp):
CTTTCAATTTTCAGCTAATCCACAAGGGAGGCCATGACAACAACTTTTCAACACTCCAACAA
Found at i:103632 original size:35 final size:35
Alignment explanation
Indices: 103585--103664 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
103575 AACAACTTTC
103585 ATTTTCAGTTGCTCACAATTGGGGGCATTATAGCA
1 ATTTTCAGTTGCTCACAATTGGGGGCATTATAGCA
*
103620 GTTTTCAGTTGCTCACAATTGGGGGCATTATAGCA
1 ATTTTCAGTTGCTCACAATTGGGGGCATTATAGCA
103655 ATTTTCAGTT
1 ATTTTCAGTT
103665 CAGCAGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (35 bp):
ATTTTCAGTTGCTCACAATTGGGGGCATTATAGCA
Found at i:104196 original size:21 final size:22
Alignment explanation
Indices: 104170--104213 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
104160 ATTGTGCATA
104170 TTCA-TTTTCTTTAATA-GAAAT
1 TTCATTTTTCTTTAA-AGGAAAT
104191 TTCATTTTTCTTTAAAGGAAAT
1 TTCATTTTTCTTTAAAGGAAAT
104213 T
1 T
104214 GCAGCATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (22 bp):
TTCATTTTTCTTTAAAGGAAAT
Found at i:108155 original size:52 final size:51
Alignment explanation
Indices: 108098--108220 Score: 149
Period size: 52 Copynumber: 2.4 Consensus size: 51
108088 ATTTCATTCA
* *
108098 AAGTTTTCAAAGCATTCAATTTA-GCCTTCTTCAAAGTGGGAAAGTTCCCATT
1 AAGTTTTCAAAACATTCAATTTAGGCCTT-TTCAAAGTGGGAAAGTTCCC-GT
** * *
108150 AAGTTTTCAAAATGTTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCCCGT
1 AAGTTTTCAAAACATTCAATTTAGGCCTTTTCAAAGTGGGAAAGTTCCCGT
*
108201 AATCTTTTCAAAACATTCAA
1 AA-GTTTTCAAAACATTCAA
108221 ACAACATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
51 3 0.05
52 53 0.88
53 4 0.07
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (51 bp):
AAGTTTTCAAAACATTCAATTTAGGCCTTTTCAAAGTGGGAAAGTTCCCGT
Found at i:109429 original size:36 final size:38
Alignment explanation
Indices: 109367--109437 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 38
109357 AGCCTGTAAT
*
109367 TTTTGCTCTCAACGTTTCACTCTTTCTT-TGTTTTATA
1 TTTTGCTCCCAACGTTTCACTCTTTCTTATGTTTTATA
*
109404 TTTTGCTCCCAAC-TTTCTCTCTTTCTTATGTTTT
1 TTTTGCTCCCAACGTTTCACTCTTTCTTATGTTTT
109438 TACTTCTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.11, C:0.24, G:0.07, T:0.58
Consensus pattern (38 bp):
TTTTGCTCCCAACGTTTCACTCTTTCTTATGTTTTATA
Found at i:112013 original size:30 final size:31
Alignment explanation
Indices: 111979--112042 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
111969 CCGCGAATGA
**
111979 CAATTCAGGTCCTGCCGTTAGCC-CTTGTGT
1 CAATTCAGGTCCTAACGTTAGCCTCTTGTGT
* * *
112009 CAATTTAGGTGCTAACGTTATCCTCTTGTGT
1 CAATTCAGGTCCTAACGTTAGCCTCTTGTGT
112040 CAA
1 CAA
112043 AACAGGTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (31 bp):
CAATTCAGGTCCTAACGTTAGCCTCTTGTGT
Found at i:113606 original size:12 final size:12
Alignment explanation
Indices: 113589--113647 Score: 100
Period size: 12 Copynumber: 4.9 Consensus size: 12
113579 TATTTGTTAG
113589 GCGGTCGGTTTA
1 GCGGTCGGTTTA
113601 GCGGTCGGTTTA
1 GCGGTCGGTTTA
*
113613 GCTGTCGGTTTA
1 GCGGTCGGTTTA
113625 GCGGTCGGTTTA
1 GCGGTCGGTTTA
*
113637 GCGGTTGGTTT
1 GCGGTCGGTTT
113648 TTAAACAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.07, C:0.15, G:0.41, T:0.37
Consensus pattern (12 bp):
GCGGTCGGTTTA
Found at i:114518 original size:21 final size:21
Alignment explanation
Indices: 114492--114536 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
114482 TAATACTGGA
114492 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
**
114513 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
114534 TTG
1 TTG
114537 ACGTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:114804 original size:32 final size:32
Alignment explanation
Indices: 114750--114847 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 32
114740 TACCGTGGCG
* *
114750 AAGCCGCCCCACTTGGGAGGCTTCGCCACGGC
1 AAGCCGCCCCACTAGGGCGGCTTCGCCACGGC
* * **
114782 AAGCCGCCCCA-TGAGGGCGGCTTCCCCATGAA
1 AAGCCGCCCCACT-AGGGCGGCTTCGCCACGGC
* *
114814 AAGGCCGCCCCACTAGGGCGGCTTAGCCAGGGC
1 AA-GCCGCCCCACTAGGGCGGCTTCGCCACGGC
114847 A
1 A
114848 GGCCTGTCCC
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
31 1 0.02
32 26 0.50
33 24 0.46
34 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.32, T:0.11
Consensus pattern (32 bp):
AAGCCGCCCCACTAGGGCGGCTTCGCCACGGC
Found at i:115036 original size:33 final size:34
Alignment explanation
Indices: 114951--115037 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 34
114941 CCCCACCAGT
114951 GCCGTCCCCCTGGGGCGG--CTGAGCCATGGCCAA
1 GCCG-CCCCCTGGGGCGGCACTGAGCCATGGCCAA
*
114984 GCCGCCCTCCTGGGGCGGCACT-A-CCATGGCCAG
1 GCCGCCC-CCTGGGGCGGCACTGAGCCATGGCCAA
115017 GCCGCCTCCCTGGGGCGGCAC
1 GCCGCC-CCCTGGGGCGGCAC
115038 CGGTACTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
32 3 0.06
33 42 0.86
34 2 0.04
35 2 0.04
ACGTcount: A:0.10, C:0.43, G:0.36, T:0.11
Consensus pattern (34 bp):
GCCGCCCCCTGGGGCGGCACTGAGCCATGGCCAA
Found at i:115157 original size:32 final size:32
Alignment explanation
Indices: 115104--115246 Score: 207
Period size: 32 Copynumber: 4.4 Consensus size: 32
115094 AAAAAACATT
* * *
115104 GCCGCCCTAGTGGGGCAGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
115136 GCCGTCGTAGTGGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
115168 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
115200 GCCGTCCTAGTGGGGA-GGCTCCGCCGTGGCAGA
1 GCCGTCCTAGT-GGGACGGCT-AGCCGTGGCAGA
115233 GCCGTCCTAGTGGG
1 GCCGTCCTAGTGGG
115247 GAGGCTCCGC
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 76 0.75
33 25 0.25
ACGTcount: A:0.13, C:0.29, G:0.43, T:0.15
Consensus pattern (32 bp):
GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
Found at i:115211 original size:64 final size:65
Alignment explanation
Indices: 115104--115252 Score: 230
Period size: 64 Copynumber: 2.3 Consensus size: 65
115094 AAAAAACATT
* * *
115104 GCCGCCCTAGTGGGGCAGCTAGCCGTGGCAGAGCCGTCGTAGT-GGGACGGCT-AGCCGTGGCAG
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGGA-GGCTCAGCCGTGGCAG
115167 A
65 A
*
115168 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGGAGGCTCAGCCGTGGCAGA
*
115233 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGCGGCT
115253 CCGCGTGGCT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
64 44 0.56
65 34 0.44
ACGTcount: A:0.13, C:0.28, G:0.43, T:0.15
Consensus pattern (65 bp):
GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTGGGGAGGCTCAGCCGTGGCAGA
Found at i:116907 original size:40 final size:42
Alignment explanation
Indices: 116852--116934 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 42
116842 CGTGCGGCTG
116852 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
116893 TTTTA-TTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
116934 T
1 T
116935 GAAATTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 18 0.44
41 23 0.56
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (42 bp):
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
Found at i:117024 original size:17 final size:17
Alignment explanation
Indices: 116999--117033 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
116989 TGGAAAAGAC
* *
116999 AAGAGAATATGGAGAAG
1 AAGAAAATATGAAGAAG
117016 AAGAAAATATGAAGAAG
1 AAGAAAATATGAAGAAG
117033 A
1 A
117034 GGAGAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (17 bp):
AAGAAAATATGAAGAAG
Found at i:117244 original size:11 final size:11
Alignment explanation
Indices: 117230--117267 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
117220 ATTCATAACA
117230 AATTTATAATT
1 AATTTATAATT
117241 AATTTATAATT
1 AATTTATAATT
117252 -ATTTGATAATT
1 AATTT-ATAATT
*
117263 TATTT
1 AATTT
117268 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.