Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000990.1 Hibiscus syriacus cultivar Beakdansim tig00001982_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: 274437
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:220176 original size:48 final size:48
Alignment explanation
Indices: 220104--220201 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
220094 TCCACAACAA
* *
220104 CAGCCTCGTTTCCAACACCATCCTTACTAATCAAATTATCCTGGCCAC
1 CAGCCTCCTTTCCAACACCATCCTTACTAATCAAATTATCCTGCCCAC
* * * * *
220152 CAGCCTCCTTTCGAACACCTTCCTTATTCATCAAATTATTCTGCCCAC
1 CAGCCTCCTTTCCAACACCATCCTTACTAATCAAATTATCCTGCCCAC
220200 CA
1 CA
220202 AGACTCAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.26, C:0.38, G:0.07, T:0.30
Consensus pattern (48 bp):
CAGCCTCCTTTCCAACACCATCCTTACTAATCAAATTATCCTGCCCAC
Found at i:221474 original size:11 final size:12
Alignment explanation
Indices: 221449--221478 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
221439 AAAGTAAGTG
221449 TTTAAATTAAAT
1 TTTAAATTAAAT
221461 TTTAAATT-AAT
1 TTTAAATTAAAT
221472 TTTAAAT
1 TTTAAAT
221479 ATTTAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAAATTAAAT
Found at i:221478 original size:18 final size:17
Alignment explanation
Indices: 221455--221497 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
221445 AGTGTTTAAA
221455 TTAAATTTTAAA-TTAATT
1 TTAAATTTTAAAGTT--TT
221473 TTAAATATTTAAAGTTTT
1 TTAAAT-TTTAAAGTTTT
221491 TTAAATT
1 TTAAATT
221498 AAAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 6 0.26
20 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTTAAAGTTTT
Found at i:225801 original size:18 final size:18
Alignment explanation
Indices: 225767--225801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
225757 ATATATCAAT
* *
225767 AACAAAATCATCTAGAAA
1 AACAAAATCACCAAGAAA
225785 AACAAAATCACCAAGAA
1 AACAAAATCACCAAGAA
225802 TTTCAAGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.11
Consensus pattern (18 bp):
AACAAAATCACCAAGAAA
Found at i:229560 original size:21 final size:19
Alignment explanation
Indices: 229544--229612 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 19
229534 GCTGTTGTCG
229544 TTGTTGTTGACGATGTTGC
1 TTGTTGTTGACGATGTTGC
*
229563 -TGTTGTTGACGATATTGC
1 TTGTTGTTGACGATGTTGC
*
229581 TGTTGTTGTTGACGACGTTGTTC
1 --TTGTTGTTGACGATGTTG--C
229604 TTGTTGTTG
1 TTGTTGTTG
229613 CCATCGTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 17 0.40
21 24 0.57
23 1 0.02
ACGTcount: A:0.10, C:0.10, G:0.30, T:0.49
Consensus pattern (19 bp):
TTGTTGTTGACGATGTTGC
Found at i:229566 original size:18 final size:18
Alignment explanation
Indices: 229545--229588 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
229535 CTGTTGTCGT
*
229545 TGTTGTTGACGATGTTGC
1 TGTTGTTGACGATATTGC
229563 TGTTGTTGACGATATTGC
1 TGTTGTTGACGATATTGC
229581 TGTTGTTG
1 TGTTGTTG
229589 TTGACGACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.09, G:0.32, T:0.48
Consensus pattern (18 bp):
TGTTGTTGACGATATTGC
Found at i:229602 original size:18 final size:18
Alignment explanation
Indices: 229543--229609 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
229533 TGCTGTTGTC
229543 GTTGTTGTTGACGATGTT
1 GTTGTTGTTGACGATGTT
* *
229561 GCTGTTGTTGACGATATTGCT
1 GTTGTTGTTGACG--A-TGTT
*
229582 GTTGTTGTTGACGACGTT
1 GTTGTTGTTGACGATGTT
*
229600 GTTCTTGTTG
1 GTTGTTGTTG
229610 TTGCCATCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 23 0.57
19 1 0.03
20 1 0.03
21 15 0.38
ACGTcount: A:0.10, C:0.10, G:0.31, T:0.48
Consensus pattern (18 bp):
GTTGTTGTTGACGATGTT
Found at i:231482 original size:68 final size:68
Alignment explanation
Indices: 231373--231506 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
231363 TTTCTATTTA
*
231373 TTCTTCCCTTCTCTCTCCATTTCTCTCCTCAACCTCAATAAATTAAGTTTTCAGCCATTACGTCG
1 TTCTTCCCTTCTCTCTCCATTTCTCTCCTCAACCTCAATAAATTAAGTTTTCAGCAATTACGTCG
231438 GAT
66 GAT
* *
231441 TTCTTCCCTTCTCTCTCCATTTCTCTCCTCAACCTCAATAAATTTAGTTTTCGGCAATTACGTCG
1 TTCTTCCCTTCTCTCTCCATTTCTCTCCTCAACCTCAATAAATTAAGTTTTCAGCAATTACGTCG
231506 G
66 G
231507 CCGCTGTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.19, C:0.32, G:0.08, T:0.40
Consensus pattern (68 bp):
TTCTTCCCTTCTCTCTCCATTTCTCTCCTCAACCTCAATAAATTAAGTTTTCAGCAATTACGTCG
GAT
Found at i:233436 original size:21 final size:20
Alignment explanation
Indices: 233350--233507 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
233340 AAATGACCAA
**
233350 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
233369 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
233389 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
233409 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
233430 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
233451 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
233471 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
233492 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
233508 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:233536 original size:20 final size:20
Alignment explanation
Indices: 233474--233666 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
233464 CGATTTTCCA
* ** *
233474 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
233494 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
233514 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
233534 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
233554 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
233574 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
233594 ATATCGTAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
233614 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
233634 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
233654 AAATCGCAACGCG
1 AAATCGCAACGCG
233667 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 140 0.98
21 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:234087 original size:33 final size:33
Alignment explanation
Indices: 234048--234118 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
234038 TTCACTTAGA
* *
234048 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
234081 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
234114 TTTCA
1 TTTCA
234119 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:234255 original size:41 final size:38
Alignment explanation
Indices: 234191--234307 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
234181 TTCAATTTGC
* *
234191 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
234229 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
234270 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
234303 AGAAT
1 AGAAT
234308 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:234271 original size:21 final size:21
Alignment explanation
Indices: 234198--234273 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
234188 TGCAGAAGAG
* *
234198 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
234219 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
234239 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
234260 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
234274 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:234277 original size:14 final size:14
Alignment explanation
Indices: 234258--234314 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
234248 GAGAAATGAC
234258 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
234272 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
234291 AATCGCAACGAGAG
1 AATCGCAACGAGAG
234305 AATCGCAACG
1 AATCGCAACG
234315 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:234295 original size:33 final size:33
Alignment explanation
Indices: 234250--234330 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
234240 CGCAACGAGA
*
234250 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
234283 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
234316 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
234331 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:234348 original size:19 final size:19
Alignment explanation
Indices: 234326--234423 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
234316 GAAACCAAAA
*
234326 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
234345 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
234359 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
234378 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
234392 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
234411 TCGCGTTGCGATT
1 TCGCGTTGCGATT
234424 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:234367 original size:14 final size:14
Alignment explanation
Indices: 234348--234437 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
234338 TTTCATTTCG
234348 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
234362 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
234381 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
234395 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
234412 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
234428 CGTTGCGATT
1 CGTTGCGATT
234438 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:234377 original size:33 final size:33
Alignment explanation
Indices: 234331--234445 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
234321 CAAAATCGCA
*
234331 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
234364 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
234397 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
234430 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
234446 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:236302 original size:93 final size:93
Alignment explanation
Indices: 236143--236616 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
236133 TAGATTGCTT
*
236143 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
236208 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
236236 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
236301 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
236329 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
236394 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
236422 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
236487 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
236515 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
236580 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
236608 AGTAAATTT
1 AGTAAATTT
236617 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:236699 original size:19 final size:19
Alignment explanation
Indices: 236660--236788 Score: 102
Period size: 19 Copynumber: 7.3 Consensus size: 19
236650 TAGTTTACTT
*
236660 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
236680 TCGCAACGCGAAACTAAAA
1 TCGCAACGCGAAACTAAAA
236699 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
236718 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
236732 TCGCAATGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
236751 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACTAAAA
*
236765 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
236784 TCGCA
1 TCGCA
236789 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 27
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.20
15 1 0.01
16 6 0.07
17 6 0.07
18 2 0.02
19 45 0.49
20 13 0.14
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:236735 original size:14 final size:14
Alignment explanation
Indices: 236716--236772 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
236706 GCGAAATGAA
*
236716 AATCGCAACGACAG
1 AATCGCAACGAAAG
236730 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
236747 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
236763 AATCGCAACG
1 AATCGCAACG
236773 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:236743 original size:33 final size:33
Alignment explanation
Indices: 236697--236788 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
236687 GCGAAACTAA
*
236697 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
236730 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
236763 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
236789 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:236806 original size:19 final size:19
Alignment explanation
Indices: 236784--236918 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
236774 GAAACCAAAA
*
236784 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
236803 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
236819 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
236836 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
236852 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
236869 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
236888 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
236908 TCGTGTTGCGA
1 TCGCGTTGCGA
236919 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:236825 original size:14 final size:14
Alignment explanation
Indices: 236806--236862 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
236796 TTTCATTTCG
236806 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
236820 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
236837 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
236853 CGTTGCGATT
1 CGTTGCGATT
236863 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:236831 original size:33 final size:33
Alignment explanation
Indices: 236789--236881 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
236779 CAAAATCGCA
*
236789 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
236822 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
236855 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
236882 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:238866 original size:14 final size:14
Alignment explanation
Indices: 238847--238882 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
238837 ATTGTTTAAT
238847 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
238861 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
238875 TGATTTGT
1 TGATTTGT
238883 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:239013 original size:19 final size:19
Alignment explanation
Indices: 238989--239138 Score: 153
Period size: 19 Copynumber: 8.4 Consensus size: 19
238979 AAAATTGACT
238989 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
239008 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239027 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
239041 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239060 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
239079 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
239093 ATCGCAATGC-AACGA-GAGA
1 ATCGCAATGCGAA--ATGAAA
239112 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
239132 ATCGCAA
1 ATCGCAA
239139 CGAGAGAATC
Statistics
Matches: 111, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
14 20 0.18
15 2 0.02
16 3 0.03
17 3 0.03
18 1 0.01
19 70 0.63
20 10 0.09
21 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:239049 original size:33 final size:33
Alignment explanation
Indices: 239007--239157 Score: 171
Period size: 33 Copynumber: 4.4 Consensus size: 33
238997 GCGAAATGAA
239007 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
239040 AATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
* * *
239078 AATCGCAACGAGAGAATCG-CAAT-GCAACGAGAG
1 AATCGCAATGCGA-AAT-GAAAATCGCAACGAGAG
239111 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
239145 AATCGCAATGCGA
1 AATCGCAATGCGA
239158 TTTTCATTTC
Statistics
Matches: 98, Mismatches: 10, Indels: 20
0.77 0.08 0.16
Matches are distributed among these distances:
32 1 0.01
33 46 0.47
34 24 0.24
35 1 0.01
36 1 0.01
37 1 0.01
38 17 0.17
39 6 0.06
40 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:239067 original size:52 final size:52
Alignment explanation
Indices: 238989--239157 Score: 279
Period size: 52 Copynumber: 3.2 Consensus size: 52
238979 AAAATTGACT
238989 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
239041 ATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
239093 ATCGCAATGC-AACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAA--ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
239146 ATCGCAATGCGA
1 ATCGCAATGCGA
239158 TTTTCATTTC
Statistics
Matches: 110, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
51 2 0.02
52 73 0.66
53 34 0.31
54 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:239105 original size:71 final size:72
Alignment explanation
Indices: 238989--239138 Score: 225
Period size: 71 Copynumber: 2.1 Consensus size: 72
238979 AAAATTGACT
* *
238989 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGA
239053 AATGAAA
66 AATGAAA
* *
239060 ATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCG-CAAT-GCAACGAGAGAATCGCAATGCG
1 ATCGCAATGCGAAATGAAAATCGCAACGAGA-AAT-GAAAATCGCAACGAGAGAATCGCAATGCG
239123 GAAATGAAA
64 GAAATGAAA
239132 ATCGCAA
1 ATCGCAA
239139 CGAGAGAATC
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
71 49 0.68
72 22 0.31
73 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGA
AATGAAA
Found at i:241491 original size:12 final size:12
Alignment explanation
Indices: 241474--241498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
241464 TCTTCGGGGA
241474 CTTTTTCTTCTT
1 CTTTTTCTTCTT
241486 CTTTTTCTTCTT
1 CTTTTTCTTCTT
241498 C
1 C
241499 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:241707 original size:24 final size:24
Alignment explanation
Indices: 241673--241719 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
241663 CTGAAACATC
241673 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
241697 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
241720 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:242649 original size:20 final size:20
Alignment explanation
Indices: 242399--242648 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
242389 AAATTTCAGT
* * *
242399 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
242419 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
242439 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
242459 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
242479 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
242499 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
242519 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
242539 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
242559 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
242579 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
242599 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
242619 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
242639 GTTGCGATTT
1 GTTGCGATTT
242649 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:242665 original size:21 final size:21
Alignment explanation
Indices: 242635--242717 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
242625 ATTTTCATAT
*
242635 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
242656 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
242677 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
242698 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
242718 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:242708 original size:42 final size:43
Alignment explanation
Indices: 242615--242713 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
242605 ATTTATGTGT
* *
242615 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
242656 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
242698 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
242714 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:242936 original size:8 final size:9
Alignment explanation
Indices: 242908--242957 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
242898 AGAAAATAAC
*
242908 AAATAATAA
1 AAATATTAA
242917 AAATATTAA
1 AAATATTAA
242926 AAATATTAA
1 AAATATTAA
*
242935 AAGATAAATAA
1 AA-AT-ATTAA
242946 AAA-ATTAA
1 AAATATTAA
242954 AAAT
1 AAAT
242958 GTTTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 7 0.20
9 19 0.54
10 3 0.09
11 6 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAATATTAA
Found at i:244178 original size:7 final size:7
Alignment explanation
Indices: 244177--244226 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
244167 TATAATAAAT
244177 AATAATA
1 AATAATA
244184 AATAAATA
1 AAT-AATA
*
244192 AGTAATA
1 AATAATA
*
244199 TATAATA
1 AATAATA
244206 TAATAAT-
1 -AATAATA
244213 AATAATA
1 AATAATA
244220 AATAATA
1 AATAATA
244227 TGATATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 6 0.17
7 19 0.53
8 11 0.31
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:244197 original size:25 final size:24
Alignment explanation
Indices: 244156--244374 Score: 95
Period size: 25 Copynumber: 9.1 Consensus size: 24
244146 TTGAAATGGT
244156 TAAATAAAATATATAATAAATAATAA
1 TAAAT-AAATA-ATAATAAATAATAA
*
244182 TAAATAAATAAGTAATATATAAT-A
1 TAAATAAATAA-TAATAAATAATAA
244206 T-AAT-AATAATAATAAATAAT-A
1 TAAATAAATAATAATAAATAATAA
* * *
244227 TGATATAATATAAT-ATATATACT-A
1 T-AAATAA-ATAATAATAAATAATAA
* ** *
244251 TAATATAAAAAAT-ATATGT-ATTA
1 TAA-ATAAATAATAATAAATAATAA
244274 TAAATATAATATATAATAAA-AATAA
1 TAAATA-AATA-ATAATAAATAATAA
* *
244299 TATATAATATAACTATATAACTATATAA
1 TAAATAA-ATAA-TA-ATAAATA-ATAA
*
244327 T-AATATAT-ATAATATAA-AATATA
1 TAAATAAATAATAATA-AATAATA-A
* * *
244350 TAACTATATAATAATATAT-ATAA
1 TAAATAAATAATAATAAATAATAA
244373 TA
1 TA
244375 GCATAATAAC
Statistics
Matches: 152, Mismatches: 20, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
21 12 0.08
22 12 0.08
23 31 0.20
24 34 0.22
25 43 0.28
26 11 0.07
27 4 0.03
28 5 0.03
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (24 bp):
TAAATAAATAATAATAAATAATAA
Found at i:244288 original size:45 final size:44
Alignment explanation
Indices: 244194--244383 Score: 131
Period size: 43 Copynumber: 4.5 Consensus size: 44
244184 AATAAATAAG
*
244194 TAATATATAATATAATAATAATAATAAATAATATGATAT-AATA
1 TAATATATAATATAATAATAATAAAAAATAATATGATATAAATA
244237 TAATATAT-ATACT-ATAAT-ATAAAAAAT-ATATGTATTATAAATA
1 TAATATATAATA-TAATAATAATAAAAAATAATATG-A-TATAAATA
* * *
244280 TAATATATAATA-AA-AATAATATATAATATAA-CT-ATATAACTA
1 TAATATATAATATAATAATAATA-A-AAAATAATATGATATAAATA
* *
244322 T-ATA-ATAATAT-AT-ATAATATAAAAT-ATATAACTATATAATA
1 TAATATATAATATAATAATAATAAAAAATAATATGA-TATA-AATA
**
244363 -ATATATATAATAGCATAATAA
1 TA-ATATATAATATAATAATAA
244384 CTATATAACA
Statistics
Matches: 117, Mismatches: 9, Indels: 40
0.70 0.05 0.24
Matches are distributed among these distances:
37 1 0.01
38 5 0.04
39 1 0.01
40 22 0.19
41 15 0.13
42 25 0.21
43 32 0.27
44 6 0.05
45 9 0.08
46 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (44 bp):
TAATATATAATATAATAATAATAAAAAATAATATGATATAAATA
Found at i:244299 original size:81 final size:79
Alignment explanation
Indices: 244194--244418 Score: 212
Period size: 81 Copynumber: 2.8 Consensus size: 79
244184 AATAAATAAG
*
244194 TAATAT-ATAATATAATAATAATAATAAATAATATGATATAATATAATATATATACTATAATATA
1 TAATATAAT-ATATAATAAAAATAATAAATAATAT-A-ATAATATAATATATATACTATAATATA
* *
244258 AAAAATATATGTATTATA
63 AAAAATATAT-AACTATA
* *
244276 -AATATAATATATAATAAAAATAATATATAATATAACT-ATATAACTATATAATAATATATATAA
1 TAATATAATATATAATAAAAATAATAAATAATATAA-TAATATAA-TATAT-ATACTATA-AT-A
*
244339 TATAAAATATATAACTATA
61 TAAAAAATATATAACTATA
** *
244358 TAATA-ATATATATAAT-AGCATAATAACT-ATATAACATAAT-TAATATATATACTATAATATA
1 TAATATA-ATATATAATAAAAATAATAAATAATAT-A-ATAATATAATATATATACTATAATATA
244419 TCTCCGAACG
Statistics
Matches: 121, Mismatches: 11, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
78 3 0.02
79 9 0.07
80 14 0.12
81 44 0.36
82 23 0.19
83 28 0.23
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (79 bp):
TAATATAATATATAATAAAAATAATAAATAATATAATAATATAATATATATACTATAATATAAAA
AATATATAACTATA
Found at i:244364 original size:34 final size:33
Alignment explanation
Indices: 244158--244419 Score: 177
Period size: 34 Copynumber: 7.7 Consensus size: 33
244148 GAAATGGTTA
*
244158 AATAAAATATATAATA-AATAATA-ATAA-ATA-
1 AATAATATATATAATATAA-AATATATAATATAT
*
244188 AATAAGTAATATATAATATAATAATA-ATAATAAAT
1 AATAA-T-ATATATAATATAA-AATATATAATATAT
*
244223 AATATGATATAATATAATAT-ATATACTATAATATA-
1 AATA--ATAT-ATATAATATAAAATA-TATAATATAT
* * *
244258 AAAAATATATGTATTAT-AAATATA-ATATATAAT
1 AATAATATATATAATATAAAATATATA-ATAT-AT
* *
244291 AAAAATAATATATAATAT-AACTATATAACTATAT
1 AATAAT-ATATATAATATAAAATATATAA-TATAT
244325 AATAATATATATAATATAAAATATATAACTATAT
1 AATAATATATATAATATAAAATATATAA-TATAT
*
244359 AATAATATATATAATAGCATAATAACTATATAACATA-
1 AATAATATATATAAT---ATAA-AA-TATATAATATAT
* * *
244396 ATTAATATATATACTATAATATAT
1 AATAATATATATAATATAAAATAT
244420 CTCCGAACGA
Statistics
Matches: 193, Mismatches: 17, Indels: 42
0.77 0.07 0.17
Matches are distributed among these distances:
30 6 0.03
31 6 0.03
32 25 0.13
33 33 0.17
34 62 0.32
35 14 0.07
36 17 0.09
37 18 0.09
38 5 0.03
39 7 0.04
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (33 bp):
AATAATATATATAATATAAAATATATAATATAT
Found at i:244365 original size:65 final size:63
Alignment explanation
Indices: 244159--244419 Score: 99
Period size: 63 Copynumber: 4.2 Consensus size: 63
244149 AAATGGTTAA
*
244159 ATAAAATATATAATAAATAATAATAAATAA-ATAAGTA-AT-A-TATAATATAATAATA-ATAAT
1 ATAAAATATATAAT-AATAATAATATATAATATAA-TATATAACTAT-ATA-AATAATATAT-AT
244219 AA-
61 AAT
* * * * ** * *
244221 ATAATATGATATAAT-ATAAT-ATATATACTATAATATAAAAAATATATGTATTATAAATATAAT
1 ATAAAAT-ATATAATAATAATAATATATAATATAATAT-ATAACTATATAAATAATATATATAAT
* * *
244284 ATATAATA-AAAATAATATATAATATA-ACTATATAACTATATAA-TAATATATATAATATA-A-
1 ATAAAATATATAATAATA-ATAATATATA--ATATAA-TATATAACT-ATATAAATAATATATAT
244344 AAT
61 AAT
* * **
244347 ATATAA-CTAT-ATAATAAT-ATATATAATAGCATA-ATAACTATATAACATAAT-TAATATATA
1 ATAAAATATATAATAATAATAATATATAATATAATATATAACTATATAA-ATAATAT-ATATA-A
244407 T
63 T
*
244408 ACTATAATATAT
1 A-TAAAATATAT
244420 CTCCGAACGA
Statistics
Matches: 153, Mismatches: 21, Indels: 49
0.69 0.09 0.22
Matches are distributed among these distances:
57 10 0.07
58 9 0.06
59 5 0.03
60 14 0.09
61 19 0.12
62 31 0.20
63 33 0.22
64 10 0.07
65 19 0.12
66 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (63 bp):
ATAAAATATATAATAATAATAATATATAATATAATATATAACTATATAAATAATATATATAAT
Found at i:244389 original size:102 final size:96
Alignment explanation
Indices: 244156--244419 Score: 275
Period size: 102 Copynumber: 2.6 Consensus size: 96
244146 TTGAAATGGT
* *
244156 TAAATAAAATATATAATAAATAATAATAAATAAATAAGTAATATATAATATAATA-ATAATAATA
1 TAAATAAAATATATAATAAATAATAATATATAAATAAATAATATATAATATAATATATAATAATA
*
244220 AATAATATGATATAATATAATATATATACTA
66 AATAATATGATATAATATAAAATATATACTA
*
244251 TAATATAAAAAATATATGTATTATAAAT-ATAATATATAATAAAAATAATATATAATATAACTAT
1 TAA-AT--AAAATATA--TA--ATAAATAATAATATATAA-ATAAATAATATATAATATAA-TAT
244315 ATAACT-ATATAATAATAT-ATATAATATAAAATATATAACTA
57 ATAA-TAATA-AATAATATGATATAATATAAAATATAT-ACTA
* * *
244356 TATAATAATATATATAATAGCATAATAACTATATAACATAATTAATATATATACTATAATATAT
1 TA-AATAAAATATATAATA-AATAATAA-TATATAA-ATAAATAATATATA-A-TATAATATAT
244420 CTCCGAACGA
Statistics
Matches: 141, Mismatches: 9, Indels: 30
0.78 0.05 0.17
Matches are distributed among these distances:
95 3 0.02
96 2 0.01
98 8 0.06
99 3 0.02
100 4 0.03
101 16 0.11
102 43 0.30
103 15 0.11
104 29 0.21
105 17 0.12
106 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (96 bp):
TAAATAAAATATATAATAAATAATAATATATAAATAAATAATATATAATATAATATATAATAATA
AATAATATGATATAATATAAAATATATACTA
Found at i:244390 original size:2 final size:2
Alignment explanation
Indices: 244196--244371 Score: 67
Period size: 2 Copynumber: 97.5 Consensus size: 2
244186 TAAATAAGTA
*
244196 AT AT AT A- AT AT A- AT A- AT A- AT A- AT AA AT A- AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * *
244233 A- AT AT A- AT AT AT AT ACT AT A- AT AT A- AA AA AT AT AT GT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
244272 -T AT AA AT AT A- AT AT AT A- AT AA AA AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
244309 A- ACT AT AT A- ACT AT AT A- AT A- AT AT AT AT A- AT AT A- AA AT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244347 AT AT A- ACT AT AT A- AT A- AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A
244372 ATAGCATAAT
Statistics
Matches: 135, Mismatches: 10, Indels: 58
0.67 0.05 0.29
Matches are distributed among these distances:
1 24 0.18
2 104 0.77
3 7 0.05
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (2 bp):
AT
Found at i:244756 original size:35 final size:35
Alignment explanation
Indices: 244715--244790 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
244705 AAAACAGTCC
* * * *
244715 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAA
*
244750 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAA
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAA
244785 TCAATT
1 TCAATT
244791 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAA
Found at i:245335 original size:130 final size:130
Alignment explanation
Indices: 245189--245436 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
245179 TATTTATATA
* **
245189 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
245254 TTAGCACATGATCATGACATGTGTCATTGGTGACCCATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
245319 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
245384 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
245437 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:245467 original size:130 final size:129
Alignment explanation
Indices: 245203--245467 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
245193 ATTTGGTCCT
* ** *
245203 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
245268 TGACATGTGTCATTGGTGACCCATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
245333 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
245398 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
245462 -A
128 CA
245463 AAATT
1 AAATT
245468 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:245797 original size:28 final size:27
Alignment explanation
Indices: 245766--245828 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
245756 AGTTGATACA
*
245766 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
245794 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
245822 ATATTTT
1 ATATTTT
245829 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:245930 original size:17 final size:19
Alignment explanation
Indices: 245908--245942 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
245898 ATTTCTTATT
245908 AAAAATA-AAAT-ATTCAA
1 AAAAATATAAATGATTCAA
245925 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
245943 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATATAAATGATTCAA
Found at i:246016 original size:16 final size:16
Alignment explanation
Indices: 245951--246017 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
245941 CATACATTAA
*
245951 TATATGAATATATTTT
1 TATATAAATATATTTT
* ** * *
245967 TTTATTTATATATCTA
1 TATATAAATATATTTT
* **
245983 AATATAAATATACATT
1 TATATAAATATATTTT
245999 TATATAAATATATTTT
1 TATATAAATATATTTT
246015 TAT
1 TAT
246018 TCGTATATAG
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (16 bp):
TATATAAATATATTTT
Found at i:246105 original size:17 final size:17
Alignment explanation
Indices: 246078--246125 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
246068 TTTATACAAG
246078 AAAAATA-AAATATATC
1 AAAAATATAAATATATC
246094 AAAAATATAAATGAT-TC
1 AAAAATATAAAT-ATATC
* *
246111 ATAAATTTAAATATA
1 AAAAATATAAATATA
246126 AATTGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 16 0.59
18 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAAATATAAATATATC
Found at i:247395 original size:14 final size:14
Alignment explanation
Indices: 247376--247402 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
247366 TCGTTCATTT
247376 AAATGAATGAACAC
1 AAATGAATGAACAC
247390 AAATGAATGAACA
1 AAATGAATGAACA
247403 TAAACGAACG
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:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (14 bp):
AAATGAATGAACAC
Found at i:247508 original size:24 final size:24
Alignment explanation
Indices: 247445--247510 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
247435 CACAATAAAT
* * *
247445 GAATGTTAACGAACAAAAACGAAC
1 GAATGTAAACGAACACAAACGAAA
*
247469 GAACGTAAACGAACACAAACGAAA
1 GAATGTAAACGAACACAAACGAAA
247493 GAATGTAAACGAACACAA
1 GAATGTAAACGAACACAA
247511 TAAATGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.56, C:0.18, G:0.17, T:0.09
Consensus pattern (24 bp):
GAATGTAAACGAACACAAACGAAA
Found at i:247984 original size:17 final size:17
Alignment explanation
Indices: 247944--247991 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
247934 TGATTCAATT
* *
247944 TATATTTAAATTTATGA
1 TATATTTATATTTTTGA
247961 -ATCATTTATATTTTTGA
1 TAT-ATTTATATTTTTGA
247978 TATATTT-TATTTTT
1 TATATTTATATTTTT
247992 CTTGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 16 0.59
18 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
TATATTTATATTTTTGA
Found at i:248071 original size:16 final size:16
Alignment explanation
Indices: 248052--248085 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
248042 CTATATACGA
248052 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
248068 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
248084 AT
1 AT
248086 TTAGATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:248160 original size:16 final size:18
Alignment explanation
Indices: 248128--248161 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
248118 TATTAATGTA
248128 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
248146 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
248162 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:248381 original size:25 final size:25
Alignment explanation
Indices: 248353--248417 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
248343 ACAATTTATC
*
248353 AAATATAATATTTTTTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
248378 AAATATAATATTTTCTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
248403 AAATATAATATTTTC
1 AAATATAATATTTTC
248418 CCATCATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
AAATATAATATTTTCTATTGTAAAA
Found at i:248860 original size:130 final size:130
Alignment explanation
Indices: 248656--248903 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
248646 AATTTTATTC
* *
248656 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
248721 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAAATTAGGACCAAATTGATAGCATATATAAA
* * *
248786 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
248851 CCTAATTAAATGATTAATTTGTTAAATTCTATTTAAATTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAAATTAGGACCAAATTGAT
248904 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAAATTAGGACCAAATTGATAGCATATATAAA
Found at i:249350 original size:35 final size:35
Alignment explanation
Indices: 249300--249375 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
249290 AATTGAATTT
* *
249300 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
249335 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
249370 AATTGA
1 AATTGA
249376 GGTCTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:252672 original size:16 final size:16
Alignment explanation
Indices: 252651--252681 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
252641 GGATCTGTGA
252651 AGGAATTGGAATATGT
1 AGGAATTGGAATATGT
252667 AGGAATTGGAATATG
1 AGGAATTGGAATATG
252682 GATCTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (16 bp):
AGGAATTGGAATATGT
Found at i:253348 original size:28 final size:28
Alignment explanation
Indices: 253274--253348 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 28
253264 TTTTCACCCT
*
253274 AAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAATATCAAACTTAAAA
253302 AAACCGACTCGACCCGAATATCAAACTTAAAA
1 AAA-C--C-CGACCCGAATATCAAACTTAAAA
*
253334 AAACCCGATCCGAAT
1 AAACCCGACCCGAAT
253349 CTGATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 12 0.29
29 2 0.05
31 2 0.05
32 25 0.61
ACGTcount: A:0.45, C:0.31, G:0.09, T:0.15
Consensus pattern (28 bp):
AAACCCGACCCGAATATCAAACTTAAAA
Found at i:254337 original size:27 final size:28
Alignment explanation
Indices: 254305--254379 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 28
254295 CTTATTTAGG
254305 GAATAATTTGTTTGAAAGAC-AATTTAA
1 GAATAATTTGTTTGAAAGACAAATTTAA
254332 GAATAATTTGTTTGAAAGACAAATTTAA
1 GAATAATTTGTTTGAAAGACAAATTTAA
* *
254360 GAACTAATTTATTAGAAAGA
1 GAA-TAATTTGTTTGAAAGA
254380 TTAAGAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.45
28 10 0.23
29 14 0.32
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (28 bp):
GAATAATTTGTTTGAAAGACAAATTTAA
Found at i:254967 original size:35 final size:35
Alignment explanation
Indices: 254921--254991 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
254911 CGTGTATACA
254921 TGTATAAGCGAAGTTTGGCCTTTAATATTTGACAC
1 TGTATAAGCGAAGTTTGGCCTTTAATATTTGACAC
254956 TGTATAAGCGAAGTTTGGCCTTTAATATTTGACAC
1 TGTATAAGCGAAGTTTGGCCTTTAATATTTGACAC
254991 T
1 T
254992 TCATTCTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (35 bp):
TGTATAAGCGAAGTTTGGCCTTTAATATTTGACAC
Found at i:257727 original size:9 final size:9
Alignment explanation
Indices: 257711--257786 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
257701 TCGTACTAAA
257711 ACATTTCTT
1 ACATTTCTT
*
257720 ATATTTCTT
1 ACATTTCTT
*
257729 ACATTTATT
1 ACATTTCTT
257738 ACATTTCTT
1 ACATTTCTT
*
257747 ATATTTCTT
1 ACATTTCTT
257756 ACATTTCTT
1 ACATTTCTT
*
257765 ATATTTCTT
1 ACATTTCTT
*
257774 ACATTTATT
1 ACATTTCTT
257783 ACAT
1 ACAT
257787 GCCAACATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (9 bp):
ACATTTCTT
Found at i:262299 original size:25 final size:25
Alignment explanation
Indices: 262248--262301 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
262238 GTTAAAATGA
**
262248 TAAA-CGAACACAAACGTGCGAACG
1 TAAACCGAACACAAACGAACGAACG
262272 TAAACCGAACACAAACGAACGAGA-G
1 TAAACCGAACACAAACGAACGA-ACG
262297 TAAAC
1 TAAAC
262302 AAACATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 21 0.81
26 1 0.04
ACGTcount: A:0.50, C:0.24, G:0.19, T:0.07
Consensus pattern (25 bp):
TAAACCGAACACAAACGAACGAACG
Found at i:262437 original size:16 final size:17
Alignment explanation
Indices: 262416--262459 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
262406 GTATTTTTAT
262416 TTGAGTTTAAA-ATTAA
1 TTGAGTTTAAATATTAA
262432 TTGAGTTTTTAAATATTAA
1 TTGAG--TTTAAATATTAA
262451 -TGAGTTTAA
1 TTGAGTTTAA
262460 TGTTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.40
18 10 0.40
19 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TTGAGTTTAAATATTAA
Found at i:262444 original size:18 final size:18
Alignment explanation
Indices: 262421--262457 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
262411 TTTATTTGAG
262421 TTTAAA-ATTAATTGAGTT
1 TTTAAATATTAA-TGAGTT
262439 TTTAAATATTAATGAGTT
1 TTTAAATATTAATGAGTT
262457 T
1 T
262458 AATGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTAAATATTAATGAGTT
Found at i:263061 original size:36 final size:36
Alignment explanation
Indices: 262988--263061 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
262978 AATACTTTAT
* * * * *
262988 TAATTAAATTTTGATAGATATATCTTTCATTTTAAA
1 TAATTAAACTCTGATAAATATATCTTTCACTTCAAA
* *
263024 TAATTAAACTCTGATAAATATATTTTTTACTTCAAA
1 TAATTAAACTCTGATAAATATATCTTTCACTTCAAA
263060 TA
1 TA
263062 TGTCGCTCGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (36 bp):
TAATTAAACTCTGATAAATATATCTTTCACTTCAAA
Found at i:264426 original size:23 final size:23
Alignment explanation
Indices: 264399--264455 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
264389 ATCGTTTCCG
* **
264399 GTTCGTTTAATGTTCGTGAACAT
1 GTTCGTTTAACGTTCACGAACAT
*
264422 GTTCGCTTAACGTTCACGAACAT
1 GTTCGTTTAACGTTCACGAACAT
* *
264445 ATTCATTTAAC
1 GTTCGTTTAAC
264456 TTTGGTGAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (23 bp):
GTTCGTTTAACGTTCACGAACAT
Found at i:265224 original size:354 final size:354
Alignment explanation
Indices: 264575--265247 Score: 1346
Period size: 354 Copynumber: 1.9 Consensus size: 354
264565 TCTCATATGT
264575 AATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAGAGCAACTTCCGTA
1 AATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAGAGCAACTTCCGTA
264640 GGATACCTCCAAATTATGAAATACCCTACATGAGACTCGATCCCATGACCTCAAGGTTAAGAACC
66 GGATACCTCCAAATTATGAAATACCCTACATGAGACTCGATCCCATGACCTCAAGGTTAAGAACC
264705 TTGTGCTCTACCAACTGAGTTGGATGGTCATTTCTTACCCTTCTATTTTCAAGCTAGAGAAAAAT
131 TTGTGCTCTACCAACTGAGTTGGATGGTCATTTCTTACCCTTCTATTTTCAAGCTAGAGAAAAAT
264770 AATGAAACTACATACTAGTCTTTAAGTTTCTTAGGCTTCACAGTTTAAACTCTAAAGTTCACTCT
196 AATGAAACTACATACTAGTCTTTAAGTTTCTTAGGCTTCACAGTTTAAACTCTAAAGTTCACTCT
264835 ATGTTAAATTTAACCCCTACATTCACCATTATTTACTTTAAATGTAATAAAAAATGAAATACCCT
261 ATGTTAAATTTAACCCCTACATTCACCATTATTTACTTTAAATGTAATAAAAAATGAAATACCCT
264900 ACATGAGACTCGATCCCATGACCTCAAAA
326 ACATGAGACTCGATCCCATGACCTCAAAA
264929 AATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAGAGCAACTTCCGTA
1 AATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAGAGCAACTTCCGTA
264994 GGATACCTCCAAATTATGAAATACCCTACATGAGACTCGATCCCATGACCTCAAGGTTAAGAACC
66 GGATACCTCCAAATTATGAAATACCCTACATGAGACTCGATCCCATGACCTCAAGGTTAAGAACC
265059 TTGTGCTCTACCAACTGAGTTGGATGGTCATTTCTTACCCTTCTATTTTCAAGCTAGAGAAAAAT
131 TTGTGCTCTACCAACTGAGTTGGATGGTCATTTCTTACCCTTCTATTTTCAAGCTAGAGAAAAAT
265124 AATGAAACTACATACTAGTCTTTAAGTTTCTTAGGCTTCACAGTTTAAACTCTAAAGTTCACTCT
196 AATGAAACTACATACTAGTCTTTAAGTTTCTTAGGCTTCACAGTTTAAACTCTAAAGTTCACTCT
265189 ATGTTAAATTTAACCCCTACATTCACCATTATTTACTTTAAATGTAATAAAAAATGAAA
261 ATGTTAAATTTAACCCCTACATTCACCATTATTTACTTTAAATGTAATAAAAAATGAAA
265248 AAGAGAATCA
Statistics
Matches: 319, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 319 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (354 bp):
AATGGGGTAAGGGGGAGGTAAGATAGTAGGCTGCCCCCAACACTAGGTTGAGAGCAACTTCCGTA
GGATACCTCCAAATTATGAAATACCCTACATGAGACTCGATCCCATGACCTCAAGGTTAAGAACC
TTGTGCTCTACCAACTGAGTTGGATGGTCATTTCTTACCCTTCTATTTTCAAGCTAGAGAAAAAT
AATGAAACTACATACTAGTCTTTAAGTTTCTTAGGCTTCACAGTTTAAACTCTAAAGTTCACTCT
ATGTTAAATTTAACCCCTACATTCACCATTATTTACTTTAAATGTAATAAAAAATGAAATACCCT
ACATGAGACTCGATCCCATGACCTCAAAA
Found at i:266712 original size:27 final size:27
Alignment explanation
Indices: 266674--266824 Score: 275
Period size: 27 Copynumber: 5.6 Consensus size: 27
266664 CAAAGAACCC
*
266674 CATAAAAGCAGTATCATCTCTTTTGTT
1 CATAAAAACAGTATCATCTCTTTTGTT
266701 CATAAAAACAGTATCATCTCTTTTGTT
1 CATAAAAACAGTATCATCTCTTTTGTT
266728 CATAAAAACAGTATCATCTCTTTTGTT
1 CATAAAAACAGTATCATCTCTTTTGTT
*
266755 CATAAAAACAGTATCAGCTCTTTTGTT
1 CATAAAAACAGTATCATCTCTTTTGTT
*
266782 CATAAAAACAGTATCAGCTCTTTTGTT
1 CATAAAAACAGTATCATCTCTTTTGTT
266809 CATAAAAACAGTATCA
1 CATAAAAACAGTATCA
266825 GCTCGCTTTT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 122 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (27 bp):
CATAAAAACAGTATCATCTCTTTTGTT
Found at i:271410 original size:29 final size:29
Alignment explanation
Indices: 271359--271418 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
271349 GAGATCACTC
*
271359 AATAAATTTGAAGTCATTAGGACTTGAGT
1 AATAAATTTGAAGTCATTAGGACTTAAGT
* * *
271388 AATAAATTTGAGGTCTTTGGGACTTAAGT
1 AATAAATTTGAAGTCATTAGGACTTAAGT
271417 AA
1 AA
271419 ATGTTTGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (29 bp):
AATAAATTTGAAGTCATTAGGACTTAAGT
Found at i:271448 original size:34 final size:34
Alignment explanation
Indices: 271405--271474 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
271395 TTGAGGTCTT
271405 TGGGACTTAAGTAAATGTTTGTAGTTAAACTCAA
1 TGGGACTTAAGTAAATGTTTGTAGTTAAACTCAA
*
271439 TGGGACTTAAGTAAATGTTTGTGGTTAAACTCAA
1 TGGGACTTAAGTAAATGTTTGTAGTTAAACTCAA
271473 TG
1 TG
271475 TTGACAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.36
Consensus pattern (34 bp):
TGGGACTTAAGTAAATGTTTGTAGTTAAACTCAA
Found at i:271795 original size:49 final size:49
Alignment explanation
Indices: 271740--271840 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
271730 TATTCTAATT
*
271740 TTAGTAATTATCACGTCAGCTCACCCATTAAATATTAACAATTAATTAA
1 TTAGTAATTATCACGTCAGCTCACCCATTAAATATTAACAATAAATTAA
*
271789 TTAGTAATTATCACGTCAGCTCATCCATTAAATATTAACAATAAATTAA
1 TTAGTAATTATCACGTCAGCTCACCCATTAAATATTAACAATAAATTAA
271838 TTA
1 TTA
271841 ATTAACATCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (49 bp):
TTAGTAATTATCACGTCAGCTCACCCATTAAATATTAACAATAAATTAA
Found at i:271855 original size:18 final size:17
Alignment explanation
Indices: 271834--271882 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
271824 TAACAATAAA
*
271834 TTAATTAATTAACATCAT
1 TTAATTAATTAAAAT-AT
*
271852 TTAAATAATTAAAATAT
1 TTAATTAATTAAAATAT
*
271869 TTTATTAA-TAAAAT
1 TTAATTAATTAAAAT
271883 TGAAAGATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 13 0.48
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTAATTAAAATAT
Found at i:273248 original size:20 final size:21
Alignment explanation
Indices: 273223--273265 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
273213 ATGGCTGTGA
273223 TTCTTTTCTTGA-TTTTTTCT
1 TTCTTTTCTTGATTTTTTTCT
* *
273243 TTCTTTTTTTTATTTTTTTCT
1 TTCTTTTCTTGATTTTTTTCT
273264 TT
1 TT
273266 TCTATATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (21 bp):
TTCTTTTCTTGATTTTTTTCT
Done.