Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009397.1 Hibiscus syriacus cultivar Beakdansim tig00113302_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: 510949
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:369852 original size:20 final size:20
Alignment explanation
Indices: 369827--369921 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
369817 AATTGAGAAA
*
369827 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
369847 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
369868 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
369888 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
369908 TTCGCAACGCGATA
1 ATCGCAACGCGATA
369922 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:370137 original size:22 final size:22
Alignment explanation
Indices: 370109--370152 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
370099 CACTCTCTCA
370109 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
370131 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
370153 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:370440 original size:20 final size:20
Alignment explanation
Indices: 370415--370452 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
370405 CGATTCTCTC
370415 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
370435 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
370453 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:370642 original size:25 final size:28
Alignment explanation
Indices: 370581--370642 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 28
370571 ACTATTTATG
*
370581 TTTATTATGTTTTTGGTATATCTTCACA
1 TTTAGTATGTTTTTGGTATATCTTCACA
*
370609 -GT-GTA-GTTTTTGGTATATC-T-A-A
1 TTTAGTATGTTTTTGGTATATCTTCACA
370631 TTTAGTATGTTT
1 TTTAGTATGTTT
370643 ATTGTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 4 0.14
25 18 0.64
26 2 0.07
27 1 0.04
ACGTcount: A:0.21, C:0.06, G:0.16, T:0.56
Consensus pattern (28 bp):
TTTAGTATGTTTTTGGTATATCTTCACA
Found at i:371786 original size:18 final size:18
Alignment explanation
Indices: 371765--371809 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
371755 TCCACTTCGG
*
371765 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
371783 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
371801 GAGCCATCA
1 GAGCCATCA
371810 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:372335 original size:19 final size:20
Alignment explanation
Indices: 372281--372347 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
372271 TAGTTTACTT
* *
372281 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
372301 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
372321 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
372340 TCGCAACG
1 TCGCAACG
372348 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:372355 original size:14 final size:14
Alignment explanation
Indices: 372336--372393 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
372326 ATGCGAAATG
372336 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
372350 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
372366 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
372382 AAAATCGCAACG
1 AAAATCGCAACG
372394 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:372378 original size:32 final size:33
Alignment explanation
Indices: 372320--372398 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
372310 GGAAATGGCT
*
372320 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
372353 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
372385 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
372399 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:372427 original size:19 final size:18
Alignment explanation
Indices: 372405--372573 Score: 128
Period size: 19 Copynumber: 9.8 Consensus size: 18
372395 GAAACACAAA
*
372405 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
372424 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
372440 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
372456 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
372472 T--CATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
372488 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
372504 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
* **
372521 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
*
372540 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGAT-TTCATT
372560 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
372574 TAAGTTTCGT
Statistics
Matches: 120, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
14 29 0.24
15 3 0.03
16 10 0.08
17 2 0.02
18 26 0.22
19 33 0.28
20 17 0.14
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:372446 original size:14 final size:14
Alignment explanation
Indices: 372427--372516 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
372417 TTTCATTTCG
372427 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
372441 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
372457 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
* *
372473 CATTGCGATTTCATTT
1 CGTTGCGATTT--TGT
372489 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
372505 CGTTGCGATTTT
1 CGTTGCGATTTT
372517 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 33 0.53
16 8 0.13
18 21 0.34
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:372457 original size:32 final size:33
Alignment explanation
Indices: 372410--372532 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
372400 ACAAATCGCA
372410 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
372443 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
372475 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
372507 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
372533 AGCCATTTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 62 0.72
33 24 0.28
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:372551 original size:20 final size:19
Alignment explanation
Indices: 372517--372571 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
372507 TTGCGATTTT
*
372517 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
372536 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
372556 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
372572 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:374459 original size:14 final size:14
Alignment explanation
Indices: 374440--374475 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
374430 ATTGTTTAAT
374440 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
374454 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
374468 TGATTTGT
1 TGATTTGT
374476 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:374601 original size:14 final size:17
Alignment explanation
Indices: 374592--374651 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 17
374582 ATCGCAACGA
374592 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
374611 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
374630 GAAAATCGCAA-CG-A-
1 GAAAATCGCAAGCGAAT
374644 GAAAATCG
1 GAAAATCG
374652 AAATGCGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.20
15 1 0.02
17 2 0.05
19 30 0.73
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (17 bp):
GAAAATCGCAAGCGAAT
Found at i:374647 original size:19 final size:19
Alignment explanation
Indices: 374592--374640 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
374582 ATCGCAACGA
374592 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
374611 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
374630 GAAAATCGCAA
1 GAAAATCGCAA
374641 CGAGAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:374703 original size:20 final size:20
Alignment explanation
Indices: 374678--374734 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
374668 TCGCATTGCG
*
374678 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
374698 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
374718 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
374735 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:375119 original size:14 final size:14
Alignment explanation
Indices: 375100--375135 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
375090 ATTGTTTAAT
375100 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
375114 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
375128 TGATTTGT
1 TGATTTGT
375136 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:375709 original size:14 final size:14
Alignment explanation
Indices: 375690--375725 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
375680 ATTGTTTAAT
375690 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
375704 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
375718 TGATTTGT
1 TGATTTGT
375726 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:376298 original size:14 final size:14
Alignment explanation
Indices: 376279--376314 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
376269 ATTGTTTAAT
376279 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
376293 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
376307 TGATTTGT
1 TGATTTGT
376315 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:376463 original size:19 final size:20
Alignment explanation
Indices: 376435--376473 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
376425 AACGAGAAAA
376435 TCGCAATGCGATTT-TCGTT
1 TCGCAATGCGATTTCTCGTT
*
376454 TCGCATTGCGATTTCTCGTT
1 TCGCAATGCGATTTCTCGTT
376474 GCGATAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (20 bp):
TCGCAATGCGATTTCTCGTT
Found at i:376884 original size:14 final size:14
Alignment explanation
Indices: 376865--376900 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
376855 ATTATTTAAT
376865 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
376879 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
376893 TGATTTGT
1 TGATTTGT
376901 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:377472 original size:14 final size:14
Alignment explanation
Indices: 377453--377488 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
377443 ATTGTTTAAT
377453 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
377467 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
377481 TGATTTGT
1 TGATTTGT
377489 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:378333 original size:589 final size:590
Alignment explanation
Indices: 374698--378453 Score: 7307
Period size: 588 Copynumber: 6.4 Consensus size: 590
374688 TGCGATAACC
*
374698 ATTTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
*
374763 AACTGAACAAATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
374828 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAAC--ATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
374891 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
*
374956 TTGTTTGAGCAAATGTTTGGTTTCTGTAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
375021 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
375086 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
375151 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
375216 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
375281 TTGCG
586 TTGCG
375286 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
*
375351 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATATATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
375416 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
375481 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
375546 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
375611 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
375676 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
*
375741 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGAAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
375806 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
375871 TTGCG
586 TTGCG
375876 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
375941 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
376006 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
376071 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
376136 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
376201 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAG-ATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
376265 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
376330 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGA-TTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
376394 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
376459 TTGCG
586 TTGCG
*
376464 A-TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAT
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
376528 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
376593 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
376658 ATGTTTGGTTAAGTACCTAGAATTCAATAA-TTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
376722 TTGTTTGAGC-AATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
376786 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
*
376851 TTTGATTATTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
*
376916 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAAGCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
376981 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
377046 TTGCG
586 TTGCG
377051 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
377116 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
377181 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
377246 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
377311 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
377376 GGGGTCAC-AAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTA-TT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
377439 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
*
377504 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATATTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
377569 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
377634 TTGCG
586 TTGCG
377639 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
*
377704 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATTCATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
377769 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
377834 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
196 ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
377899 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
261 TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
377964 -GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
326 GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
* *
378028 TTTGATTGTTTAATTGATTTGTGAAAGATGATTTGTAAATGTTGATTTGTTTGATTGATGTGTAC
391 TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
378093 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
456 ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
*
378158 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGATAAAATCGCAATGCGATTTTCGTTTCGCA
521 ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
378223 TTGCG
586 TTGCG
378228 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
1 ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
378293 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
66 AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
378358 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
131 AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
*
378423 ATATTTGGTTAAGTACCTAGAATTCAATAAT
196 ATGTTTGGTTAAGTACCTAGAATTCAATAAT
378454 AATTGTTAAA
Statistics
Matches: 3137, Mismatches: 22, Indels: 17
0.99 0.01 0.01
Matches are distributed among these distances:
585 105 0.03
586 157 0.05
587 327 0.10
588 1064 0.34
589 633 0.20
590 851 0.27
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (590 bp):
ATTTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGAC
AACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAA
AAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAA
ATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTC
TTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTAC
GGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTT
TTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTAC
ATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAA
ACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCA
TTGCG
Found at i:379375 original size:24 final size:24
Alignment explanation
Indices: 379325--379377 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
379315 GTATTCGAAA
* * *
379325 TTGATCTTGGTCAATACCCGGACT
1 TTGATATTGGTCAATACACGAACT
*
379349 TTGATATTGGTCAATACACGAATT
1 TTGATATTGGTCAATACACGAACT
379373 TTGAT
1 TTGAT
379378 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGATATTGGTCAATACACGAACT
Found at i:379569 original size:12 final size:12
Alignment explanation
Indices: 379552--379576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
379542 ATATAATCCT
379552 GAAGAAGAAAAA
1 GAAGAAGAAAAA
379564 GAAGAAGAAAAA
1 GAAGAAGAAAAA
379576 G
1 G
379577 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:381889 original size:19 final size:19
Alignment explanation
Indices: 381867--381931 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
381857 GGAAATTACT
381867 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
381886 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
381900 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
381919 ATCGCAACGCGAA
1 ATCGCAATGCGAA
381932 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:381890 original size:39 final size:33
Alignment explanation
Indices: 381867--381929 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
381857 GGAAATTACT
*
381867 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
381900 ATCGCAATGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCGCAACGCG
381930 AATTTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
Found at i:382001 original size:19 final size:18
Alignment explanation
Indices: 381931--382002 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
381921 CGCAACGCGA
*
381931 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
381949 ATTTCATTTTCGCGTTGCG
1 ATTTCA-TTTCGCGTTGCG
*
381968 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
381982 ATTTTCATTTCGCATTGCG
1 A-TTTCATTTCGCGTTGCG
382001 AT
1 AT
382003 AGTACTTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
18 9 0.20
19 22 0.50
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:382127 original size:14 final size:14
Alignment explanation
Indices: 382108--382144 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
382098 CATCAATTAA
382108 ACAAATCAACTTGT
1 ACAAATCAACTTGT
* *
382122 ACAAATCACCTTTT
1 ACAAATCAACTTGT
382136 ACAAATCAA
1 ACAAATCAA
382145 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTGT
Found at i:383568 original size:21 final size:21
Alignment explanation
Indices: 383502--383568 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
383492 GTGAATCAGG
*
383502 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
383522 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
383544 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
383565 CTCT
1 CTCT
383569 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:383587 original size:42 final size:41
Alignment explanation
Indices: 383502--383624 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
383492 GTGAATCAGG
* * * * *
383502 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
383544 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
383586 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
383625 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:385699 original size:33 final size:33
Alignment explanation
Indices: 385645--385743 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
385635 ACGAGATAAT
* *
385645 GAGAATTGCAATGCGGAAATGACTATCGCAATGA
1 GAGAATTGCAACGC-GAAATGACTATCGCAACGA
* *
385679 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATTGCAACGCGAAATGACTATCGCAACGA
**
385712 GAGAATTGCAACGCGAAATGAAAATCGCAACG
1 GAGAATTGCAACGCGAAATGACTATCGCAACG
385744 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (33 bp):
GAGAATTGCAACGCGAAATGACTATCGCAACGA
Found at i:385741 original size:19 final size:19
Alignment explanation
Indices: 385719--385784 Score: 123
Period size: 19 Copynumber: 3.5 Consensus size: 19
385709 CGAGAGAATT
385719 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
385738 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
385757 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
385776 GCAATGCGA
1 GCAACGCGA
385785 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:385813 original size:19 final size:19
Alignment explanation
Indices: 385780--385846 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
385770 AAAATCGCAA
**
385780 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
385799 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
385818 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
385838 TGCGATTTT
1 TGCGATTTT
385847 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:386436 original size:21 final size:21
Alignment explanation
Indices: 386403--386482 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
386393 TGCGAAAGTA
* * *
386403 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
386424 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
386444 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
386466 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
386483 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:386459 original size:20 final size:20
Alignment explanation
Indices: 386366--386459 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
386356 CGCTAAGTAA
*
386366 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
386386 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
386406 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
386427 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
386447 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
386460 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:386478 original size:41 final size:41
Alignment explanation
Indices: 386387--386521 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
386377 AAAGTCAGTA
* * * * *
386387 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
386427 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * *
386469 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
386510 TCGCGTTGCGAT
1 TCGCGTTGCGAT
386522 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.92
42 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:386492 original size:20 final size:20
Alignment explanation
Indices: 386448--386540 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
386438 ATAGTCAGTA
*
386448 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
386469 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
386489 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
386510 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
386530 TCGCATTGCGA
1 TCGCATTGCGA
386541 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:386522 original size:41 final size:41
Alignment explanation
Indices: 386448--386543 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
386438 ATAGTCAGTA
* *
386448 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
386489 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
386530 TCGCATTGCGAATT
1 TCGCATTGCGAATT
386544 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:387409 original size:3 final size:3
Alignment explanation
Indices: 387403--387482 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
387393 TATTATAAAT
387403 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
387451 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
387483 GTTAGATATC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:393927 original size:46 final size:46
Alignment explanation
Indices: 393860--393950 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
393850 TTTGAAATTT
393860 AATTTAATTTTCTCATTGACTGTGTTTGATTCAAATAAAATATATC
1 AATTTAATTTTCTCATTGACTGTGTTTGATTCAAATAAAATATATC
* *
393906 AATTTATTTTTCTCATTGACTGTGTTTGATTCGAATAAAATATAT
1 AATTTAATTTTCTCATTGACTGTGTTTGATTCAAATAAAATATAT
393951 TAGTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (46 bp):
AATTTAATTTTCTCATTGACTGTGTTTGATTCAAATAAAATATATC
Found at i:394343 original size:20 final size:20
Alignment explanation
Indices: 394318--394356 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
394308 ATTCTCTTCA
394318 TTTTTTACTATAATATATTG
1 TTTTTTACTATAATATATTG
* *
394338 TTTTTTATTATAATCTATT
1 TTTTTTACTATAATATATT
394357 CCTTTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTTACTATAATATATTG
Found at i:394362 original size:20 final size:20
Alignment explanation
Indices: 394319--394364 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
394309 TTCTCTTCAT
**
394319 TTTTTACTATAATATATTGT
1 TTTTTACTATAATATATTCC
* *
394339 TTTTTATTATAATCTATTCC
1 TTTTTACTATAATATATTCC
394359 TTTTTA
1 TTTTTA
394365 AGAGTGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTACTATAATATATTCC
Found at i:399123 original size:6 final size:6
Alignment explanation
Indices: 399112--399136 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
399102 TCTCGTCTCG
399112 GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT G
399137 AATTAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:400109 original size:29 final size:29
Alignment explanation
Indices: 400075--400133 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
400065 CCTAAATTAA
400075 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
400104 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
400133 T
1 T
400134 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:404788 original size:29 final size:29
Alignment explanation
Indices: 404754--404812 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
404744 CCTAAATTAA
404754 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
404783 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
404812 T
1 T
404813 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:412808 original size:29 final size:29
Alignment explanation
Indices: 412766--412854 Score: 153
Period size: 29 Copynumber: 3.1 Consensus size: 29
412756 GACTTCTTAA
412766 TAATAGGGTATACCCAATATCTCCTGGAG
1 TAATAGGGTATACCCAATATCTCCTGGAG
*
412795 TAATAGGGTATACCCAACATCTCCTGGAG
1 TAATAGGGTATACCCAATATCTCCTGGAG
412824 TAATAGGGTATACCC-ATCATCTCCTGGAG
1 TAATAGGGTATACCCAAT-ATCTCCTGGAG
412853 TA
1 TA
412855 GTCATCAATA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
28 1 0.02
29 56 0.98
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27
Consensus pattern (29 bp):
TAATAGGGTATACCCAATATCTCCTGGAG
Found at i:417051 original size:14 final size:14
Alignment explanation
Indices: 417032--417059 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
417022 TCATTTATAT
417032 TCATTTATGTTCGA
1 TCATTTATGTTCGA
417046 TCATTTATGTTCGA
1 TCATTTATGTTCGA
417060 ACATATGGCA
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:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TCATTTATGTTCGA
Found at i:417351 original size:34 final size:34
Alignment explanation
Indices: 417313--417393 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
417303 CATAGGTCTC
417313 GTTCGTTCATTTACGTTC-GTGAACATTCGGTTAT
1 GTTCGTTCATTTACGTTCGGT-AACATTCGGTTAT
* * ** *
417347 GTTCGTTTATGTT-CGTTCGGTTATGTTCGTTTAT
1 GTTCGTTCAT-TTACGTTCGGTAACATTCGGTTAT
417381 GTTCGTTCATTTA
1 GTTCGTTCATTTA
417394 TGTTTAACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 2 0.05
34 32 0.84
35 4 0.11
ACGTcount: A:0.14, C:0.15, G:0.21, T:0.51
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCGGTAACATTCGGTTAT
Found at i:417353 original size:24 final size:24
Alignment explanation
Indices: 417326--417377 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
417316 CGTTCATTTA
*
417326 CGTTCGTGAACATTCGGTTATGTT
1 CGTTCATGAACATTCGGTTATGTT
* ** *
417350 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACATTCGGTTATGTT
417374 CGTT
1 CGTT
417378 TATGTTCGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACATTCGGTTATGTT
Found at i:417378 original size:24 final size:24
Alignment explanation
Indices: 417338--417397 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
417328 TTCGTGAACA
417338 TTCGGTTATGTTCGTTTATGTTCG
1 TTCGGTTATGTTCGTTTATGTTCG
417362 TTCGGTTATGTTCGTTTATGTTCG
1 TTCGGTTATGTTCGTTTATGTTCG
**
417386 TTCATTTATGTT
1 TTCGGTTATGTT
417398 TAACCCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (24 bp):
TTCGGTTATGTTCGTTTATGTTCG
Found at i:417386 original size:10 final size:10
Alignment explanation
Indices: 417338--417387 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
417328 TTCGTGAACA
*
417338 TTCGGTTATG
1 TTCGTTTATG
417348 TTCGTTTATG
1 TTCGTTTATG
417358 TTCGTTCGGTTATG
1 TTCG-T---TTATG
417372 TTCGTTTATG
1 TTCGTTTATG
417382 TTCGTT
1 TTCGTT
417388 CATTTATGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 24 0.69
11 1 0.03
13 1 0.03
14 9 0.26
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:417388 original size:14 final size:14
Alignment explanation
Indices: 417347--417397 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
417337 ATTCGGTTAT
417347 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
417361 GTTCGGTTA---T-
1 GTTCGTTTATGTTC
417371 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
417385 GTTCATTTATGTT
1 GTTCGTTTATGTT
417398 TAACCCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:418489 original size:16 final size:15
Alignment explanation
Indices: 418468--418522 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
418458 GTCTCCAACG
418468 TTTATGTTCGTGTTC
1 TTTATGTTCGTGTTC
418483 ATTTATGTTCGTGTTC
1 -TTTATGTTCGTGTTC
*
418499 ---GTGTTCGTGTTC
1 TTTATGTTCGTGTTC
418511 GTTTATGTTCGT
1 -TTTATGTTCGT
418523 TTATTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 11 0.33
16 22 0.67
ACGTcount: A:0.07, C:0.13, G:0.24, T:0.56
Consensus pattern (15 bp):
TTTATGTTCGTGTTC
Found at i:418497 original size:6 final size:6
Alignment explanation
Indices: 418488--418512 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
418478 TGTTCATTTA
418488 TGTTCG TGTTCG TGTTCG TGTTCG T
1 TGTTCG TGTTCG TGTTCG TGTTCG T
418513 TTATGTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTTCG
Found at i:418903 original size:14 final size:14
Alignment explanation
Indices: 418884--418914 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
418874 CATTTATTAT
*
418884 GTTCGTTTATGTTC
1 GTTCGTTTATATTC
418898 GTTCGTTTATATTC
1 GTTCGTTTATATTC
418912 GTT
1 GTT
418915 TATCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATATTC
Found at i:434165 original size:2 final size:2
Alignment explanation
Indices: 434158--434209 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
434148 AAATTTATTA
434158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434200 AT AT AT AT AT
1 AT AT AT AT AT
434210 TTAATATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439469 original size:17 final size:19
Alignment explanation
Indices: 439428--439472 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
439418 ATTTTACGAA
439428 TTAAAAAA-ATAATATGAT
1 TTAAAAAATATAATATGAT
439446 TGT-AAAAATATAAT-T-AT
1 T-TAAAAAATATAATATGAT
439463 TTAAAAAATA
1 TTAAAAAATA
439473 ATCTTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 10 0.42
18 7 0.29
19 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TTAAAAAATATAATATGAT
Found at i:441652 original size:36 final size:36
Alignment explanation
Indices: 441610--441679 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
441600 CGGTCGTGTC
* **
441610 GAGCTTCGACTGTCCCAACGTGATCTCTAGGATCAG
1 GAGCTTCAACTGTCCCAACGTGATAACTAGGATCAG
441646 GAGCTTCAACTGTCCCAACGTGATAACTAGGATC
1 GAGCTTCAACTGTCCCAACGTGATAACTAGGATC
441680 GGCAGTGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (36 bp):
GAGCTTCAACTGTCCCAACGTGATAACTAGGATCAG
Found at i:442977 original size:31 final size:33
Alignment explanation
Indices: 442942--443004 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 33
442932 ACATGTTTAA
442942 ATATGAATTTTTT-TT-ATTCATATTCTAAAGT
1 ATATGAATTTTTTATTAATTCATATTCTAAAGT
*
442973 ATATGAATTTTTTATTAAATTCATATTTTAAA
1 ATATGAATTTTTTATT-AATTCATATTCTAAA
443005 CTTTATATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 2 0.07
34 13 0.46
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (33 bp):
ATATGAATTTTTTATTAATTCATATTCTAAAGT
Found at i:448319 original size:29 final size:30
Alignment explanation
Indices: 448249--448308 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
448239 CAATTTAAGG
*
448249 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
448280 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
448309 TTCAAGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:448416 original size:20 final size:20
Alignment explanation
Indices: 448393--448435 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
448383 TTCAAGATTG
* *
448393 CCCAGAGGGTATAGATTCCC
1 CCCAGAGGGTACAGATACCC
*
448413 CCCAGGGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
448433 CCC
1 CCC
448436 TGCAGGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (20 bp):
CCCAGAGGGTACAGATACCC
Found at i:448509 original size:20 final size:21
Alignment explanation
Indices: 448469--448511 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
448459 AACAGAATGT
448469 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
448490 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
448511 C
1 C
448512 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:448573 original size:21 final size:21
Alignment explanation
Indices: 448547--448589 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
448537 ATTTAAATAT
*
448547 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
448568 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
448589 T
1 T
448590 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:449640 original size:146 final size:147
Alignment explanation
Indices: 449374--449666 Score: 563
Period size: 145 Copynumber: 2.0 Consensus size: 147
449364 CCAATCCAAT
449374 GATCTTGATGTATGGGAGATAATCGAGAATGGCTACTCTTCTCCAAAGAAGAAGGAGAAGAGCGG
1 GATCTTGATGTATGGGAGATAATCGAGAATGGCTACTCTTCTCCAAAGAAGAAGGAGAAGAGCGG
449439 AGTGACAAAGAACAGAAGAAATCTCAACTTAATGCCAAGGCCATGAACATGTTG-TTTGTGCATT
66 AGTGACAAAGAACAGAAGAAATCTCAACTTAATGCCAAGGCCATGAACATGTTGTTTTGTGCATT
449503 TGGTCC-GAAATCTATG
131 TGGTCCTGAAATCTATG
449519 GATCTTGATGTATGGGAGATAATCGAGAATGGCTACTCTTCTCCAAAGAAGAAGGAGAAGAAGCG
1 GATCTTGATGTATGGGAGATAATCGAGAATGGCTACTCTTCTCCAAAGAAGAAGGAGAAG-AGCG
449584 GAGTGACAAAGAACAGAAGAAATCTCAACTTAATGCCAAGGCCATGAACATGTTGTTTTGTGCAT
65 GAGTGACAAAGAACAGAAGAAATCTCAACTTAATGCCAAGGCCATGAACATGTTGTTTTGTGCAT
449649 TTGGTCCTGAAATCTATG
130 TTGGTCCTGAAATCTATG
449667 AAGGAGTTTC
Statistics
Matches: 145, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
145 60 0.41
146 59 0.41
147 16 0.11
148 10 0.07
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (147 bp):
GATCTTGATGTATGGGAGATAATCGAGAATGGCTACTCTTCTCCAAAGAAGAAGGAGAAGAGCGG
AGTGACAAAGAACAGAAGAAATCTCAACTTAATGCCAAGGCCATGAACATGTTGTTTTGTGCATT
TGGTCCTGAAATCTATG
Found at i:449951 original size:19 final size:20
Alignment explanation
Indices: 449927--449974 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
449917 AACGATTTTC
*
449927 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
449946 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
449966 TTTTGAAAA
1 TTTTGAAAA
449975 AGGATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:451150 original size:29 final size:30
Alignment explanation
Indices: 451079--451138 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
451069 CAATTTAAGG
*
451079 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
451110 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
451139 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:451274 original size:15 final size:15
Alignment explanation
Indices: 451254--451283 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
451244 CCCCCCCAGG
451254 GGGTACAGATACCCC
1 GGGTACAGATACCCC
451269 GGGTACAGATACCCC
1 GGGTACAGATACCCC
451284 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:451311 original size:22 final size:21
Alignment explanation
Indices: 451227--451305 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
451217 TTCAAGATTG
* * *
451227 CCCAGGGAGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
451248 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
451266 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
451284 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
451305 C
1 C
451306 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 30 0.61
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:451380 original size:19 final size:20
Alignment explanation
Indices: 451343--451380 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
451333 GAATGTCCAG
451343 GGGGTACCGATTCCCCCCCA
1 GGGGTACCGATTCCCCCCCA
451363 GGGGTACCGATTCCCCCC
1 GGGGTACCGATTCCCCCC
451381 TGTTCACAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.45, G:0.26, T:0.16
Consensus pattern (20 bp):
GGGGTACCGATTCCCCCCCA
Found at i:451441 original size:21 final size:21
Alignment explanation
Indices: 451415--451457 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
451405 ATTTGAATAT
*
451415 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
451436 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
451457 T
1 T
451458 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:451522 original size:20 final size:22
Alignment explanation
Indices: 451484--451523 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
451474 TTTTGAGTAT
451484 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
451506 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
451524 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:451773 original size:34 final size:32
Alignment explanation
Indices: 451734--451803 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
451724 TTTTGTAAAG
*
451734 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
451768 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
451800 GGGA
1 GGGA
451804 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:452159 original size:22 final size:21
Alignment explanation
Indices: 452126--452166 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
452116 AATTATCTAT
*
452126 TTTTTATATATACATATTACG
1 TTTTAATATATACATATTACG
*
452147 TTTTAATATTATATATATTA
1 TTTTAATA-TATACATATTA
452167 TTATTATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAATATATACATATTACG
Found at i:452266 original size:19 final size:17
Alignment explanation
Indices: 452234--452270 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
452224 TAGTATTTCA
452234 TTTTATTATATTACTAT
1 TTTTATTATATTACTAT
452251 TTTTATTTACTATTACTAT
1 TTTTA-TTA-TATTACTAT
452270 T
1 T
452271 ATTAAGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATTATATTACTAT
Found at i:452513 original size:17 final size:18
Alignment explanation
Indices: 452491--452525 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
452481 ATGTGTTCTA
452491 TTCATT-TTTTTTCCTTC
1 TTCATTGTTTTTTCCTTC
*
452508 TTCATTGTTTTTTTCTTC
1 TTCATTGTTTTTTCCTTC
452526 CAGTATTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (18 bp):
TTCATTGTTTTTTCCTTC
Found at i:454322 original size:94 final size:94
Alignment explanation
Indices: 454161--454342 Score: 301
Period size: 94 Copynumber: 1.9 Consensus size: 94
454151 GGTATAATTT
* *
454161 AGAAAGGGTATTTGGCTTAAGTAAGGCAGAAGAGTTAGGAAAAGTGATGGTTTTAAAAGTAAGTA
1 AGAAAGGGTATTGGGCTTAAGTAAGGCACAAGAGTTAGGAAAAGTGATGGTTTTAAAAGTAAGTA
454226 AATAGGAGAAGGACCTAAAGTGTAGTTTA
66 AATAGGAGAAGGACCTAAAGTGTAGTTTA
* * * *
454255 AGAAAGGGTATTGGGCTTAAGTAAGGCCCAATAGTTAGGAGAAGTGGTGGTTTTAAAAGTAAGTA
1 AGAAAGGGTATTGGGCTTAAGTAAGGCACAAGAGTTAGGAAAAGTGATGGTTTTAAAAGTAAGTA
*
454320 AATAGGAGAATGACCTAAAGTGT
66 AATAGGAGAAGGACCTAAAGTGT
454343 TGATTACCCT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.39, C:0.05, G:0.30, T:0.25
Consensus pattern (94 bp):
AGAAAGGGTATTGGGCTTAAGTAAGGCACAAGAGTTAGGAAAAGTGATGGTTTTAAAAGTAAGTA
AATAGGAGAAGGACCTAAAGTGTAGTTTA
Found at i:454440 original size:3 final size:3
Alignment explanation
Indices: 454432--454460 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
454422 TCTCACCCAC
454432 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
454461 CTTCCATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:456613 original size:16 final size:16
Alignment explanation
Indices: 456592--456623 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
456582 ATTAAGGATT
456592 GAAATTTTAGGATTTG
1 GAAATTTTAGGATTTG
*
456608 GAAATTTTAGGTTTTG
1 GAAATTTTAGGATTTG
456624 AGATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (16 bp):
GAAATTTTAGGATTTG
Found at i:457423 original size:31 final size:31
Alignment explanation
Indices: 457382--457448 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
457372 ATGTTACATA
*
457382 ATTTATAAACAAGTCATCAAACACTGTATTT
1 ATTTACAAACAAGTCATCAAACACTGTATTT
*
457413 ATTTACAAACAAGTCATCAAACATTGTATTT
1 ATTTACAAACAAGTCATCAAACACTGTATTT
457444 ATTTA
1 ATTTA
457449 GAGCTCACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.37
Consensus pattern (31 bp):
ATTTACAAACAAGTCATCAAACACTGTATTT
Found at i:459507 original size:43 final size:44
Alignment explanation
Indices: 459455--459541 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
459445 AAATAAGACG
*
459455 ATAACGGGTCTCTCTGTTTAATA-CCCGAAACGGTATAAACGCT
1 ATAACGGGTCTCTCTGTCTAATACCCCGAAACGGTATAAACGCT
459498 ATAACGGGTCTCTCTGTCTAATACCCCGAAACGGTATAAACGCT
1 ATAACGGGTCTCTCTGTCTAATACCCCGAAACGGTATAAACGCT
459542 TATGTCATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 22 0.52
44 20 0.48
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (44 bp):
ATAACGGGTCTCTCTGTCTAATACCCCGAAACGGTATAAACGCT
Found at i:460732 original size:37 final size:32
Alignment explanation
Indices: 460691--460765 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 32
460681 AAATAAATCA
*
460691 ATAATATTTTTATCAAAATAATATTATTTAAATTATT
1 ATAATA-TTTTA--AAAATAATAATA-TT-AATTATT
*
460728 ATAATATTTTAAAAATAATAATATTAATTTTT
1 ATAATATTTTAAAAATAATAATATTAATTATT
460760 ATAATA
1 ATAATA
460766 AAAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 12 0.33
33 2 0.06
34 11 0.31
36 5 0.14
37 6 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
ATAATATTTTAAAAATAATAATATTAATTATT
Found at i:460748 original size:17 final size:17
Alignment explanation
Indices: 460685--460752 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
460675 TAGTACAAAT
460685 AAATCAATAATATTTTTATCA
1 AAAT-AATAATA-TTTTA--A
*
460706 AAATAATATTA-TTTAA
1 AAATAATAATATTTTAA
* *
460722 ATTATTATAATATTTTAA
1 A-AATAATAATATTTTAA
460740 AAATAATAATATT
1 AAATAATAATATT
460753 AATTTTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.05
17 17 0.44
18 10 0.26
20 6 0.15
21 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAATAATATTTTAA
Found at i:460765 original size:21 final size:21
Alignment explanation
Indices: 460741--460783 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
460731 ATATTTTAAA
*
460741 AATAATAATATTAATTT-TTAT
1 AATAAAAATATT-ATTTATTAT
460762 AATAAAAATATTATTTATTAT
1 AATAAAAATATTATTTATTAT
460783 A
1 A
460784 TTTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAAAAATATTATTTATTAT
Found at i:461949 original size:2 final size:2
Alignment explanation
Indices: 461942--461985 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
461932 TTCTTTTTAT
461942 TA TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
461984 TA
1 TA
461986 GTCTTTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:462110 original size:33 final size:33
Alignment explanation
Indices: 461998--462298 Score: 192
Period size: 33 Copynumber: 8.8 Consensus size: 33
461988 CTTTTTTCTC
* * *
461998 AAACATTTTGACAAAGTATAATATATAGTTTTCAGA
1 AAACATTTTTAAAAATTAT-ATATATAGTTTT--GA
* * * *
462034 AAACGGTTTTTCAAAATATATATTGTATAATTTTGA
1 AAAC-ATTTTTAAAAAT-TATA-TATATAGTTTTGA
*
462070 AAACATTTTTAAAAATTATATATATAGTTTCGA
1 AAACATTTTTAAAAATTATATATATAGTTTTGA
*
462103 AAACA----T-----TTATATATATAGTTTTTTA
1 AAACATTTTTAAAAATTATATATATAG-TTTTGA
* *
462128 AAAGTCATTTTGAAAATATATATAATATATAGTTTTTA
1 AAA--CATTTTTAAAA-AT-TAT-ATATATAGTTTTGA
*
462166 AAACATTTTGAAAATTATATATAGTATATAGTTTTGA
1 AAACATTTTTAAAA--AT-TATA-TATATAGTTTTGA
*
462203 AAACA-TTTTGAAAATTATAATATATAGTTTTGA
1 AAACATTTTTAAAAATTAT-ATATATAGTTTTGA
* *
462236 AAACA-TTTTGAAAATTATAATATATAATTTTGA
1 AAACATTTTTAAAAATTAT-ATATATAGTTTTGA
462269 AAACATTTTTGAAAATATTTATATTATATA
1 AAACATTTTT-AAAA-A-TTATA-TATATA
462299 AGACATTTGA
Statistics
Matches: 219, Mismatches: 20, Indels: 51
0.76 0.07 0.18
Matches are distributed among these distances:
24 12 0.05
25 7 0.03
27 2 0.01
29 1 0.00
33 68 0.31
34 11 0.05
35 13 0.06
36 30 0.14
37 43 0.20
38 24 0.11
39 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (33 bp):
AAACATTTTTAAAAATTATATATATAGTTTTGA
Found at i:462185 original size:37 final size:36
Alignment explanation
Indices: 462113--462403 Score: 241
Period size: 33 Copynumber: 8.2 Consensus size: 36
462103 AAACATTTAT
462113 ATATATAGTTTTTTAAAAGTCATTTTGAAAATATATATA
1 ATATATAG-TTTTTAAAA--CATTTTGAAAATATATATA
462152 ATATATAGTTTTTAAAACATTTTGAAAATTATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAA-TATATATA
* *
462189 GTATATAGTTTTGAAAACATTTTG-AAA-AT-TATA
1 ATATATAGTTTTTAAAACATTTTGAAAATATATATA
*
462222 ATATATAGTTTTGAAAACATTTTG-AAA-AT-TATA
1 ATATATAGTTTTTAAAACATTTTGAAAATATATATA
* *
462255 ATATATAATTTTGAAAACATTTTTGAAAATAT-T-T-
1 ATATATAGTTTTTAAAACA-TTTTGAAAATATATATA
* *
462289 ATAT-TA---TATAAGACA-TTTGAAAATATATATA
1 ATATATAGTTTTTAAAACATTTTGAAAATATATATA
* * **
462320 ATATATATTTTTTAAAAAATATTTTTGAAGTTATATATA
1 ATATATAGTTTTT--AAAACA-TTTTGAAAATATATATA
* * * **
462359 TTGTATATGTTTTTAAAAACGTTTCTGAAAATACGTATA
1 ATATATA-GTTTTT-AAAACATTT-TGAAAATATATATA
462398 ATATAT
1 ATATAT
462404 TTTAAAAAAA
Statistics
Matches: 212, Mismatches: 23, Indels: 34
0.79 0.09 0.13
Matches are distributed among these distances:
28 11 0.05
29 1 0.00
30 7 0.03
31 4 0.02
32 2 0.01
33 56 0.26
34 11 0.05
35 6 0.03
36 17 0.08
37 34 0.16
38 12 0.06
39 46 0.22
40 5 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
ATATATAGTTTTTAAAACATTTTGAAAATATATATA
Found at i:462291 original size:70 final size:73
Alignment explanation
Indices: 462110--462298 Score: 250
Period size: 70 Copynumber: 2.6 Consensus size: 73
462100 CGAAAACATT
* * *
462110 TATA-TATATAGTTTTTTAAAAGTCATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
1 TATAGTATATAG-TTTTGAAAA--CATTTTGAAAATATTTATAATATATAGTTTTGAAAACATTT
462174 TGAAAATTATA
63 TGAAAATTATA
462185 TATAGTATATAGTTTTGAAAACATTTTG-AAA-A-TTATAATATATAGTTTTGAAAACATTTTGA
1 TATAGTATATAGTTTTGAAAACATTTTGAAAATATTTATAATATATAGTTTTGAAAACATTTTGA
462247 AAATTATA
66 AAATTATA
*
462255 -ATA-TATA-A-TTTTGAAAACATTTTTGAAAATATTTATATTATATA
1 TATAGTATATAGTTTTGAAAACA-TTTTGAAAATATTTATAATATATA
462299 AGACATTTGA
Statistics
Matches: 105, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
66 11 0.10
67 6 0.06
68 7 0.07
69 4 0.04
70 47 0.45
71 1 0.01
72 3 0.03
73 7 0.07
75 12 0.11
76 7 0.07
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (73 bp):
TATAGTATATAGTTTTGAAAACATTTTGAAAATATTTATAATATATAGTTTTGAAAACATTTTGA
AAATTATA
Found at i:462469 original size:3 final size:3
Alignment explanation
Indices: 462463--462505 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
462453 ATTTATATAG
* *
462463 ATT ATT ATT ATTT ATT ATT ACT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
462506 TCTTATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:462511 original size:19 final size:22
Alignment explanation
Indices: 462470--462531 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
462460 TAGATTATTA
*
462470 TTATTTA-TTATTACTATTATTA-
1 TTATTTATTTATTA-T-TTCTTAT
462492 TTA-TTATTT-TTATTTCTTAT
1 TTATTTATTTATTATTTCTTAT
*
462512 TTATTTATTTATTTTTTCTT
1 TTATTTATTTATTATTTCTT
462532 TTCTCTACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 12 0.35
22 13 0.38
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTTATTTATTATTTCTTAT
Found at i:463639 original size:23 final size:22
Alignment explanation
Indices: 463601--463656 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
463591 ATTCTTATTT
* *
463601 TATTTTATTTATTTATTATTA-
1 TATTTTTTTTAATTATTATTAG
463622 TCATGTTTTTTTAATTATTATTAG
1 T-AT-TTTTTTTAATTATTATTAG
463646 TATTTTTTTTA
1 TATTTTTTTTA
463657 CCTCATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 18 0.60
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTAATTATTATTAG
Found at i:463651 original size:20 final size:20
Alignment explanation
Indices: 463606--463653 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
463596 TATTTTATTT
463606 TATTTATTTATTATTATCATG
1 TATTT-TTTATTATTATCATG
*
463627 T-TTTTTTAATTATTATTA-G
1 TATTTTTT-ATTATTATCATG
463646 TATTTTTT
1 TATTTTTT
463654 TTACCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTATTATCATG
Found at i:465415 original size:22 final size:22
Alignment explanation
Indices: 465385--465431 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
465375 TTCGCAGTGT
*
465385 GATAGTCTACAGTTGTCGTTGC
1 GATAATCTACAGTTGTCGTTGC
* *
465407 GATAATCTACGGTTGTTGTTGC
1 GATAATCTACAGTTGTCGTTGC
465429 GAT
1 GAT
465432 TTTCCAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (22 bp):
GATAATCTACAGTTGTCGTTGC
Found at i:466027 original size:5 final size:5
Alignment explanation
Indices: 466017--466052 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
466007 GCCGCCGCCA
466017 TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG T
1 TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG TCTCG T
466053 GGTCGTGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.19, T:0.42
Consensus pattern (5 bp):
TCTCG
Found at i:466249 original size:21 final size:21
Alignment explanation
Indices: 466143--466249 Score: 67
Period size: 20 Copynumber: 5.1 Consensus size: 21
466133 TCTTTTTTTT
*
466143 AACTATCGCAACGCGAAATGT
1 AACTATCGCAACGCGAAATGC
* * *
466164 AA-AATTGCAACGCGAAATGG
1 AACTATCGCAACGCGAAATGC
* * * *
466184 AA-AAACGCAACGAC-AACTGT
1 AACTATCGCAACG-CGAAATGC
* ** *
466204 AGACTATCGCACCGCGATTTTC
1 A-ACTATCGCAACGCGAAATGC
466226 AACTATCGCAACGCGAAATGC
1 AACTATCGCAACGCGAAATGC
466247 AAC
1 AAC
466250 GCGAATTTGT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
20 30 0.47
21 24 0.38
22 10 0.16
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (21 bp):
AACTATCGCAACGCGAAATGC
Found at i:469538 original size:135 final size:129
Alignment explanation
Indices: 469283--469614 Score: 412
Period size: 135 Copynumber: 2.5 Consensus size: 129
469273 CAATAGTTCA
* * * * * **
469283 GTTCCATTTTGCTGCCCTTCATTCAGTCTAGTTTCGTCAAGCATACCACGATTGCTTTCACCATC
1 GTTCCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATAACACGATCACTTTCACCATC
* * * * * *
469348 ACTATCTCCGAATGTATTTCGATCCTTCTCGTAGCGATCTAATGATTCCACCCGCAACAATCCG
66 ACTATATCCGAACGTATTTCGATCCTTCTCGCACCAATCTAAAGATTCCACCCGCAACAATCCG
* *
469412 GTTTCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATATCACGATCACTTCCATCATC
1 GTTCCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATAACACGATCACTT---TCA--
* * **
469477 GCCATCACTATATCCGGACGTATTTCGATCCTTCTCGCACCAATCTAAAGTTTCCGTCCGCAACA
61 -CCATCACTATATCCGAACGTATTTCGATCCTTCTCGCACCAATCTAAAGATTCCACCCGCAACA
469542 ATCCG
125 ATCCG
* **
469547 GTTCCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATAACACGACCACTTAAACCATC
1 GTTCCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATAACACGATCACTTTCACCATC
469612 ACT
66 ACT
469615 CTCTCCGGAT
Statistics
Matches: 174, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
129 57 0.33
132 4 0.02
135 113 0.65
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.32
Consensus pattern (129 bp):
GTTCCATTCTGCTGCCCTTCATTCAATCTACTTTCATCAAGCATAACACGATCACTTTCACCATC
ACTATATCCGAACGTATTTCGATCCTTCTCGCACCAATCTAAAGATTCCACCCGCAACAATCCG
Found at i:470718 original size:25 final size:24
Alignment explanation
Indices: 470690--470737 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
470680 TTTTTTCATT
470690 TGTGTATTTCCCAAGTAATATTTTA
1 TGTGTATTTCCCAAG-AATATTTTA
*
470715 TGTGTATTTCCCAAGAATCTTTT
1 TGTGTATTTCCCAAGAATATTTT
470738 GATGCATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (24 bp):
TGTGTATTTCCCAAGAATATTTTA
Found at i:471075 original size:4 final size:4
Alignment explanation
Indices: 471068--471128 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
471058 TTATTTAATT
* * * *
471068 GTGC GTGC GTGT GTGC GTGC GTGC GTGC TTGC GCGC GT-- GTGT GTGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
*
471114 GTGT GTGC GTGC GTG
1 GTGC GTGC GTGC GTG
471129 TGAAAAAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.04
4 44 0.96
ACGTcount: A:0.00, C:0.20, G:0.49, T:0.31
Consensus pattern (4 bp):
GTGC
Found at i:471084 original size:12 final size:12
Alignment explanation
Indices: 471067--471130 Score: 74
Period size: 12 Copynumber: 5.2 Consensus size: 12
471057 TTTATTTAAT
471067 TGTGCGTGCGTG
1 TGTGCGTGCGTG
471079 TGTGCGTGCGTG
1 TGTGCGTGCGTG
* * *
471091 CGTGCTTGCGCGCG
1 TGTGC--GTGCGTG
*
471105 TGTGTGTGCGTG
1 TGTGCGTGCGTG
471117 TGTGCGTGCGTG
1 TGTGCGTGCGTG
471129 TG
1 TG
471131 AAAAAGCCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 34 0.81
14 8 0.19
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (12 bp):
TGTGCGTGCGTG
Found at i:471116 original size:22 final size:22
Alignment explanation
Indices: 471088--471130 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
471078 GTGTGCGTGC
471088 GTGCGTGCT-TGCGCGCGTGTGT
1 GTGCGTG-TGTGCGCGCGTGTGT
*
471110 GTGCGTGTGTGCGTGCGTGTG
1 GTGCGTGTGTGCGCGCGTGTG
471131 AAAAAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.00, C:0.19, G:0.49, T:0.33
Consensus pattern (22 bp):
GTGCGTGTGTGCGCGCGTGTGT
Found at i:473639 original size:10 final size:9
Alignment explanation
Indices: 473604--473706 Score: 98
Period size: 10 Copynumber: 10.6 Consensus size: 9
473594 GCTGCTGGAA
*
473604 ACCGGTTTA
1 ACCGGTTTG
*
473613 ACCGGTTTTCA
1 ACCGG-TTT-G
473624 ACCGGTTCTG
1 ACCGGTT-TG
473634 ACCGGTTTCG
1 ACCGGTTT-G
473644 ACCGGTTCTG
1 ACCGGTT-TG
473654 ACCGGTTTCG
1 ACCGGTTT-G
*
473664 ACCGGTTCG
1 ACCGGTTTG
473673 AACCGGTTTG
1 -ACCGGTTTG
*
473683 ACCGGTCTG
1 ACCGGTTTG
473692 AACCGGTTTG
1 -ACCGGTTTG
473702 ACCGG
1 ACCGG
473707 CCTGACCCGA
Statistics
Matches: 81, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
9 21 0.26
10 52 0.64
11 8 0.10
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:473687 original size:19 final size:20
Alignment explanation
Indices: 473604--473706 Score: 126
Period size: 20 Copynumber: 5.2 Consensus size: 20
473594 GCTGCTGGAA
* *
473604 ACCGGTT-TAACCGGTTTTCA
1 ACCGGTTCTGACCGG-TTTCG
473624 ACCGGTTCTGACCGGTTTCG
1 ACCGGTTCTGACCGGTTTCG
473644 ACCGGTTCTGACCGGTTTCG
1 ACCGGTTCTGACCGGTTTCG
473664 ACCGGTTC-GAACCGGTTT-G
1 ACCGGTTCTG-ACCGGTTTCG
473683 ACCGG-TCTGAACCGGTTT-G
1 ACCGGTTCTG-ACCGGTTTCG
473702 ACCGG
1 ACCGG
473707 CCTGACCCGA
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
18 2 0.03
19 23 0.29
20 47 0.60
21 6 0.08
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGACCGGTTTCG
Found at i:473747 original size:22 final size:22
Alignment explanation
Indices: 473722--473764 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
473712 CCCGACCGTT
473722 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
473744 GACCCGACCCGACTGTTGACC
1 GACCCGACCCGACCGTTGACC
473765 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:473764 original size:17 final size:17
Alignment explanation
Indices: 473710--473752 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
473700 TGACCGGCCT
473710 GACCCGACCGTTGACCC
1 GACCCGACCGTTGACCC
473727 GACCCGACCGTTGACCC
1 GACCCGACCGTTGACCC
473744 GACCCGACC
1 GACCCGACC
473753 CGACTGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (17 bp):
GACCCGACCGTTGACCC
Found at i:481003 original size:19 final size:19
Alignment explanation
Indices: 480979--481018 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
480969 TTCGATGTTC
480979 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
*
480998 GAACCGGTTTGATCGGTCT
1 GAACCGGTTTGACCGGTCT
481017 GA
1 GA
481019 CCCGACCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.28
Consensus pattern (19 bp):
GAACCGGTTTGACCGGTCT
Found at i:481098 original size:7 final size:7
Alignment explanation
Indices: 481086--481116 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
481076 GACCCGACCC
481086 GACCGTT
1 GACCGTT
481093 GACCGTT
1 GACCGTT
481100 GACCGTT
1 GACCGTT
481107 GACCGTT
1 GACCGTT
481114 GAC
1 GAC
481117 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:487525 original size:17 final size:15
Alignment explanation
Indices: 487498--487534 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
487488 ATACATAATA
487498 TATATATATATATTT
1 TATATATATATATTT
487513 TCATATCATATATATTT
1 T-ATAT-ATATATATTT
487530 TATAT
1 TATAT
487535 TTTTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 8 0.40
17 11 0.55
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATATATATTT
Found at i:487542 original size:21 final size:24
Alignment explanation
Indices: 487495--487552 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 24
487485 ATAATACATA
487495 ATATATATATATATATTTTCATATC
1 ATATATATATATATATTTT-ATATC
*
487520 ATATATAT-TTTATATTTT-T-TC
1 ATATATATATATATATTTTATATC
*
487541 ATATGT-TATATA
1 ATATATATATATA
487553 CATATATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.03
21 10 0.34
22 1 0.03
24 9 0.31
25 8 0.28
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (24 bp):
ATATATATATATATATTTTATATC
Found at i:487550 original size:26 final size:27
Alignment explanation
Indices: 487495--487560 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
487485 ATAATACATA
487495 ATATATATATATATATTTTCATATCAT
1 ATATATATATATATATTTTCATATCAT
* * **
487522 ATATAT-TTTATATTTTTTCATATGTT
1 ATATATATATATATATTTTCATATCAT
*
487548 ATATACATATATA
1 ATATATATATATA
487561 CAATAGACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATATATATATATATTTTCATATCAT
Found at i:490885 original size:129 final size:130
Alignment explanation
Indices: 490709--490955 Score: 406
Period size: 129 Copynumber: 1.9 Consensus size: 130
490699 TATTTATATA
*
490709 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
490774 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
490839 ATCAATTTGGTCCTAAATTAAATAATA-TTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
490903 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
490956 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 82 0.76
130 26 0.24
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:490986 original size:129 final size:129
Alignment explanation
Indices: 490723--490986 Score: 291
Period size: 129 Copynumber: 2.0 Consensus size: 129
490713 ATTTGGTCCT
* *
490723 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
490788 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
490853 AAATTAAATAATA-TTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
490917 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
490981 -A
128 CA
490982 AAATT
1 AAATT
490987 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
129 86 0.77
130 12 0.11
131 8 0.07
132 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:491590 original size:21 final size:21
Alignment explanation
Indices: 491566--491609 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
491556 TATTACCTTA
491566 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
491587 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
491608 AA
1 AA
491610 GGTTTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:492853 original size:179 final size:181
Alignment explanation
Indices: 492525--492995 Score: 703
Period size: 179 Copynumber: 2.6 Consensus size: 181
492515 GATCCAAATT
* * * * *
492525 AAAAATATGTCGATCCAAAACGATATAAGAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-TCAAATGATA
* * * * *
492590 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
492655 GTGAATTTAAAATAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
492707 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
* * *
492772 AACCGGTAAAACGTTACCGGATATA-TGAAAGTGTTGATACTTT-ATATAAGGATCGACACTTTG
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
** *
492835 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
492886 AAAAATATATTGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATC-AAATGATA
492951 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
492996 CGTAAATACG
Statistics
Matches: 261, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
179 116 0.44
180 48 0.18
181 49 0.19
182 48 0.18
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:492939 original size:20 final size:19
Alignment explanation
Indices: 492916--492962 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
492906 CGATATAACA
492916 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
492936 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
492956 GGTAAAA
1 GGTAAAA
492963 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:492967 original size:17 final size:19
Alignment explanation
Indices: 492927--492967 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
492917 GTAAAAATAT
*
492927 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
492947 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
492964 GATA
1 GATA
492968 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:494047 original size:183 final size:183
Alignment explanation
Indices: 493705--494476 Score: 1386
Period size: 183 Copynumber: 4.2 Consensus size: 183
493695 CAAAGTTTTC
*
493705 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
493770 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
493833 TATAATCGGTATAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
493889 ACACATTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
493954 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
494019 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
494072 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
494137 CAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
494202 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
494255 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
494320 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
494385 AACCGGTATAAATATACCGATTTTATGAGTGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
494438 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
494477 TATAATGTAC
Statistics
Matches: 572, Mismatches: 14, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
183 494 0.86
184 75 0.13
186 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:494563 original size:120 final size:120
Alignment explanation
Indices: 494350--494596 Score: 415
Period size: 120 Copynumber: 2.1 Consensus size: 120
494340 ACATCGGAAC
* *
494350 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGT
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGAGTTTATGAGC
*
494415 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * *
494470 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAACCGGTATAAGTATACCG-GTTTATTAG
1 CCAGAATTATAATGTAATAGATAATTTTGTAATAT-AACCGGTATAAATATACCGAGTTTATGAG
*
494534 CGAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
65 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
494590 CCAGAAT
1 CCAGAAT
494597 GGAAGAAAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 101 0.85
121 18 0.15
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGAGTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:494714 original size:303 final size:303
Alignment explanation
Indices: 494167--494761 Score: 1102
Period size: 303 Copynumber: 2.0 Consensus size: 303
494157 ACATCGGAAC
494167 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
494232 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
494297 AGAAAAATGTGTCGATACATTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACATTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
*
494362 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGTGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTAC
*
494427 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * *
494470 CCAGAATTATAATGTACTAGATAATTTTGTAATATAAACCGGTATAAGTATACCGG-TTTATTAG
1 CCAGAATTATAATGTAATAGATAATTTTGTAATAT-AACCGGTATAAATATACCGGTTTTATGAG
*
494534 CGAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGG
65 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGG
*
494599 AAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATA
130 AAGAAAAATGTGTCGATACATTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATA
*
494664 ATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTA
195 ATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTA
494729 CAACCTATATCGACACTTTTTAATATTGTGTCG
260 CAACCTATATCGACACTTTTTAATATTGTGTCG
494762 CTAATTTTAA
Statistics
Matches: 283, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
303 264 0.93
304 19 0.07
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (303 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
AGAAAAATGTGTCGATACATTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTAC
AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:498197 original size:87 final size:87
Alignment explanation
Indices: 498093--498255 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
498083 AAATAGGTCA
498093 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
498158 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* *
498180 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
498245 TCGGTTAAATA
66 CCCGTTAAATA
498256 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:498227 original size:23 final size:23
Alignment explanation
Indices: 498177--498221 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
498167 TACCTATTTT
* *
498177 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
498200 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
498222 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Done.