Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005168.1 Hibiscus syriacus cultivar Beakdansim tig00011662_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: 818383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:459910 original size:26 final size:25
Alignment explanation
Indices: 459881--459934 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
459871 AATGGAGATT
* *
459881 CTACGAGGCACTTTCTAGTGCAAATA
1 CTACGAGACACTTTCGAGTGC-AATA
459907 CTACGAGACACTTTCGAGTGCAATA
1 CTACGAGACACTTTCGAGTGCAATA
459932 CTA
1 CTA
459935 TATATAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (25 bp):
CTACGAGACACTTTCGAGTGCAATA
Found at i:483851 original size:30 final size:30
Alignment explanation
Indices: 483794--483867 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
483784 ATAAAACCGG
*
483794 CGGTTCACACC-AGTTTTGTCAGATCCCAAC
1 CGGTTCACACCGA-TTTTATCAGATCCCAAC
* *
483824 CGGTTCACACCGATTTTATCGGTTCCCAAC
1 CGGTTCACACCGATTTTATCAGATCCCAAC
* *
483854 TGGTTC-TACCGATT
1 CGGTTCACACCGATT
483868 CCCAACCGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 7 0.18
30 30 0.79
31 1 0.03
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (30 bp):
CGGTTCACACCGATTTTATCAGATCCCAAC
Found at i:484198 original size:17 final size:16
Alignment explanation
Indices: 484169--484203 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
484159 GATGAGGGCT
*
484169 TTAGTTTTATTTTAGG
1 TTAGGTTTATTTTAGG
484185 TTAGGTTTAGTTTTAGG
1 TTAGGTTTA-TTTTAGG
484202 TT
1 TT
484204 CTTCTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (16 bp):
TTAGGTTTATTTTAGG
Found at i:488766 original size:21 final size:21
Alignment explanation
Indices: 488734--488788 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
488724 ATTCTGACTA
*
488734 TCGCATTACGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
488755 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
488776 TCGCATTGCGATT
1 TCGCATTGCGATT
488789 ACGTAAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:489714 original size:24 final size:24
Alignment explanation
Indices: 489663--489716 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
489653 GTATTCGAAA
*
489663 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
489687 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
489711 TTTGAT
1 TTTGAT
489717 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:492416 original size:20 final size:20
Alignment explanation
Indices: 492388--492520 Score: 113
Period size: 20 Copynumber: 7.0 Consensus size: 20
492378 GGTTGAAATA
492388 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAATG
** *
492408 ACTATCGCAACGCG-GAAATG
1 AAAATCGCAACGAGAG-AATG
*
492428 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAGAATG
**
492448 ATTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAG-AATG
492469 AAAATCGCAAC--GAG-A-G
1 AAAATCGCAACGAGAGAATG
*
492485 --AATCGCAACGTGA-AATG
1 AAAATCGCAACGAGAGAATG
492502 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
492521 CGTAACGCGA
Statistics
Matches: 88, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
14 9 0.10
16 4 0.05
17 2 0.02
19 16 0.18
20 43 0.49
21 14 0.16
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAATG
Found at i:492426 original size:40 final size:41
Alignment explanation
Indices: 492382--492520 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 41
492372 TCTTTTGGTT
* *
492382 GAAATAAAAATCGCAACGAGAGAATGACTATCGCAACGCG-
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGAGA
* *
492422 GAAATGAAAATCGCAAC-ACGAAAATGATTATCGCAACGAGA
1 GAAATGAAAATCGCAACGA-GAGAATGACTATCGCAACGAGA
*
492463 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAAC--GT
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGAGA
492496 GAAATGAAAATCGCAACGAGAGAAT
1 GAAATGAAAATCGCAACGAGAGAAT
492521 CGTAACGCGA
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
33 18 0.21
35 11 0.13
36 1 0.01
37 2 0.02
38 1 0.01
39 3 0.03
40 34 0.39
41 17 0.20
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (41 bp):
GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGAGA
Found at i:492469 original size:21 final size:21
Alignment explanation
Indices: 492382--492486 Score: 119
Period size: 20 Copynumber: 5.1 Consensus size: 21
492372 TCTTTTGGTT
*
492382 GAAATAAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
** *
492403 G-AATGACTATCGCAACGCG-
1 GAAATGAAAATCGCAACGAGA
492422 GAAATGAAAATCGCAAC-ACGA
1 GAAATGAAAATCGCAACGA-GA
**
492443 -AAATGATTATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
492463 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
492484 GAA
1 GAA
492487 TCGCAACGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
19 1 0.01
20 44 0.65
21 23 0.34
ACGTcount: A:0.49, C:0.17, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:492490 original size:14 final size:14
Alignment explanation
Indices: 492471--492527 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
492461 GAGAAATGAA
492471 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
492485 AATCGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
492504 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
492518 AATCGTAACG
1 AATCGCAACG
492528 CGAAATACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:492504 original size:33 final size:33
Alignment explanation
Indices: 492411--492544 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 33
492401 GAGAATGACT
*
492411 ATCGCAACGCGGAAATGAAAATCGCAACACGAAAATGA
1 ATCGCAACGC-GAAATGAAAATCGC-A-ACG-AGA-GA
*
492449 TTATCGCAACGAGAGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAAC--GCGAAATGAAAATCGCAACGAGAGA
*
492486 ATCGCAACGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
492519 ATCGTAACGCGAAAT-ACAAATCGCAA
1 ATCGCAACGCGAAATGA-AAATCGCAA
492545 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
32 1 0.01
33 46 0.53
35 8 0.09
37 2 0.02
38 2 0.02
39 3 0.03
40 9 0.10
41 14 0.16
42 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:492580 original size:14 final size:14
Alignment explanation
Indices: 492561--492616 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
492551 TTTGGTTTCG
492561 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
492575 CGTTGCGATTTTCATTCG
1 CGTTGCGA--TT-A-TCT
*
492593 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
492607 CGTTGCGATT
1 CGTTGCGATT
492617 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.57
16 4 0.11
17 1 0.03
18 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:492597 original size:32 final size:32
Alignment explanation
Indices: 492557--492622 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
492547 CGATTTTGGT
492557 TTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTCGCGTTGCGATTATCTCGTTGCGATTTTCA
*
492589 TTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTCGCGTTGCGATTATCTCGTTGCGATTTTCA
492621 TT
1 TT
492623 TCTCTCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (32 bp):
TTCGCGTTGCGATTATCTCGTTGCGATTTTCA
Found at i:492627 original size:21 final size:21
Alignment explanation
Indices: 492601--492664 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
492591 CGCGTTGCGA
492601 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
492622 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
492643 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
492663 TT
1 TT
492665 TCATGTTACG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:492677 original size:20 final size:19
Alignment explanation
Indices: 492608--492679 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
492598 CGATTCTCTC
492608 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
492628 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
492649 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
*
492669 GTTACGATTTT
1 GTTGCGATTTT
492680 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:493251 original size:20 final size:20
Alignment explanation
Indices: 493205--493338 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
493195 CGATAGTCAG
* *
493205 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
493225 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
493246 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
493266 AATAGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
493286 AATAGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
493306 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
493326 ATTCGCATTGCGA
1 ATTCGCATTGCGA
493339 ATTAGGAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
20 87 0.83
21 18 0.17
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:493359 original size:21 final size:21
Alignment explanation
Indices: 493335--493380 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
493325 TATTCGCATT
493335 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
493356 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
493377 GCGA
1 GCGA
493381 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:495332 original size:67 final size:67
Alignment explanation
Indices: 495211--495511 Score: 410
Period size: 67 Copynumber: 4.5 Consensus size: 67
495201 TTTGTATCCC
* *
495211 TTGAGATAGTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
495275 CT
66 CT
*
495277 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGA-AAGTTTATCTTGAAACATAAA
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAA-TTTCTCTTGAAACATAAA
495341 CCT
65 CCT
* * * * *
495344 TTGAGATTGTTTCTCTCAAAACAAAGTTTCGTCTCTCTTAAGACAATATCTCTT-ATAACATAAA
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGA-AACATAAA
495408 CCT
65 CCT
* * *
495411 TTGATATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTCAAACATATAA
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAAC--ATAA
495476 ACCT
64 ACCT
* * * *
495480 TTGAGATTATTTCACTCAAAACAAAATTTTGT
1 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGT
495512 TTCACCTAAG
Statistics
Matches: 207, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
66 26 0.13
67 143 0.69
68 3 0.01
69 35 0.17
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (67 bp):
TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAAC
CT
Found at i:498687 original size:9 final size:9
Alignment explanation
Indices: 498673--498703 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
498663 GAATTATTAA
498673 ATATTAAAT
1 ATATTAAAT
*
498682 ATATTATAT
1 ATATTAAAT
498691 ATATTAAAT
1 ATATTAAAT
498700 ATAT
1 ATAT
498704 ATTTTAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATATTAAAT
Found at i:499496 original size:2 final size:2
Alignment explanation
Indices: 499491--499515 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
499481 ATGTATTTTA
499491 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
499516 ATACTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:500557 original size:19 final size:19
Alignment explanation
Indices: 500522--500570 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
500512 CTCAAAACAT
500522 TATTATTTT-ATA-T-ATA
1 TATTATTTTAATATTAATA
500538 TA-TA-TTTAATATTAATA
1 TATTATTTTAATATTAATA
500555 TATTATTTTAATATTA
1 TATTATTTTAATATTA
500571 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 3 0.11
17 5 0.18
18 2 0.07
19 10 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTTTAATATTAATA
Found at i:500585 original size:28 final size:32
Alignment explanation
Indices: 500522--500607 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
500512 CTCAAAACAT
*
500522 TATTATTTTATATATATATATTTAATATTAATA
1 TATTATTTTATATATATATATTTAATA-TAAAA
500555 TATTATTTTA-ATAT-TAT-TTTAATA-AAAA
1 TATTATTTTATATATATATATTTAATATAAAA
*
500583 TATTAATTATTAAATATAATATATT
1 TATT-ATT-TTATATAT-ATATATT
500608 GATAATGTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
28 7 0.15
29 3 0.07
30 10 0.22
31 7 0.15
32 4 0.09
33 13 0.28
34 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTATTTTATATATATATATTTAATATAAAA
Found at i:500585 original size:30 final size:33
Alignment explanation
Indices: 500522--500607 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 33
500512 CTCAAAACAT
**
500522 TATTATTTTATATATATATATTTAATATTAATA
1 TATTATTTTATATATATATATTTAATAAAAATA
500555 TATTATTTTA-ATAT-TAT-TTTAATAAAAATA
1 TATTATTTTATATATATATATTTAATAAAAATA
* *
500585 T-TAATTATTAAATATAATATATT
1 TATTATT-TTATATAT-ATATATT
500608 GATAATGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 4 0.09
30 15 0.33
31 7 0.16
32 4 0.09
33 13 0.29
34 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTATTTTATATATATATATTTAATAAAAATA
Found at i:500603 original size:19 final size:18
Alignment explanation
Indices: 500544--500664 Score: 57
Period size: 16 Copynumber: 7.1 Consensus size: 18
500534 TATATATATT
* *
500544 TAATATTAATATATTATTT
1 TAATATTAAT-TATTAATA
500563 TAATATT-ATT-TTAATAA
1 TAATATTAATTATTAAT-A
*
500580 AAATATTAATTATTAAATA
1 TAATATTAATTATT-AATA
*
500599 TAATA-T-ATTGA-TAATG
1 TAATATTAATT-ATTAATA
*
500615 T--TAATAA-TA-TAATA
1 TAATATTAATTATTAATA
* *
500629 TAATATTTATTATTATTA
1 TAATATTAATTATTAATA
*
500647 TTATATT-ATTA-TAATA
1 TAATATTAATTATTAATA
500663 TA
1 TA
500665 TAATTTTATT
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
14 8 0.10
15 2 0.03
16 18 0.23
17 17 0.22
18 17 0.22
19 14 0.18
20 3 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATATTAATTATTAATA
Found at i:512249 original size:19 final size:18
Alignment explanation
Indices: 512208--512262 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
512198 AGTTAGATCC
512208 TTATATATTTTAATTTTCT
1 TTAT-TATTTTAATTTTCT
512227 TTATTATTTGTAATTTT-T
1 TTATTATTT-TAATTTTCT
*
512245 ATTATTTTGTTTAATTTT
1 -TTATTAT-TTTAATTTT
512263 AGTAGTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.19
19 24 0.75
20 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (18 bp):
TTATTATTTTAATTTTCT
Found at i:516732 original size:21 final size:21
Alignment explanation
Indices: 516692--516731 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
516682 TTGAAAATAT
516692 AATATATTATATAATTTTTTA
1 AATATATTATATAATTTTTTA
*
516713 AATATATTAT-TATTTTTTT
1 AATATATTATATAATTTTTT
516732 TTTCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATATATTATATAATTTTTTA
Found at i:516886 original size:30 final size:30
Alignment explanation
Indices: 516817--516887 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
516807 AGCCAGCAGA
* *
516817 CCTGACCCAACAAGCCATCTCTGTTAGGGG
1 CCTGACCCAGCAAGCCATCCCTGTTAGGGG
516847 CCTGACCCAGCAAGCCATCCCTGTTAGGGG
1 CCTGACCCAGCAAGCCATCCCTGTTAGGGG
516877 CCTGACCCAGC
1 CCTGACCCAGC
516888 CTGGAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (30 bp):
CCTGACCCAGCAAGCCATCCCTGTTAGGGG
Found at i:522905 original size:28 final size:28
Alignment explanation
Indices: 522865--522929 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
522855 TTCAAGTTCA
*
522865 TCTTGAGTTGATGAAGGGGATATTGATT
1 TCTTGTGTTGATGAAGGGGATATTGATT
* *
522893 TCTTTTGTTGATGAAGGGGATGTTGATT
1 TCTTGTGTTGATGAAGGGGATATTGATT
522921 TCTTGTGTT
1 TCTTGTGTT
522930 TTATGGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.18, C:0.05, G:0.31, T:0.46
Consensus pattern (28 bp):
TCTTGTGTTGATGAAGGGGATATTGATT
Found at i:523881 original size:16 final size:18
Alignment explanation
Indices: 523842--523882 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
523832 AGCATGATAT
*
523842 TATGTCATTTATCATAAA
1 TATGTCATATATCATAAA
*
523860 TTTGTCATAT-TC-TAAA
1 TATGTCATATATCATAAA
523876 TATGTCA
1 TATGTCA
523883 AAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 10 0.50
17 2 0.10
18 8 0.40
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (18 bp):
TATGTCATATATCATAAA
Found at i:524407 original size:45 final size:45
Alignment explanation
Indices: 524313--524636 Score: 524
Period size: 45 Copynumber: 7.2 Consensus size: 45
524303 AATGATAAAC
* * * *
524313 TGGTAAAATAAGCTTACTAGCGTATGGAA-TAATGGCAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
524357 TGGTAAAATAAGCTTACGAGATTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
524402 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
524447 TGGTAAAATAAGCTTACGAGCTTATGCAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
* *
524492 TGTTAAAATAAGCTTACGAGCTTATGGAACAAATGGTTAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
**
524537 TGGTAAAATAAGCTTGTGAGCTTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
**
524582 TGGTAAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
524627 TGATAAAATA
1 TGGTAAAATA
524637 TTGGATATGT
Statistics
Matches: 260, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
44 26 0.10
45 234 0.90
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
Found at i:530793 original size:21 final size:23
Alignment explanation
Indices: 530768--530813 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
530758 GATTTTTTTC
*
530768 ATATGA-TGTTGTCATGAA-CAT
1 ATATGATTGTTATCATGAATCAT
*
530789 ATATGATTTTTATCATGAATCAT
1 ATATGATTGTTATCATGAATCAT
530812 AT
1 AT
530814 TGCGAGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (23 bp):
ATATGATTGTTATCATGAATCAT
Found at i:531290 original size:45 final size:45
Alignment explanation
Indices: 531196--531519 Score: 524
Period size: 45 Copynumber: 7.2 Consensus size: 45
531186 AATGATAAAC
* * * *
531196 TGGTAAAATAAGCTTACTAGCGTATGGAA-TAATGGCAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
531240 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAATTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
531285 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
531330 CGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
* *
531375 TGTTAAAATAAGCTTACGAGCTTATGGAACAAATGGTTAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
**
531420 TGGTAAAATAAGCTTGTGAGCTTATGGAACAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
**
531465 TGGTAAAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
*
531510 TGATAAAATA
1 TGGTAAAATA
531520 TTGGATATGT
Statistics
Matches: 260, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
44 27 0.10
45 233 0.90
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATAT
Found at i:531318 original size:25 final size:25
Alignment explanation
Indices: 531290--531363 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
531280 TATATTGGTA
531290 AAATAAGCTTACGAGCTTATGGAAC
1 AAATAAGCTTACGAGCTTATGGAAC
* *
531315 AAAT--G-GTA--AG-TATATCGGTA-
1 AAATAAGCTTACGAGCT-TAT-GGAAC
531335 AAATAAGCTTACGAGCTTATGGAAC
1 AAATAAGCTTACGAGCTTATGGAAC
531360 AAAT
1 AAAT
531364 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 9 0.25
21 3 0.08
22 3 0.08
23 3 0.08
24 3 0.08
25 13 0.36
26 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGAAC
Found at i:534274 original size:60 final size:60
Alignment explanation
Indices: 534202--534400 Score: 305
Period size: 60 Copynumber: 3.4 Consensus size: 60
534192 AAAAATCTCA
* * *
534202 GTTAGGCA-TTAACTTACCATCTACCTTGCATTAATGGAACATTTCTACCAAAATGCACC
1 GTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGAACATTTCTACCAAAATGCACC
*
534261 GTTAGGCATTTAACTTATCATCTAACTTGCATTAGT-GACACATTTCTACCAAAATGCATC
1 GTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGA-ACATTTCTACCAAAATGCACC
* * *
534321 GTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGCACCTTTCTACAAAAATGCACC
1 GTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGAACATTTCTACCAAAATGCACC
534381 GTTAGGCATTTAACTT-TCAT
1 GTTAGGCATTTAACTTATCAT
534401 TTTAGAGCAT
Statistics
Matches: 129, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
59 14 0.11
60 114 0.88
61 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (60 bp):
GTTAGGCATTTAACTTATCATCTAACTTGCATTAGTGGAACATTTCTACCAAAATGCACC
Found at i:540270 original size:59 final size:60
Alignment explanation
Indices: 540088--540330 Score: 319
Period size: 60 Copynumber: 4.1 Consensus size: 60
540078 GCATTGTTTT
* * * * * * * * *
540088 TCATCTAAATTGAATTAGTGGCACATTTCCAGCAAAAATGCTCAGTTAGGCAATTAACTTA
1 TCATCTAACTTGCATTAGTGGTACCTTT-CTGCCAAAATGCACCGTTAGGCATTTAACTTA
* * * *
540149 TCATCTAACTTGCATTAATGGCACCTTTCTGACAAAATGCACCGTTAGGCATTCAACTTA
1 TCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACCGTTAGGCATTTAACTTA
* *
540209 TCATCTAACTTGCATTAGTGATACCTTT-TGCCAAAAAGCACCGTTAGGCATTTAACTTA
1 TCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACCGTTAGGCATTTAACTTA
*
540268 TCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACCGTTAGGCATTTAGCTT-
1 TCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACCGTTAGGCATTTAACTTA
540327 TCAT
1 TCAT
540331 TTTAGAGCAT
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
59 59 0.37
60 78 0.48
61 24 0.15
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (60 bp):
TCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACCGTTAGGCATTTAACTTA
Found at i:542395 original size:20 final size:19
Alignment explanation
Indices: 542372--542419 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
542362 CGGCAAACAC
*
542372 TTTTCATTCTTCATTTATTT
1 TTTTCATTCCT-ATTTATTT
* *
542392 TTTTCTTTCCTGTTTATTT
1 TTTTCATTCCTATTTATTT
542411 TTATTCATT
1 TT-TTCATT
542420 TTGTGTGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTCATTCCTATTTATTT
Found at i:542893 original size:60 final size:61
Alignment explanation
Indices: 542768--543011 Score: 318
Period size: 60 Copynumber: 4.1 Consensus size: 61
542758 TGTATTTTTT
* ** * *
542768 TCATTTAACTTGCATTAGTGGCACATTTCTGCCAAAAATGCTCAGTTAGGCATTTAACTTA
1 TCATCTAACTTGCATTAACGGCACCTTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
* * *
542829 TCATCTAACTTGCATTAACGGCACCTTTCTGAC-AAAATGCACCGTTAGGCATTTAACTTG
1 TCATCTAACTTGCATTAACGGCACCTTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
** * *
542889 TCATCTAACTTGCATTAGTGGCATCTTTCTGCC-AAAATGCACCGTTAGGCATTTAACTTA
1 TCATCTAACTTGCATTAACGGCACCTTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
* *
542949 TCATCTAACTTGC-TTTACTGGCACCTTTCTG-CAAAAATGCATAGTTAGGCATTTAACTT-
1 TCATCTAACTTGCATTAAC-GGCACCTTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
543008 TCAT
1 TCAT
543012 TTTAGAGCAT
Statistics
Matches: 162, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
59 7 0.04
60 127 0.78
61 28 0.17
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (61 bp):
TCATCTAACTTGCATTAACGGCACCTTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
Found at i:542987 original size:120 final size:120
Alignment explanation
Indices: 542766--543011 Score: 374
Period size: 120 Copynumber: 2.0 Consensus size: 120
542756 TTTGTATTTT
* *
542766 TTTCATTTAACTTGCATTAGTGGCACATTTCTGCCAAAAATGCTCAGTTAGGCATTTAACTTATC
1 TTTCATCTAACTTGCATTAGTGGCACATTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTATC
*
542831 ATCTAACTTGCATTAACGGCACCTTTCTGACAAAATGCACCGTTAGGCATTTAAC
66 ATCTAACTTGCATTAACGGCACCTTTCTGACAAAATGCACAGTTAGGCATTTAAC
*
542886 TTGTCATCTAACTTGCATTAGTGGCATC-TTTCTGCC-AAAATGCACCGTTAGGCATTTAACTTA
1 TT-TCATCTAACTTGCATTAGTGGCA-CATTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTA
* *
542949 TCATCTAACTTGC-TTTACTGGCACCTTTCTG-CAAAAATGCATAGTTAGGCATTTAAC
64 TCATCTAACTTGCATTAAC-GGCACCTTTCTGAC-AAAATGCACAGTTAGGCATTTAAC
543006 TTTCAT
1 TTTCAT
543012 TTTAGAGCAT
Statistics
Matches: 116, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
119 9 0.08
120 76 0.66
121 30 0.26
122 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (120 bp):
TTTCATCTAACTTGCATTAGTGGCACATTTCTGCCAAAAATGCACAGTTAGGCATTTAACTTATC
ATCTAACTTGCATTAACGGCACCTTTCTGACAAAATGCACAGTTAGGCATTTAAC
Found at i:548450 original size:73 final size:73
Alignment explanation
Indices: 548293--548451 Score: 185
Period size: 73 Copynumber: 2.2 Consensus size: 73
548283 ATTCAATATT
* * * * * *
548293 GACTCAACTTCACGACGAATGAGTCACCCACGATTTTAACTTCACAACGAAGGATATCGTACCCA
1 GACTTAACTTCACGAAGAAGGAGTCACCCACGATTTCAACTTCACAACAAAGGATATCATACCCA
*
548358 AAAGTTTC
66 AAAGTATC
* * * * *
548366 GATTTAACTTCACGAAGAAGGAGTCAGCCCCCGATTTCAACTTCACAATAAAGGATATCATGCCT
1 GACTTAACTTCACGAAGAAGGAGTCA-CCCACGATTTCAACTTCACAACAAAGGATATCATACCC
*
548431 AATAG-ATC
65 AAAAGTATC
548439 GACTTAACTTCAC
1 GACTTAACTTCAC
548452 AGCAAATGAG
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
73 36 0.51
74 35 0.49
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (73 bp):
GACTTAACTTCACGAAGAAGGAGTCACCCACGATTTCAACTTCACAACAAAGGATATCATACCCA
AAAGTATC
Found at i:549215 original size:31 final size:30
Alignment explanation
Indices: 549152--549312 Score: 116
Period size: 30 Copynumber: 5.2 Consensus size: 30
549142 AAAAAGTATA
* **
549152 ATATATGGTTTTTAAAATGGTTTTGAAAAC
1 ATATATAGTTTTTAAAATATTTTTGAAAAC
549182 ATATATAGTTTTTAAAATAATTTTT-AAAA-
1 ATATATAGTTTTTAAAAT-ATTTTTGAAAAC
*
549211 ACATATAGTTTTTAAAAAATAGTTTTT-AAAAC
1 ATATATAGTTTTT--AAAATA-TTTTTGAAAAC
* * *
549243 GTATAATAGGTAGTTTTAAAATGGTTTTTCAAAAC
1 ATAT-ATA-GT--TTTTAAAAT-ATTTTTGAAAAC
549278 ATATAGTA-TATTTT-AAATATTTTTGAAAAC
1 ATATA-TAGT-TTTTAAAATATTTTTGAAAAC
*
549308 GTATA
1 ATATA
549313 GTTTTCAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
29 12 0.11
30 36 0.34
31 22 0.21
32 6 0.06
33 4 0.04
34 13 0.12
35 10 0.09
36 4 0.04
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (30 bp):
ATATATAGTTTTTAAAATATTTTTGAAAAC
Found at i:549234 original size:14 final size:15
Alignment explanation
Indices: 549186--549242 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
549176 GAAAACATAT
*
549186 ATAGTTTTTAAAATA
1 ATAGTTTTTAAAACA
*
549201 AT--TTTTAAAAACA
1 ATAGTTTTTAAAACA
549214 TATAGTTTTTAAAA-A
1 -ATAGTTTTTAAAACA
549229 ATAGTTTTTAAAAC
1 ATAGTTTTTAAAAC
549243 GTATAATAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 9 0.26
14 15 0.43
15 3 0.09
16 8 0.23
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (15 bp):
ATAGTTTTTAAAACA
Found at i:549323 original size:95 final size:96
Alignment explanation
Indices: 549137--549342 Score: 258
Period size: 95 Copynumber: 2.2 Consensus size: 96
549127 TGAAAGCTTT
* * * *
549137 TTTTTAAAAAGTATAATATATGGTTTTTAAAATGGTTTTGAAAACATATATAGTTTTTAAAATAA
1 TTTTTAAAACGTATAATAGATAGTTTTTAAAATGGTTTTCAAAACATATATAGTTTTTAAAATAA
* *
549202 TTTTTAAAAACATATAGTTTTTAAAAAATAG
66 TTTTTAAAAACATATAGTTTTCAAAAAACAG
*
549233 TTTTTAAAACGTATAATAGGTAG-TTTTAAAATGGTTTTTCAAAACATATAGTA-TATTTT-AAA
1 TTTTTAAAACGTATAATAGATAGTTTTTAAAATGG-TTTTCAAAACATATA-TAGT-TTTTAAAA
* * *
549295 T-ATTTTTGAAAACGTATAGTTTTCAAAAAACGG
63 TAATTTTTAAAAACATATAGTTTTCAAAAAACAG
*
549328 TTTTTAAAACATATA
1 TTTTTAAAACGTATA
549343 GTATATATTA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
95 52 0.54
96 38 0.40
97 6 0.06
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (96 bp):
TTTTTAAAACGTATAATAGATAGTTTTTAAAATGGTTTTCAAAACATATATAGTTTTTAAAATAA
TTTTTAAAAACATATAGTTTTCAAAAAACAG
Found at i:549487 original size:3 final size:3
Alignment explanation
Indices: 549479--549503 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
549469 TTTTAAAATA
549479 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
549504 TTTTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:549682 original size:20 final size:20
Alignment explanation
Indices: 549659--549699 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
549649 ATTAGGGTTT
549659 CCACACATTAACCAGGGGTG
1 CCACACATTAACCAGGGGTG
549679 CCACACATTAACCAGGGGTG
1 CCACACATTAACCAGGGGTG
549699 C
1 C
549700 TGAAAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (20 bp):
CCACACATTAACCAGGGGTG
Found at i:550584 original size:40 final size:39
Alignment explanation
Indices: 550527--550624 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 39
550517 CGATTTTCCA
*
550527 AATTTGCAACACTGAATTTCAAAT-TAGCAACTCAATTTCTG
1 AATTCGCAACAC-GAATTT-AAATGTAGCAACTCAATTT-TG
** *** *
550568 AATTCGCAATGCGAATTTTGTTGTAGCAACTCGATTTTG
1 AATTCGCAACACGAATTTAAATGTAGCAACTCAATTTTG
550607 AATTCGCAACACGAATTT
1 AATTCGCAACACGAATTT
550625 TAATTTCGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 19 0.40
40 19 0.40
41 9 0.19
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (39 bp):
AATTCGCAACACGAATTTAAATGTAGCAACTCAATTTTG
Found at i:550615 original size:19 final size:20
Alignment explanation
Indices: 550548--550629 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
550538 CTGAATTTCA
550548 AATTAGCAACTC-AATTTCTG
1 AATTAGCAACTCGAATTT-TG
*
550568 AATTCGCAA-TGCGAATTTTG
1 AATTAGCAACT-CGAATTTTG
*
550588 -TTGTAGCAACTCG-ATTTTG
1 AAT-TAGCAACTCGAATTTTG
* *
550607 AATTCGCAACACGAATTTT-
1 AATTAGCAACTCGAATTTTG
550626 AATT
1 AATT
550630 TCGTAACACA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
19 20 0.40
20 24 0.48
21 6 0.12
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (20 bp):
AATTAGCAACTCGAATTTTG
Found at i:551438 original size:12 final size:12
Alignment explanation
Indices: 551406--551439 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
551396 TCACCATTTC
*
551406 CAATACCAAACA
1 CAATATCAAACA
551418 CAATATCAAACA
1 CAATATCAAACA
*
551430 CAATCTCAAA
1 CAATATCAAA
551440 ACCTGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:551596 original size:24 final size:24
Alignment explanation
Indices: 551564--551617 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
551554 GTATTTGAAA
*
551564 TTTGATCTTGGTTAATACTCAGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
551588 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
551612 TTTGAT
1 TTTGAT
551618 GATGTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:553853 original size:12 final size:12
Alignment explanation
Indices: 553838--553878 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
553828 AGAAAAAGGA
*
553838 AATCAAAATCGC
1 AATCAAAATCAC
*
553850 AATCAAAATCAA
1 AATCAAAATCAC
*
553862 AATCAAAATCCC
1 AATCAAAATCAC
553874 AATCA
1 AATCA
553879 CAACCCGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:553859 original size:6 final size:6
Alignment explanation
Indices: 553837--553871 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
553827 AAGAAAAAGG
* *
553837 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
553872 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:554094 original size:19 final size:19
Alignment explanation
Indices: 554063--554116 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 19
554053 CGATTGTTGT
554063 GAAAGTCAAATTCGCAACGC
1 GAAAGT-AAATTCGCAACGC
554083 GAAAGTAAATTCGCAACGC
1 GAAAGTAAATTCGCAACGC
*
554102 GAATGTTAAATTCGC
1 GAAAG-TAAATTCGC
554117 GTTGCGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
GAAAGTAAATTCGCAACGC
Found at i:554175 original size:20 final size:20
Alignment explanation
Indices: 554112--554177 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
554102 GAATGTTAAA
* * *
554112 TTCGCGTTGCGAATTTGGCT
1 TTCGCATTGCAAATTTGACT
* *
554132 TTCACATTGCAAATCTGACT
1 TTCGCATTGCAAATTTGACT
554152 TTCGCATTGCAAATTTGACT
1 TTCGCATTGCAAATTTGACT
554172 TTCGCA
1 TTCGCA
554178 ACCATCGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (20 bp):
TTCGCATTGCAAATTTGACT
Found at i:554310 original size:14 final size:14
Alignment explanation
Indices: 554293--554329 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
554283 ATTTAAAAAA
554293 ACAAATCAACTTTT
1 ACAAATCAACTTTT
554307 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
554321 ACAAGTCAA
1 ACAAATCAA
554330 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:555764 original size:21 final size:20
Alignment explanation
Indices: 555735--555804 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
555725 ATGAATCGGG
* *
555735 CTCTCGAACAGTGGGAGGGAC
1 CTCTTGAAC-GTGGGAGGGGC
**
555756 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACG-TGGGAGGGGC
555777 CTCTTGAACG-GTGGAGGGGC
1 CTCTTGAACGTG-GGAGGGGC
555797 CTCTTGAA
1 CTCTTGAA
555805 GGATGATAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
21 25 0.61
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.20
Consensus pattern (20 bp):
CTCTTGAACGTGGGAGGGGC
Found at i:555810 original size:41 final size:41
Alignment explanation
Indices: 555748--555856 Score: 137
Period size: 41 Copynumber: 2.6 Consensus size: 41
555738 TCGAACAGTG
* *
555748 GGAGGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGT
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
* * * * *
555789 GGAGGGGCCTCTTGAAGGATGATAGGGGCTTTTTGAATGAT
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
*
555830 GATAGGGGCCTCTTGAACGATGACAGG
1 G-GAGGGGCCTCTTGAACGATGACAGG
555857 TGCTTCGGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 35 0.61
42 22 0.39
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (41 bp):
GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT
Found at i:555817 original size:21 final size:21
Alignment explanation
Indices: 555750--555852 Score: 127
Period size: 21 Copynumber: 5.0 Consensus size: 21
555740 GAACAGTGGG
* *
555750 AGGGACCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAT
* *
555771 AGGGGCCTCTTGAACGGTG-G
1 AGGGGCCTCTTGAACGATGAT
*
555791 AGGGGCCTCTTGAAGGATGAT
1 AGGGGCCTCTTGAACGATGAT
* * *
555812 AGGGGCTTTTTGAATGATGAT
1 AGGGGCCTCTTGAACGATGAT
555833 AGGGGCCTCTTGAACGATGA
1 AGGGGCCTCTTGAACGATGA
555853 CAGGTGCTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
20 17 0.25
21 52 0.75
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAT
Found at i:556283 original size:21 final size:21
Alignment explanation
Indices: 556259--556308 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
556249 ACCATTGTCT
* *
556259 TCACGTAAAGTATCGACCTCC
1 TCACGTAAAGCATCGACCTCA
* *
556280 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCATCGACCTCA
556301 TCACGTAA
1 TCACGTAA
556309 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCATCGACCTCA
Found at i:557895 original size:19 final size:19
Alignment explanation
Indices: 557853--557953 Score: 148
Period size: 19 Copynumber: 5.3 Consensus size: 19
557843 TCTGAAACTT
*
557853 AAAATCACAACGCGAAAATG
1 AAAATCGCAACGCG-AAATG
* *
557873 AAAATCGCAACGCTAAATA
1 AAAATCGCAACGCGAAATG
557892 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
557911 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
557930 AAAATCACAACGCGAAATG
1 AAAATCGCAACGCGAAATG
557949 AAAAT
1 AAAAT
557954 TTCGTGTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 61 0.84
20 12 0.16
ACGTcount: A:0.52, C:0.19, G:0.16, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:558497 original size:20 final size:20
Alignment explanation
Indices: 558472--558520 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
558462 TAAACGTGCT
558472 TTGCGAATTTCACTTCTGTG
1 TTGCGAATTTCACTTCTGTG
* *
558492 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTCACTTCTGTG
*
558512 TTACGAATT
1 TTGCGAATT
558521 ACAAATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTCACTTCTGTG
Found at i:561462 original size:17 final size:18
Alignment explanation
Indices: 561429--561463 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
561419 AAATTTCATG
*
561429 TATAATGATATATAATAT
1 TATAATGATAAATAATAT
561447 TATAATG-TAAATAATAT
1 TATAATGATAAATAATAT
561464 ACAACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAATGATAAATAATAT
Found at i:563212 original size:2 final size:2
Alignment explanation
Indices: 563205--563233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
563195 TACCCTAGGT
563205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563234 GTGGTCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:563328 original size:3 final size:3
Alignment explanation
Indices: 563320--563392 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
563310 GGCATTTCTT
563320 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
563367 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
563393 TATGTATTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:563618 original size:26 final size:29
Alignment explanation
Indices: 563571--563629 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 29
563561 AGCTTTAATT
*
563571 TTAAAAATACTTATAATCTTATTTTTAAC
1 TTAAAAATACTTATAATCTTATTCTTAAC
*
563600 TTAAAAA-A-TTAT-ATCTTATTCTTATC
1 TTAAAAATACTTATAATCTTATTCTTAAC
563626 TTAA
1 TTAA
563630 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 16 0.57
27 4 0.14
28 1 0.04
29 7 0.25
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAAAAATACTTATAATCTTATTCTTAAC
Found at i:563692 original size:30 final size:30
Alignment explanation
Indices: 563593--563708 Score: 121
Period size: 29 Copynumber: 3.9 Consensus size: 30
563583 ATAATCTTAT
*
563593 TTTTAACTTAAAAAATTATATCTTA-TTCTTA
1 TTTTAACTTAAAAAA-TATATTTTATTTC-TA
* * ** * *
563624 TCTTAATTTTTAAAATATATTTTGTTTTTA
1 TTTTAACTTAAAAAATATATTTTATTTCTA
*
563654 -TATAACTTAAAAAATATATTTTATTTCTA
1 TTTTAACTTAAAAAATATATTTTATTTCTA
563683 TTTTAACTT-AAAAATATATTTTATTT
1 TTTTAACTTAAAAAATATATTTTATTT
563709 TTATCCTAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
29 39 0.57
30 16 0.24
31 13 0.19
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTTAACTTAAAAAATATATTTTATTTCTA
Found at i:563808 original size:12 final size:12
Alignment explanation
Indices: 563791--563826 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
563781 TAATGTAAAT
563791 TCCTTTAACCTG
1 TCCTTTAACCTG
563803 TCCTTTAACCTG
1 TCCTTTAACCTG
563815 TCCTTTAACCTG
1 TCCTTTAACCTG
563827 ACCATGCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.08, T:0.42
Consensus pattern (12 bp):
TCCTTTAACCTG
Found at i:565727 original size:278 final size:277
Alignment explanation
Indices: 565231--565761 Score: 936
Period size: 278 Copynumber: 1.9 Consensus size: 277
565221 AATCATGATT
* *
565231 CAGGTGTGTATACCGTGCGTTCGGCCTATTGGTGGCTGCAAAAGCCAACCCATACAACGGATGCT
1 CAGGTGTGTATACCCTGAGTTCGGCCTATTGGTGGCTGCAAAAGCCAACCCATACAACGGATGCT
* *
565296 ACATCCAAATTATGGAGGAATATTGTTAAACTGAAAGTAGTACCTAAAACACGTATTTTCACGTG
66 ACATCCAAATTATGGAGGAATATTGTTAAACTGAAAGTACTACCTAAAACACATATTTTCACGTG
*
565361 GCGGTTGGCGCATAGAACTCTTCCGATGGGTAATTGGGTTCGAGAGGCCTTTGTAATGTAGAGCT
131 GCGGTTGGCGCATAGAACTCTTCCGATGGGTAATTGGGTTCGAGAGGCCTTCGTAATGTAGAGCT
* *
565426 TGAAACGATAATGCATGCGATGCGAGAATGTGGCTTTACACAGGAGGTTTCGCAACTATTGGTGT
196 TGAAACGATAATACACGCGATGCGAGAATGTGGCTTTACACAGGAGGTTTCGCAACTATTGGTGT
565491 GTATCAATAGCAAGATG
261 GTATCAATAGCAAGATG
* *
565508 CAGGTGTGTATACCCTGAGTTCGGCCTATTGGTGGCTGCAAAATCCAACCCATACAACGGATTCT
1 CAGGTGTGTATACCCTGAGTTCGGCCTATTGGTGGCTGCAAAAGCCAACCCATACAACGGATGCT
*
565573 ACATCCAAATTATGGAGGAATATTGTTAAAACTGAAAGTACTACCTAAAACACATATTTTCGCGT
66 ACATCCAAATTATGGAGGAATATTGTT-AAACTGAAAGTACTACCTAAAACACATATTTTCACGT
*
565638 GGCGGTTGGCGCATAGCACTCTTCCGATGGGTAATTGGGTTCGAGAGGCCTTCGTAATGTAGAGC
130 GGCGGTTGGCGCATAGAACTCTTCCGATGGGTAATTGGGTTCGAGAGGCCTTCGTAATGTAGAGC
* *
565703 TTGAAACGATAATACACGCGATGCGAGACTGTGGTTTTACACAGGAGGTTTCGCAACTA
195 TTGAAACGATAATACACGCGATGCGAGAATGTGGCTTTACACAGGAGGTTTCGCAACTA
565762 GCTGGTATTT
Statistics
Matches: 240, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
277 88 0.37
278 152 0.63
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (277 bp):
CAGGTGTGTATACCCTGAGTTCGGCCTATTGGTGGCTGCAAAAGCCAACCCATACAACGGATGCT
ACATCCAAATTATGGAGGAATATTGTTAAACTGAAAGTACTACCTAAAACACATATTTTCACGTG
GCGGTTGGCGCATAGAACTCTTCCGATGGGTAATTGGGTTCGAGAGGCCTTCGTAATGTAGAGCT
TGAAACGATAATACACGCGATGCGAGAATGTGGCTTTACACAGGAGGTTTCGCAACTATTGGTGT
GTATCAATAGCAAGATG
Found at i:568271 original size:41 final size:42
Alignment explanation
Indices: 568217--568319 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
568207 GTCATTAACT
* *
568217 TTAG-ACATATAGCGGCGTTTT-TTAATAAACGTCGC-AATAGA
1 TTAGTACAT-TAGCGGCGTTTTGATAACAAACGTCGCAAAT-GA
* * *
568258 TTAGTACTTTAGCGACGTTTTGATAACAAACGTCGTAAATGA
1 TTAGTACATTAGCGGCGTTTTGATAACAAACGTCGCAAATGA
* *
568300 TTCGTACATTAGTGGCGTTT
1 TTAGTACATTAGCGGCGTTT
568320 AGACAAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 15 0.30
42 32 0.64
43 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (42 bp):
TTAGTACATTAGCGGCGTTTTGATAACAAACGTCGCAAATGA
Found at i:568313 original size:148 final size:147
Alignment explanation
Indices: 568127--568416 Score: 409
Period size: 148 Copynumber: 2.0 Consensus size: 147
568117 TATAGCAGCA
* * * * * * * * *
568127 TTTTGGTATCAAACGCCGCAAATGATTCGGACTTTAGTGGTGTTTTGATAGAAAATGCCGCAATT
1 TTTTGATAACAAACGCCGCAAATGATTCGGACATTAGTGGCGTTTAGACAAAAAATGCCACAAAT
* * * *
568192 GTTTTTTATTTAAACGTCATTAACTTTAGACATATAGCGGCGTTTTTTAATAAACGTCGCAATAG
66 GTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGC-ATTTTTAATAAACGCCGCAATAA
568257 ATTAGTACTTTAGCGACG
130 ATTAGTACTTTAGCGACG
* * *
568275 TTTTGATAACAAACGTCGTAAATGATTCGTACATTAGTGGCGTTTAGACAAAAAATGCCACAAAT
1 TTTTGATAACAAACGCCGCAAATGATTCGGACATTAGTGGCGTTTAGACAAAAAATGCCACAAAT
* *
568340 GTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAATGCCGTAATAAA
66 GTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAACGCCGCAATAAA
568405 TTAGTACTTTAG
131 TTAGTACTTTAG
568417 GGGTGTTTTG
Statistics
Matches: 124, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
147 31 0.25
148 93 0.75
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (147 bp):
TTTTGATAACAAACGCCGCAAATGATTCGGACATTAGTGGCGTTTAGACAAAAAATGCCACAAAT
GTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAACGCCGCAATAAA
TTAGTACTTTAGCGACG
Found at i:568592 original size:187 final size:188
Alignment explanation
Indices: 568267--568662 Score: 521
Period size: 187 Copynumber: 2.1 Consensus size: 188
568257 ATTAGTACTT
* * * * *
568267 TAGCGACGTTTTGATAACAAACGTCGTAAATGATTCGTACATTAGTGGCGTTTAGACAAAAAATG
1 TAGCGGCGTTTTGGTAACAAACCTCGCAAATGATTCGTACATTAGTGGCATTTAGACAAAAAATG
* *
568332 CCACAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAATGCC
66 ACACAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAAAGCC
* ** * * *
568397 GTAATAAATTAGTACTTTAGGGGTGTTTTGACAAAAATACCGTAATAGGGTT-CACATA
131 GCAATAAATTAGTACTTTAGCAGCGTTTTGACAAAAACACCGCAATA-GGTTGCACATA
**
568455 TAGCGGCGTTTTGGTAACAAACACT-GCAAATGATTCGTACA-TAGTGGCATTTAGATGAAAAAT
1 TAGCGGCGTTTTGGTAACAAAC-CTCGCAAATGATTCGTACATTAGTGGCATTTAGACAAAAAAT
*** * *
568518 GATGTAAATGTTTTTTATTT-AACGTCATTAACTTTAGACATATATCGGCGTTTTTCAATAAAAG
65 GACACAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTT-AATAAAAG
* *
568582 CCGCAATAAATTAGTACTTTAGCAGCGTTTTGACAAAAACGCCGCAATAGGTTGCATATA
129 CCGCAATAAATTAGTACTTTAGCAGCGTTTTGACAAAAACACCGCAATAGGTTGCACATA
* *
568642 TAGCGGCGTTGTAGTAACAAA
1 TAGCGGCGTTTTGGTAACAAA
568663 TGCCATAAAT
Statistics
Matches: 181, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
186 37 0.20
187 108 0.60
188 35 0.19
189 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (188 bp):
TAGCGGCGTTTTGGTAACAAACCTCGCAAATGATTCGTACATTAGTGGCATTTAGACAAAAAATG
ACACAAATGTTTTTTATTTAAACGTCATTAACTTTAGACATATAACGGCATTTTTAATAAAAGCC
GCAATAAATTAGTACTTTAGCAGCGTTTTGACAAAAACACCGCAATAGGTTGCACATA
Found at i:575825 original size:130 final size:128
Alignment explanation
Indices: 575635--575875 Score: 464
Period size: 130 Copynumber: 1.9 Consensus size: 128
575625 ATGATCTCAG
575635 CCTTGAAGAGAAGCTGCAAACAGTCCCACCAGGAATGCTCAGGTACCAATGGGAAGATGCAGTCA
1 CCTTGAAGAGAAGCTGCAAACAGTCCCACCAGGAATGCTCAGGTACCAATGGGAAGATGCAGTCA
575700 GATTTTAGAGTTCATAAAAAAGACAAGTATGATGTATTTTTAAGAAATAATTATAACAAATTGTA
66 GATTTT--AGTTCATAAAAAAGACAAGTATGATGTATTTTTAAGAAATAATTATAACAAATTGTA
575765 CCTTGAAGAGAAGCTGCAAACAGTCCCACCAGGAATGCTCAGGTACCAATGGGAAGATGCAGTCA
1 CCTTGAAGAGAAGCTGCAAACAGTCCCACCAGGAATGCTCAGGTACCAATGGGAAGATGCAGTCA
575830 GATTTTAGTTCATAAAAAAGACAAGTATGATGTATTTTTAAGAAAT
66 GATTTTAGTTCATAAAAAAGACAAGTATGATGTATTTTTAAGAAAT
575876 CATCAGGACA
Statistics
Matches: 111, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
128 40 0.36
130 71 0.64
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (128 bp):
CCTTGAAGAGAAGCTGCAAACAGTCCCACCAGGAATGCTCAGGTACCAATGGGAAGATGCAGTCA
GATTTTAGTTCATAAAAAAGACAAGTATGATGTATTTTTAAGAAATAATTATAACAAATTGTA
Found at i:576976 original size:44 final size:41
Alignment explanation
Indices: 576924--577021 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 41
576914 GTTTGTAACA
* * *
576924 AAAAATGCCACAATATACCATACATTTAGCGGCTTTTTTATCC
1 AAAAATGCCACAATATA-CAGACATTTACCGGCGTTTTTA-CC
* * *
576967 TAAAAATGCCACTATATACAGACCTTTACCGGCGTTTTTAGC
1 -AAAAATGCCACAATATACAGACATTTACCGGCGTTTTTACC
577009 AAAAATGCCACAA
1 AAAAATGCCACAA
577022 AACATCAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 12 0.26
42 1 0.02
43 18 0.38
44 16 0.34
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (41 bp):
AAAAATGCCACAATATACAGACATTTACCGGCGTTTTTACC
Found at i:577043 original size:43 final size:42
Alignment explanation
Indices: 576996--577261 Score: 176
Period size: 43 Copynumber: 6.2 Consensus size: 42
576986 AGACCTTTAC
* *
576996 CGGCGTTTTTAGCAAAAATGCCACAAAACATCAATATCTACTA
1 CGGCGTTTTTAG-AAAAATGCCACAAAACATCAACACCTACTA
* * *
577039 CGGCGTTTGTGAGAAAAACGCCGCAAAACATCAACACCTACTA
1 CGGCGTTT-TTAGAAAAATGCCACAAAACATCAACACCTACTA
* * * * *
577082 CGACGTTTGTGGGAAAATGCCACAAAACATCAACACCTACTG
1 CGGCGTTTTTAGAAAAATGCCACAAAACATCAACACCTACTA
* * * * * * *
577124 CGGCG-TTTAAGAGAAAATCACCTCTAAACATCATA-ACATATTG
1 CGGCGTTTTTAGA-AAAAT-GCCACAAAACATCA-ACACCTACTA
* * ** * * * *
577167 TGGCGTTTGTCTAAAAATGCCGCTAAATATCAACACCTATTA
1 CGGCGTTTTTAGAAAAATGCCACAAAACATCAACACCTACTA
* * * * * *
577209 CAGCGTTTTTATGACAAATGCCGCTAAATATCAACACCTATTA
1 CGGCGTTTTTA-GAAAAATGCCACAAAACATCAACACCTACTA
*
577252 CGGTGTTTTT
1 CGGCGTTTTT
577262 TATGACAAAC
Statistics
Matches: 175, Mismatches: 41, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
41 4 0.02
42 60 0.34
43 104 0.59
44 7 0.04
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (42 bp):
CGGCGTTTTTAGAAAAATGCCACAAAACATCAACACCTACTA
Found at i:577121 original size:42 final size:43
Alignment explanation
Indices: 576996--577140 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
576986 AGACCTTTAC
* * *
576996 CGGCGTTT-TTAGCAAAAATGCCACAAAACATCAATATCTACTA
1 CGGCGTTTGTGAG-AAAAATGCCACAAAACATCAACACCTACTA
* *
577039 CGGCGTTTGTGAGAAAAACGCCGCAAAACATCAACACCTACTA
1 CGGCGTTTGTGAGAAAAATGCCACAAAACATCAACACCTACTA
* * *
577082 CGACGTTTGTG-GGAAAATGCCACAAAACATCAACACCTACTG
1 CGGCGTTTGTGAGAAAAATGCCACAAAACATCAACACCTACTA
**
577124 CGGCGTTTAAGAGAAAA
1 CGGCGTTTGTGAGAAAA
577141 TCACCTCTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 35 0.41
43 48 0.56
44 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (43 bp):
CGGCGTTTGTGAGAAAAATGCCACAAAACATCAACACCTACTA
Found at i:577141 original size:42 final size:42
Alignment explanation
Indices: 577010--577141 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 42
577000 GTTTTTAGCA
* *
577010 AAAATGCCACAAAACATCAATATCTACTACGGCGTTTGTGAG
1 AAAATGCCACAAAACATCAACACCTACTACGGCGTTTGTGAG
* * * *
577052 AAAAACGCCGCAAAACATCAACACCTACTACGACGTTTGTGGG
1 -AAAATGCCACAAAACATCAACACCTACTACGGCGTTTGTGAG
* **
577095 AAAATGCCACAAAACATCAACACCTACTGCGGCGTTTAAGAG
1 AAAATGCCACAAAACATCAACACCTACTACGGCGTTTGTGAG
577137 AAAAT
1 AAAAT
577142 CACCTCTAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
42 40 0.53
43 36 0.47
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (42 bp):
AAAATGCCACAAAACATCAACACCTACTACGGCGTTTGTGAG
Found at i:577174 original size:85 final size:85
Alignment explanation
Indices: 577009--577216 Score: 202
Period size: 85 Copynumber: 2.4 Consensus size: 85
576999 CGTTTTTAGC
* * ** *
577009 AAAAATGCCACAAAACATCAATATCTACTACGGCGTTTGTGAGAAAAACGCCGCAAAACATCAAC
1 AAAAATGCCACAAAACATCAACACCTACTACGGCGTTTAAGAGAAAAACACCGCAAAACATCAAC
* *
577074 ACCTACTACGACGTTTGTGG
66 ACATACTACGACGTTTGTCG
* * * * *
577094 GAAAATGCCACAAAACATCAACACCTACTGCGGCGTTTAAGAGAAAATCACCTCTAAACATCATA
1 AAAAATGCCACAAAACATCAACACCTACTACGGCGTTTAAGAGAAAAACACCGCAAAACATCA-A
* ** * *
577159 -ACATATTGTGGCGTTTGTCT
65 CACATACTACGACGTTTGTCG
* * * * *
577179 AAAAATGCCGCTAAATATCAACACCTATTACAGCGTTT
1 AAAAATGCCACAAAACATCAACACCTACTACGGCGTTT
577217 TTATGACAAA
Statistics
Matches: 98, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
85 97 0.99
86 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (85 bp):
AAAAATGCCACAAAACATCAACACCTACTACGGCGTTTAAGAGAAAAACACCGCAAAACATCAAC
ACATACTACGACGTTTGTCG
Found at i:577277 original size:44 final size:44
Alignment explanation
Indices: 577181--577349 Score: 207
Period size: 43 Copynumber: 3.9 Consensus size: 44
577171 GTTTGTCTAA
*
577181 AAATGCCGCTAAATATCAACACCTATTACAGCG-TTTTTATGAC
1 AAATGCCGCTAAATATCAACACCTATTACGGCGTTTTTTATGAC
*
577224 AAATGCCGCTAAATATCAACACCTATTACGGTGTTTTTTATGAC
1 AAATGCCGCTAAATATCAACACCTATTACGGCGTTTTTTATGAC
** * * * * * *
577268 AAACACCGCTAAATATAAACACCTATTGCGGTGTTTGTCA-CAC
1 AAATGCCGCTAAATATCAACACCTATTACGGCGTTTTTTATGAC
* * *
577311 AAATGCCGCTAAATATCAATACTTATTGCGGCGTTTTTT
1 AAATGCCGCTAAATATCAACACCTATTACGGCGTTTTTT
577350 GTTAAAAAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 64 0.59
44 44 0.41
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (44 bp):
AAATGCCGCTAAATATCAACACCTATTACGGCGTTTTTTATGAC
Found at i:577294 original size:87 final size:87
Alignment explanation
Indices: 577186--577349 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 87
577176 TCTAAAAATG
* * *
577186 CCGCTAAATATCAACACCTATTACAGCGTTT-TTATGACAAATGCCGCTAAATATCAACACCTAT
1 CCGCTAAATATAAACACCTATTACAGCGTTTGTCA-CACAAATGCCGCTAAATATCAACACCTAT
*
577250 TACGGTGTTTTTTATGACAAACA
65 TACGGCGTTTTTTATGACAAACA
* * * * *
577273 CCGCTAAATATAAACACCTATTGCGGTGTTTGTCACACAAATGCCGCTAAATATCAATACTTATT
1 CCGCTAAATATAAACACCTATTACAGCGTTTGTCACACAAATGCCGCTAAATATCAACACCTATT
*
577338 GCGGCGTTTTTT
66 ACGGCGTTTTTT
577350 GTTAAAAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
87 64 0.97
88 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (87 bp):
CCGCTAAATATAAACACCTATTACAGCGTTTGTCACACAAATGCCGCTAAATATCAACACCTATT
ACGGCGTTTTTTATGACAAACA
Found at i:579739 original size:22 final size:21
Alignment explanation
Indices: 579696--579774 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
579686 ATGATCATAC
579696 ATATAATATGTTTTCAAAATT
1 ATATAATATGTTTTCAAAATT
*
579717 ATATTATATGTTTTCAAAA--
1 ATATAATATGTTTTCAAAATT
*
579736 AT-T-ATATGCTTTCAAAAGTT
1 ATATAATATGTTTTCAAAA-TT
* * *
579756 ATATTATATATTTTAAAAA
1 ATATAATATGTTTTCAAAA
579775 ACTATATAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.27
18 1 0.02
19 2 0.04
20 2 0.04
21 19 0.40
22 11 0.23
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATAATATGTTTTCAAAATT
Found at i:579741 original size:17 final size:17
Alignment explanation
Indices: 579719--579759 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
579709 TCAAAATTAT
*
579719 ATTATATGTTTTCAAAA
1 ATTATATGCTTTCAAAA
579736 ATTATATGCTTTCAAAA
1 ATTATATGCTTTCAAAA
*
579753 GTTATAT
1 ATTATAT
579760 TATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (17 bp):
ATTATATGCTTTCAAAA
Found at i:579775 original size:39 final size:38
Alignment explanation
Indices: 579701--579781 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
579691 CATACATATA
* * * *
579701 ATATGTTTTCAAAATTATATTATATGTTTTCAAAAATT
1 ATATGCTTTCAAAATTATATTATATATTTTAAAAAACT
579739 ATATGCTTTCAAAAGTTATATTATATATTTTAAAAAACT
1 ATATGCTTTCAAAA-TTATATTATATATTTTAAAAAACT
579778 ATAT
1 ATAT
579782 AGTATATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
38 13 0.34
39 25 0.66
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (38 bp):
ATATGCTTTCAAAATTATATTATATATTTTAAAAAACT
Found at i:579793 original size:20 final size:20
Alignment explanation
Indices: 579757--579808 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
579747 TCAAAAGTTA
*
579757 TATTATA-TATTTTAAAAAAC
1 TATTATAGTATATT-AAAAAC
*
579777 TA-TATAGTATATTAAAAAT
1 TATTATAGTATATTAAAAAC
579796 TATTATAGTATAT
1 TATTATAGTATAT
579809 AATATAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TATTATAGTATATTAAAAAC
Found at i:585482 original size:16 final size:17
Alignment explanation
Indices: 585443--585482 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
585433 GACTTGACCC
585443 GTTGACTTCGACCAGAA
1 GTTGACTTCGACCAGAA
*
585460 -TTAACTTCGACCA-AA
1 GTTGACTTCGACCAGAA
585475 GTTGACTT
1 GTTGACTT
585483 TAACCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (17 bp):
GTTGACTTCGACCAGAA
Found at i:586347 original size:31 final size:31
Alignment explanation
Indices: 586309--586385 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
586299 TAAGGCGACC
* *
586309 CTTGGGTAGGCTCTGCGGCCCTG-GAATTTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAA-TTGT
** *
586340 CTTGGGTAAGATTCTGTGGCCCCGAGAATTGT
1 CTTGGGT-AGGCTCTGCGGCCCCGAGAATTGT
586372 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
586386 CATGCGCCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 12 0.32
32 22 0.59
33 3 0.08
ACGTcount: A:0.13, C:0.21, G:0.32, T:0.34
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAATTGT
Found at i:591535 original size:21 final size:21
Alignment explanation
Indices: 591511--591572 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
591501 ATGATAATAC
*
591511 ATATAATATGTTTTCAATATT
1 ATATAATATGTTTTCAAAATT
591532 ATATTATATAT-TTTTCAAAATT
1 ATA-TA-ATATGTTTTCAAAATT
*
591554 ATATAATATGATTTCAAAA
1 ATATAATATGTTTTCAAAA
591573 GCCATATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 15 0.42
23 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (21 bp):
ATATAATATGTTTTCAAAATT
Found at i:591683 original size:25 final size:25
Alignment explanation
Indices: 591649--591749 Score: 195
Period size: 25 Copynumber: 4.1 Consensus size: 25
591639 AGTGCATATA
591649 CTATTCATGTTAATTGTAATCAATT
1 CTATTCATGTTAATTGTAATCAATT
591674 CTATTCATGTTAATTGTAATCAATT
1 CTATTCATGTTAATTGTAATCAATT
591699 CTATTCATGTTAATTGTAATCAATT
1 CTATTCATGTTAATTGTAATCAATT
591724 CTATTCATGTTAATTGTAAT-AATT
1 CTATTCATGTTAATTGTAATCAATT
591748 CT
1 CT
591750 TAAGTTTGTA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
24 6 0.08
25 70 0.92
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (25 bp):
CTATTCATGTTAATTGTAATCAATT
Found at i:594033 original size:49 final size:50
Alignment explanation
Indices: 593974--594077 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
593964 TAATAAGTAG
593974 TACTCTACAGTC-GGGGACCATTCGTGTACTTTGCCCTAATAATAATAAC
1 TACTCTACAGTCGGGGGACCATTCGTGTACTTTGCCCTAATAATAATAAC
594023 TACTCTACAGTCGGGGGACCATTCGTGTACTTTGCCCTAATAATAATAAC
1 TACTCTACAGTCGGGGGACCATTCGTGTACTTTGCCCTAATAATAATAAC
594073 T-CTCT
1 TACTCT
594078 TGTTTTGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 16 0.30
50 38 0.70
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (50 bp):
TACTCTACAGTCGGGGGACCATTCGTGTACTTTGCCCTAATAATAATAAC
Found at i:601499 original size:13 final size:13
Alignment explanation
Indices: 601481--601507 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
601471 TATTCACCCA
601481 TAAAGAAAAATAT
1 TAAAGAAAAATAT
601494 TAAAGAAAAATAT
1 TAAAGAAAAATAT
601507 T
1 T
601508 GAAAATTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (13 bp):
TAAAGAAAAATAT
Found at i:601700 original size:21 final size:21
Alignment explanation
Indices: 601661--601709 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
601651 CAATTATGGG
* **
601661 TATTCAATGTTAATGTTTAAA
1 TATTGAATGTTAAAATTTAAA
*
601682 TATTGAATGTTAAAATTTAAG
1 TATTGAATGTTAAAATTTAAA
601703 T-TTGAAT
1 TATTGAAT
601710 ATTTATTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (21 bp):
TATTGAATGTTAAAATTTAAA
Found at i:602908 original size:31 final size:32
Alignment explanation
Indices: 602853--602917 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
602843 TATGTTCGTG
602853 TACATTATGAATGGCACCGTTGGTGCAAATGA
1 TACATTATGAATGGCACCGTTGGTGCAAATGA
*
602885 TACATTATGAATGGCA-CGTTGGTGGAAATGA
1 TACATTATGAATGGCACCGTTGGTGCAAATGA
602916 TA
1 TA
602918 AGATATCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (32 bp):
TACATTATGAATGGCACCGTTGGTGCAAATGA
Found at i:604986 original size:29 final size:29
Alignment explanation
Indices: 604940--605006 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
604930 AAAACAATAG
*
604940 AATTTAAGGGATTGAAATATAAATGTTGGA
1 AATTTAAAGGATTGAAATATAAA-GTTGGA
* *
604970 AATTTAAAGG-TTGAAATTTAAAGTTTGA
1 AATTTAAAGGATTGAAATATAAAGTTGGA
*
604998 AATTAAAAG
1 AATTTAAAG
605007 TACATAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 13 0.39
29 11 0.33
30 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.34
Consensus pattern (29 bp):
AATTTAAAGGATTGAAATATAAAGTTGGA
Found at i:604987 original size:14 final size:14
Alignment explanation
Indices: 604940--605006 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
604930 AAAACAATAG
*
604940 AATTTAAGGGATTGA
1 AATTTAAAGG-TTGA
* *
604955 AATATAAATGTTGGA
1 AATTTAAAGGTT-GA
604970 AATTTAAAGGTTGA
1 AATTTAAAGGTTGA
*
604984 AATTTAAAGTTTGA
1 AATTTAAAGGTTGA
*
604998 AATTAAAAG
1 AATTTAAAG
605007 TACATAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 25 0.57
15 19 0.43
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.34
Consensus pattern (14 bp):
AATTTAAAGGTTGA
Found at i:606509 original size:13 final size:13
Alignment explanation
Indices: 606484--606515 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
606474 GTCACATTCT
606484 AATAATTTAAAAA
1 AATAATTTAAAAA
606497 AATATATTTAAAAA
1 AATA-ATTTAAAAA
606511 AATAA
1 AATAA
606516 AATTAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATTTAAAAA
Found at i:606521 original size:14 final size:14
Alignment explanation
Indices: 606490--606523 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
606480 TTCTAATAAT
* *
606490 TTAAAAAAATATAT
1 TTAAAAAAATAAAA
606504 TTAAAAAAATAAAA
1 TTAAAAAAATAAAA
606518 TTAAAA
1 TTAAAA
606524 TCATATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAAAATAAAA
Found at i:607537 original size:18 final size:18
Alignment explanation
Indices: 607514--607549 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
607504 ATTTATAAGA
607514 GCTAACAATTGGTATCAG
1 GCTAACAATTGGTATCAG
607532 GCTAACAATTGGTATCAG
1 GCTAACAATTGGTATCAG
607550 AGCGGGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
GCTAACAATTGGTATCAG
Found at i:608680 original size:90 final size:88
Alignment explanation
Indices: 608566--608741 Score: 307
Period size: 89 Copynumber: 2.0 Consensus size: 88
608556 TCCTGAATAT
*
608566 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
*
608631 GGTAACTTGGATATAAGAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
608655 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
608720 GGTAACTTGGCTATAAAAGGAT
65 GGTAACTTGGATATAAAAGGAT
608742 GTGTTAGGTC
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 42 0.51
90 41 0.49
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:610553 original size:18 final size:18
Alignment explanation
Indices: 610530--610718 Score: 87
Period size: 20 Copynumber: 10.5 Consensus size: 18
610520 TAATTTTGAA
610530 ATATATATTTTAATATAT
1 ATATATATTTTAATATAT
*
610548 ATATATATATATTAAAATAT
1 ATATATAT-T-TTAATATAT
*
610568 ATATATA-TAT-ATATAT
1 ATATATATTTTAATATAT
** *
610584 ATATTATATTTTTTTGAAAT
1 ATA-TATATTTTAAT-ATAT
*
610604 CACATATAGTTTTGAA-ATAT
1 -ATATATA-TTTT-AATATAT
610624 ATATATA---T-ATATAT
1 ATATATATTTTAATATAT
*
610638 ATATATA-TAT-ATATAT
1 ATATATATTTTAATATAT
*
610654 AT-TATATTTTAAAATAT
1 ATATATATTTTAATATAT
* * *
610671 ATATGGTTTTATTGAAAATAT
1 ATAT-ATATT-TT-AATATAT
610692 ATTATATATTTTGAATA-AT
1 A-TATATATTTT-AATATAT
610711 ATAT-TATT
1 ATATATATT
610719 AATTATTTTT
Statistics
Matches: 134, Mismatches: 18, Indels: 39
0.70 0.09 0.20
Matches are distributed among these distances:
13 1 0.01
14 11 0.08
15 5 0.04
16 19 0.14
17 16 0.12
18 15 0.11
19 14 0.10
20 33 0.25
21 17 0.13
22 3 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (18 bp):
ATATATATTTTAATATAT
Found at i:610674 original size:2 final size:2
Alignment explanation
Indices: 610530--610660 Score: 96
Period size: 2 Copynumber: 67.0 Consensus size: 2
610520 TAATTTTGAA
* *
610530 AT AT AT AT -T TT A- AT AT AT AT AT AT AT AT AT -T A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
610568 AT AT AT AT AT AT AT AT AT AT -T AT AT TT TT TT GAA AT CAC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT
* *
610611 AGT -T TT GAA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610654 AT -T AT AT
1 AT AT AT AT
610661 TTTAAAATAT
Statistics
Matches: 107, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
1 7 0.07
2 98 0.92
3 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621977 original size:23 final size:23
Alignment explanation
Indices: 621947--621993 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
621937 ATAGCAAAGA
621947 TAGTGCGGTTGCATGGGGTTCTT
1 TAGTGCGGTTGCATGGGGTTCTT
621970 TAGTGCGGTTGCATGGGGTTCTT
1 TAGTGCGGTTGCATGGGGTTCTT
621993 T
1 T
621994 TGTCGATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.13, G:0.38, T:0.40
Consensus pattern (23 bp):
TAGTGCGGTTGCATGGGGTTCTT
Found at i:623334 original size:12 final size:13
Alignment explanation
Indices: 623300--623336 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
623290 TGACACAAAA
623300 TTTAGGTCAGTAG
1 TTTAGGTCAGTAG
623313 TTTCAGGTCAGTAG
1 TTT-AGGTCAGTAG
623327 -TTAGGTCAGT
1 TTTAGGTCAGT
623337 TTCTGAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 5 0.22
14 10 0.43
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (13 bp):
TTTAGGTCAGTAG
Found at i:623652 original size:15 final size:16
Alignment explanation
Indices: 623632--623675 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
623622 AATTAATCTC
623632 ATTTTCATTTTCT-TA
1 ATTTTCATTTTCTGTA
623647 ATTTTCATTTAT-TGTA
1 ATTTTCATTT-TCTGTA
*
623663 TTTTTCATTTTCT
1 ATTTTCATTTTCT
623676 CTCTTCTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTTCATTTTCTGTA
Found at i:626138 original size:21 final size:20
Alignment explanation
Indices: 626096--626174 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
626086 ACTGATTTGC
**
626096 AAAGGATCGATCCCCCGTAAA
1 AAAGGATCGAT-CCCTTTAAA
*
626117 AAAGGATCGATCCTTTTCAAA
1 AAAGGATCGATCCCTTT-AAA
*
626138 AAAGGATTGATCCCTTTACAA
1 AAAGGATCGATCCCTTTA-AA
*
626159 AAAGGATGGATCCCTT
1 AAAGGATCGATCCCTT
626175 CGTTGTTGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.08
21 46 0.92
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTAAA
Found at i:627097 original size:26 final size:26
Alignment explanation
Indices: 627063--627143 Score: 153
Period size: 26 Copynumber: 3.1 Consensus size: 26
627053 CACCTTTCGA
627063 TTTAGATCTACGCTAAGAGGGTTCAT
1 TTTAGATCTACGCTAAGAGGGTTCAT
627089 TTTAGATCTACGCTAAGAGGGTTCAT
1 TTTAGATCTACGCTAAGAGGGTTCAT
*
627115 TTTAGATCTACACTAAGAGGGTTCAT
1 TTTAGATCTACGCTAAGAGGGTTCAT
627141 TTT
1 TTT
627144 TTTTGGTGAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (26 bp):
TTTAGATCTACGCTAAGAGGGTTCAT
Found at i:631729 original size:20 final size:20
Alignment explanation
Indices: 631704--631750 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
631694 TAAGGTCTAA
631704 GAGCTAAAATGAATGAACAT
1 GAGCTAAAATGAATGAACAT
631724 GAGCTAAAATGAATGAACAT
1 GAGCTAAAATGAATGAACAT
631744 GAGCTAA
1 GAGCTAA
631751 TCAAATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (20 bp):
GAGCTAAAATGAATGAACAT
Found at i:640829 original size:2 final size:2
Alignment explanation
Indices: 640822--640849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
640812 CTTCAAATAC
640822 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
640850 TAAATAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:648175 original size:29 final size:29
Alignment explanation
Indices: 648143--648229 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 29
648133 AAATGTAATA
* *
648143 TTTTAAAATTATCATTTTTGTCCTTAAAC
1 TTTTAAAATTATCATTTTGGTCATTAAAC
*
648172 TTTTCCAAAATTTAT-ACTTTGGTCATTAAAC
1 TTTT--AAAA-TTATCATTTTGGTCATTAAAC
648203 TTTTAAAATT-TGCATTTTGGTCATTAA
1 TTTTAAAATTAT-CATTTTGGTCATTAA
648230 CCAAATCCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 21 0.43
31 21 0.43
32 4 0.08
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTTAAAATTATCATTTTGGTCATTAAAC
Found at i:664823 original size:7 final size:7
Alignment explanation
Indices: 664811--664840 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
664801 ATATTGATTG
664811 AGGTGAA
1 AGGTGAA
664818 AGGTGAA
1 AGGTGAA
664825 AGGTGAA
1 AGGTGAA
664832 AGGTGAA
1 AGGTGAA
664839 AG
1 AG
664841 AAGTGTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (7 bp):
AGGTGAA
Found at i:674956 original size:28 final size:28
Alignment explanation
Indices: 674919--674975 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
674909 TTCCACACAC
*
674919 AAAAAATTAAA-GTGTCAAGTTCAATAA
1 AAAAAATTAAATGTGTAAAGTTCAATAA
* *
674946 AAAAAATTTAAATTTTTAAAGTTCAATAA
1 AAAAAA-TTAAATGTGTAAAGTTCAATAA
674975 A
1 A
674976 CAAAGCTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.24
28 5 0.20
29 14 0.56
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAATTAAATGTGTAAAGTTCAATAA
Found at i:675013 original size:2 final size:2
Alignment explanation
Indices: 675006--675035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
674996 TGTAAAAATA
675006 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
675036 GAGACGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:681337 original size:82 final size:82
Alignment explanation
Indices: 681251--681553 Score: 275
Period size: 82 Copynumber: 3.8 Consensus size: 82
681241 ACAAATATCG
*
681251 CAATAGAAT-GGTAAATTAGCGGCGTTTATACCATAAACGCCATAATAGATTAACATATAGTGGC
1 CAATAGAATCGGTAAATTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTGGC
*
681315 GTTTTGGGTAAAACGCCA
66 GTTTT-GCTAAAACGCCA
* * ** **** * *
681333 CAATA-AATCGGTAAATTAGCGGCG-TT-TA--A-AAACGTCGCAATAGGGTGGTTTATTGCGGC
1 CAATAGAATCGGTAAATTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTGGC
* * *
681392 G-TTTGTTAACAAACGGCG
66 GTTTTGCT-A-AAACGCCA
* * *
681410 CAATAGAAT-GGTAAATTAGTGGCGTTTATACCATAAATGCCACAATAGATTAACATATAGTAGC
1 CAATAGAATCGGTAAATTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTGGC
*
681474 ATTTTAGCTAAAACGCCA
66 GTTTT-GCTAAAACGCCA
* * * **
681492 TAATAG-ATCGGCAAATTAGCGGCGTTTATACCACAAACGCCGTAATAGATTACACATATAGT
1 CAATAGAATCGGTAAATTAGCGGCGTTTATACCATAAACGCCACAATAGATTA-ACATATAGT
681554 TATTCTTAAA
Statistics
Matches: 170, Mismatches: 38, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
75 2 0.01
76 4 0.02
77 45 0.26
78 6 0.04
79 2 0.01
80 2 0.01
81 8 0.05
82 86 0.51
83 13 0.08
84 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (82 bp):
CAATAGAATCGGTAAATTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTGGC
GTTTTGCTAAAACGCCA
Found at i:681490 original size:159 final size:159
Alignment explanation
Indices: 681201--681519 Score: 485
Period size: 159 Copynumber: 2.0 Consensus size: 159
681191 CGTTTTTACA
* * * * * *
681201 AAAAATGTCGCAATAGTGTGGTTTATTGCGGTGTTTTTTAACAAATATCGCAATAGAATGGTAAA
1 AAAAACGTCGCAATAGGGTGGTTTATTGCGGCGTTTGTTAACAAACAGCGCAATAGAATGGTAAA
* * * * *
681266 TTAGCGGCGTTTATACCATAAACGCCATAATAGATTAACATATAGTGGCGTTTTGGGTAAAACGC
66 TTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTAGCATTTTAGCTAAAACGC
*
681331 CACAATAAATCGGTAAATTAGCGGCGTTT
131 CACAATAAATCGGCAAATTAGCGGCGTTT
*
681360 AAAAACGTCGCAATAGGGTGGTTTATTGCGGCGTTTGTTAACAAACGGCGCAATAGAATGGTAAA
1 AAAAACGTCGCAATAGGGTGGTTTATTGCGGCGTTTGTTAACAAACAGCGCAATAGAATGGTAAA
* *
681425 TTAGTGGCGTTTATACCATAAATGCCACAATAGATTAACATATAGTAGCATTTTAGCTAAAACGC
66 TTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTAGCATTTTAGCTAAAACGC
* *
681490 CATAATAGATCGGCAAATTAGCGGCGTTT
131 CACAATAAATCGGCAAATTAGCGGCGTTT
681519 A
1 A
681520 TACCACAAAC
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
159 143 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (159 bp):
AAAAACGTCGCAATAGGGTGGTTTATTGCGGCGTTTGTTAACAAACAGCGCAATAGAATGGTAAA
TTAGCGGCGTTTATACCATAAACGCCACAATAGATTAACATATAGTAGCATTTTAGCTAAAACGC
CACAATAAATCGGCAAATTAGCGGCGTTT
Found at i:684304 original size:2 final size:2
Alignment explanation
Indices: 684297--684327 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
684287 CAATCATTTA
684297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
684328 GGCTGATCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:684604 original size:9 final size:9
Alignment explanation
Indices: 684567--684609 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
684557 GAAAGAAAAG
684567 AAAATAAAT
1 AAAATAAAT
684576 AATAAT-AAT
1 AA-AATAAAT
684585 AATAATAAAAT
1 AA-AAT-AAAT
684596 AAAATAAAT
1 AAAATAAAT
684605 AAAAT
1 AAAAT
684610 TATACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 20 0.65
10 6 0.19
11 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATAAAT
Found at i:684711 original size:9 final size:9
Alignment explanation
Indices: 684680--684723 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
684670 AAATGTTAGT
684680 AAAAATAAA
1 AAAAATAAA
*
684689 ATAAAAGCAGAA
1 A-AAAA-TA-AA
684701 AAAAATAAA
1 AAAAATAAA
684710 AAAAATAAA
1 AAAAATAAA
684719 AAAAA
1 AAAAA
684724 GGTCTAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 17 0.57
10 5 0.17
11 5 0.17
12 3 0.10
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (9 bp):
AAAAATAAA
Found at i:686197 original size:3 final size:3
Alignment explanation
Indices: 686169--686217 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
686159 GGGCCTACAA
* *
686169 AAT AAT TAT AAT ATAT AA- ATT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
686213 -AT AAT
1 AAT AAT
686218 TTTTTTGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 30 0.79
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:686529 original size:94 final size:94
Alignment explanation
Indices: 686368--686554 Score: 302
Period size: 94 Copynumber: 2.0 Consensus size: 94
686358 GACGACATCG
* *
686368 CTCATACATGATGAAGAGTTATGGTCGTCTAAGGGATGAGTAATAACTCGGTTCCTATGTGATGA
1 CTCATACATGATGAAGAGTTATGGTCGTCTAAGGGAAGAGTAATAACTCGGTTCCTACGTGATGA
*
686433 GGACAATTGGTTATCTAAGGGTGACACGA
66 GGACAATTGGTTATCTAAGGGTAACACGA
* * * *
686462 CTCATACGTGATGAAGAGTTATGGTCGTCTAAGGGAAGGGTGATAACTCTGTTCCTACGTGATGA
1 CTCATACATGATGAAGAGTTATGGTCGTCTAAGGGAAGAGTAATAACTCGGTTCCTACGTGATGA
*
686527 GGACAGTTGGTTATCTAAGGGTAACACG
66 GGACAATTGGTTATCTAAGGGTAACACG
686555 GTTGCTGTGA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (94 bp):
CTCATACATGATGAAGAGTTATGGTCGTCTAAGGGAAGAGTAATAACTCGGTTCCTACGTGATGA
GGACAATTGGTTATCTAAGGGTAACACGA
Found at i:692047 original size:16 final size:16
Alignment explanation
Indices: 692028--692061 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
692018 AAAGCATAAT
*
692028 AAAATAAAATGAGAAA
1 AAAATAAAAGGAGAAA
*
692044 AAAATGAAAGGAGAAA
1 AAAATAAAAGGAGAAA
692060 AA
1 AA
692062 GAAAAAGTTA
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:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAATAAAAGGAGAAA
Found at i:692869 original size:2 final size:2
Alignment explanation
Indices: 692862--692892 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
692852 ACCGATCATT
692862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
692893 TTAGGTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:693148 original size:10 final size:10
Alignment explanation
Indices: 693135--693160 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
693125 AAAAGAAAAG
693135 AAAATAAATA
1 AAAATAAATA
693145 AAAATAAATA
1 AAAATAAATA
693155 AAAATA
1 AAAATA
693161 TACAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:693251 original size:20 final size:21
Alignment explanation
Indices: 693209--693257 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
693199 GAACTGAAAC
* *
693209 AAAAC-AAATAAAAGTTAGTA
1 AAAACAAAATAAAAGTAAGAA
693229 AAAACAAAATAAAAG-AAGAA
1 AAAACAAAATAAAAGTAAGAA
*
693249 AAAATAAAA
1 AAAACAAAA
693258 AAAGGTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.76, C:0.04, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAACAAAATAAAAGTAAGAA
Found at i:702156 original size:25 final size:27
Alignment explanation
Indices: 702128--702192 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
702118 ATAGAGAGAC
702128 TTAAAAATATTTTACTATTAACA-T-A-
1 TTAAAAATATTTTACTATTAA-ATTAAT
* *
702153 TTAAATATATTTTATTATTAAATTAAT
1 TTAAAAATATTTTACTATTAAATTAAT
702180 TTAAAAATATTTT
1 TTAAAAATATTTT
702193 TTATTTTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 20 0.59
26 1 0.03
27 12 0.35
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAAAAATATTTTACTATTAAATTAAT
Found at i:702230 original size:26 final size:24
Alignment explanation
Indices: 702177--702231 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
702167 TTATTAAATT
* *
702177 AATTT-AAAAATATTTTTTATTTT
1 AATTTAAAAAATATATTTTATTTG
*
702200 CATTTAAAAAATATATTTTATGTTAG
1 AATTTAAAAAATATATTTTAT-TT-G
702226 AATTTA
1 AATTTA
702232 TTTAAAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 2 0.08
26 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
AATTTAAAAAATATATTTTATTTG
Done.