Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004367.1 Hibiscus syriacus cultivar Beakdansim tig00009567_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: 97286
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:699 original size:2 final size:2
Alignment explanation
Indices: 692--725 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
682 CAATTTTGTA
*
692 AT AT AT AT AT AT AT AT AG 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
726 TAAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1587 original size:20 final size:20
Alignment explanation
Indices: 1562--1625 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1552 ACATTTCGCA
1562 TTGCGATAGTCCAAGTTGCG
1 TTGCGATAGTCCAAGTTGCG
* * *
1582 TTGCGATTTATTACAAATT--G
1 TTGCGA--TAGTCCAAGTTGCG
*
1602 TTCCGATAGTCCAAGTTGCG
1 TTGCGATAGTCCAAGTTGCG
1622 TTGC
1 TTGC
1626 ATTTGTTTCT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 8 0.25
20 16 0.50
22 8 0.25
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTGCG
Found at i:2463 original size:21 final size:19
Alignment explanation
Indices: 2431--2620 Score: 182
Period size: 21 Copynumber: 9.3 Consensus size: 19
2421 CGTTGCGATT
2431 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
2450 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
2473 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
2492 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
2515 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
2536 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
2555 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
2578 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
2597 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
2616 TTGGA
1 TTGGA
2621 AAATCGCATT
Statistics
Matches: 144, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
19 53 0.37
21 62 0.43
23 29 0.20
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:2528 original size:63 final size:63
Alignment explanation
Indices: 2459--2628 Score: 285
Period size: 63 Copynumber: 2.8 Consensus size: 63
2449 CTTGGAATAA
* *
2459 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
2522 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
2585 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGG-A-AAATCGCA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCA
2629 TTGCGATAGT
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
59 8 0.08
60 1 0.01
61 28 0.27
63 67 0.64
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:2653 original size:21 final size:21
Alignment explanation
Indices: 2624--2676 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2614 ATTTGGAAAA
* *
2624 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAATCGAAGT
*
2645 TCGCGTTGCGATAATCGATGT
1 TCGCGTTGCGATAATCGAAGT
2666 TCGCGTTGCGA
1 TCGCGTTGCGA
2677 ATCTAGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATCGAAGT
Found at i:13767 original size:2 final size:2
Alignment explanation
Indices: 13762--13829 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
13752 AGATTGTGTG
13762 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
13804 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
13830 GAATTGTTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14306 original size:22 final size:23
Alignment explanation
Indices: 14269--14320 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
14259 TGAATAATTT
14269 AATATT-TTTTATTTTAACTTAA
1 AATATTATTTTATTTTAACTTAA
*
14291 AATATTATTTTA-TTTAATTTAA
1 AATATTATTTTATTTTAACTTAA
*
14313 AAAATTAT
1 AATATTAT
14321 GCACTTCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTATTTTATTTTAACTTAA
Found at i:16312 original size:23 final size:21
Alignment explanation
Indices: 16257--16302 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
16247 ATCTAGAGAC
16257 GATCCCTTTCATCTTTCTAAT
1 GATCCCTTTCATCTTTCTAAT
*
16278 GATCCCTTTCATCTTTTTAAT
1 GATCCCTTTCATCTTTCTAAT
16299 GATC
1 GATC
16303 GCCCTCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.48
Consensus pattern (21 bp):
GATCCCTTTCATCTTTCTAAT
Found at i:18570 original size:30 final size:30
Alignment explanation
Indices: 18535--18622 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 30
18525 TAACCAACAT
**
18535 TTTTGTAACAATTA-AATAGTTCAATAACTA
1 TTTTGTAACTTTTACAA-AGTTCAATAACTA
* *
18565 TTTTGTAA-TTTTATAAAGTTCAATGACTA
1 TTTTGTAACTTTTACAAAGTTCAATAACTA
*
18594 TTTCGTAACTTTTACAAAAGTTCAATAAC
1 TTTTGTAACTTTTAC-AAAGTTCAATAAC
18623 CATTAATGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.45
30 15 0.31
31 12 0.24
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTTGTAACTTTTACAAAGTTCAATAACTA
Found at i:18588 original size:29 final size:31
Alignment explanation
Indices: 18552--18622 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 31
18542 ACAATTAAAT
* *
18552 AGTTCAATAACTATTTTGTAA-TTTTA-TAA
1 AGTTCAATAACTATTTCGTAACTTTTACAAA
*
18581 AGTTCAATGACTATTTCGTAACTTTTACAAA
1 AGTTCAATAACTATTTCGTAACTTTTACAAA
18612 AGTTCAATAAC
1 AGTTCAATAAC
18623 CATTAATGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
30 5 0.14
31 12 0.33
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (31 bp):
AGTTCAATAACTATTTCGTAACTTTTACAAA
Found at i:19223 original size:31 final size:29
Alignment explanation
Indices: 19146--19227 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
19136 TCGATAATAA
* *
19146 AATAATTATTTTATAGTATTTATATAAATTT
1 AATAA-TATTTTATAATTTTTA-ATAAATTT
* *
19177 ATTAATAATTTATAATCTTTTAATAAATTT
1 AATAATATTTTATAAT-TTTTAATAAATTT
19207 AATAAGTATTTTATAATTTTT
1 AATAA-TATTTTATAATTTTT
19228 TAAACTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 25 0.58
31 18 0.42
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (29 bp):
AATAATATTTTATAATTTTTAATAAATTT
Found at i:19224 original size:19 final size:18
Alignment explanation
Indices: 19178--19225 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
19168 TATAAATTTA
*
19178 TTAATAATTTATAATCTT
1 TTAATAATTTATAATATT
19196 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTT-ATAA-TATT
19217 TT-ATAATTT
1 TTAATAATTT
19226 TTTAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 10 0.38
20 6 0.23
21 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAATAATTTATAATATT
Found at i:19227 original size:9 final size:10
Alignment explanation
Indices: 19147--19229 Score: 55
Period size: 10 Copynumber: 8.1 Consensus size: 10
19137 CGATAATAAA
19147 ATAATTATTTT
1 ATAA-TATTTT
*
19158 ATAGTATTTAT
1 ATAATATTT-T
19169 ATAA-A-TTT
1 ATAATATTTT
*
19177 ATTAATAATTT
1 A-TAATATTTT
*
19188 ATAATCTTTT
1 ATAATATTTT
*
19198 AATAA-ATTTA
1 -ATAATATTTT
19208 ATAAGTATTTT
1 ATAA-TATTTT
*
19219 ATAATTTTTT
1 ATAATATTTT
19229 A
1 A
19230 AACTTTATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.04
9 9 0.16
10 23 0.40
11 23 0.40
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:19229 original size:31 final size:30
Alignment explanation
Indices: 19146--19230 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
19136 TCGATAATAA
* *
19146 AATAATTATTTTAT-AGTATTTATATAAATTT
1 AATAA-TATTTTATAATTTTTTA-ATAAATTT
* * *
19177 ATTAATAATTTATAATCTTTTAATAAATTT
1 AATAATATTTTATAATTTTTTAATAAATTT
19207 AATAAGTATTTTATAATTTTTTAA
1 AATAA-TATTTTATAATTTTTTAA
19231 ACTTTATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
30 19 0.43
31 25 0.57
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (30 bp):
AATAATATTTTATAATTTTTTAATAAATTT
Found at i:19872 original size:31 final size:28
Alignment explanation
Indices: 19824--19914 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 28
19814 TTCGTCAATA
19824 AAATTTA--AAAAACTATAAAATACTTATT
1 AAATTTATTAAAAA-TATAAAATA-TTATT
*
19852 AAATTTATTAAAAGATTATAAAATTATTAAT
1 AAATTTATTAAAA-A-TATAAAA-TATTATT
19883 AAATTTATCTAAATAATATAAAATAATTATT
1 AAATTTAT-TAAA-AATATAAAAT-ATTATT
19914 A
1 A
19915 TATTATCGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
28 7 0.13
30 5 0.09
31 33 0.62
32 7 0.13
33 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (28 bp):
AAATTTATTAAAAATATAAAATATTATT
Found at i:20513 original size:8 final size:8
Alignment explanation
Indices: 20500--20530 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
20490 AGACAATGGT
20500 GAGCTATA
1 GAGCTATA
20508 GAGCTATA
1 GAGCTATA
20516 GAGCTATA
1 GAGCTATA
20524 GAGCTAT
1 GAGCTAT
20531 GTGTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (8 bp):
GAGCTATA
Found at i:20770 original size:20 final size:21
Alignment explanation
Indices: 20731--20772 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
20721 CGAGACCTCT
*
20731 AAAGAGAGGCCTACACAGAAA
1 AAAGAGAGGCCTAAACAGAAA
20752 AAAGAGAGG-CTAAACAGAAA
1 AAAGAGAGGCCTAAACAGAAA
20772 A
1 A
20773 CAAAATAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (21 bp):
AAAGAGAGGCCTAAACAGAAA
Found at i:20842 original size:17 final size:15
Alignment explanation
Indices: 20799--20846 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
20789 GGGCTGTTTG
*
20799 TTAAAACTGAATGAT
1 TTAACACTGAATGAT
*
20814 TTAGCACTGAATGAT
1 TTAACACTGAATGAT
20829 TTAACAGTCTGAATGAT
1 TTAACA--CTGAATGAT
20846 T
1 T
20847 AAGAGGCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 18 0.64
17 10 0.36
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (15 bp):
TTAACACTGAATGAT
Found at i:21298 original size:18 final size:18
Alignment explanation
Indices: 21260--21336 Score: 109
Period size: 18 Copynumber: 4.1 Consensus size: 18
21250 GTTCTAATTC
21260 AAAGTATTTCTAATCATCAA
1 AAAGTATTTCTAATC--CAA
*
21280 AAAGTATTTCTACTCCAAA
1 AAAGTATTTCTAATCC-AA
21299 AAAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
*
21317 AGAGTATTTCTAATCCAA
1 AAAGTATTTCTAATCCAA
21335 AA
1 AA
21337 TACACATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
18 21 0.40
19 17 0.33
20 14 0.27
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (18 bp):
AAAGTATTTCTAATCCAA
Found at i:21302 original size:19 final size:19
Alignment explanation
Indices: 21260--21336 Score: 104
Period size: 19 Copynumber: 4.1 Consensus size: 19
21250 GTTCTAATTC
21260 AAAGTATTTCTAAT-CATCAA
1 AAAGTATTTCTAATCCA--AA
*
21280 AAAGTATTTCTACTCCAAA
1 AAAGTATTTCTAATCCAAA
21299 AAAGTATTTCTAATCC-AA
1 AAAGTATTTCTAATCCAAA
*
21317 AGAGTATTTCTAATCCAAA
1 AAAGTATTTCTAATCCAAA
21336 A
1 A
21337 TACACATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
18 17 0.33
19 20 0.38
20 13 0.25
21 2 0.04
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (19 bp):
AAAGTATTTCTAATCCAAA
Found at i:21334 original size:37 final size:38
Alignment explanation
Indices: 21260--21336 Score: 120
Period size: 37 Copynumber: 2.0 Consensus size: 38
21250 GTTCTAATTC
*
21260 AAAGTATTTCTAATCATCAAAAAGTATTTCTACTCCAAA
1 AAAGTATTTCTAATCA-CAAAAAGTATTTCTAATCCAAA
*
21299 AAAGTATTTCTAATC-CAAAGAGTATTTCTAATCCAAA
1 AAAGTATTTCTAATCACAAAAAGTATTTCTAATCCAAA
21336 A
1 A
21337 TACACATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 21 0.58
39 15 0.42
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (38 bp):
AAAGTATTTCTAATCACAAAAAGTATTTCTAATCCAAA
Found at i:22497 original size:17 final size:17
Alignment explanation
Indices: 22475--22525 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
22465 ATATATCCAT
22475 TGGTCTATTAATTTCTA
1 TGGTCTATTAATTTCTA
* *
22492 TGGTCTAATAACATATCTA
1 TGGTCT-ATTA-ATTTCTA
22511 -GG-CTATTAATTTCTA
1 TGGTCTATTAATTTCTA
22526 GTCTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 8 0.29
18 5 0.18
19 6 0.21
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (17 bp):
TGGTCTATTAATTTCTA
Found at i:24477 original size:9 final size:9
Alignment explanation
Indices: 24363--24471 Score: 71
Period size: 9 Copynumber: 11.8 Consensus size: 9
24353 TGTTAGATAA
24363 AAATGAAAAT
1 AAAT-AAAAT
*
24373 TAATAAAAT
1 AAATAAAAT
*
24382 AAAGAAAAT
1 AAATAAAAT
24391 AAATCAAAAT
1 AAAT-AAAAT
* *
24401 AAA-ACAAC
1 AAATAAAAT
*
24409 AAATGAAAT
1 AAATAAAAT
*
24418 AAAGCAAAGA-
1 AAA-TAAA-AT
24428 AAATAAAA-
1 AAATAAAAT
*
24436 AGATAAAAAGT
1 AAAT-AAAA-T
*
24447 GAATAAAAT
1 AAATAAAAT
24456 AAATAAAAT
1 AAATAAAAT
24465 AAATAAA
1 AAATAAA
24472 GAAAATGAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
8 10 0.13
9 43 0.57
10 20 0.26
11 3 0.04
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:24534 original size:14 final size:13
Alignment explanation
Indices: 24517--24606 Score: 66
Period size: 14 Copynumber: 6.8 Consensus size: 13
24507 TAAGATATAA
24517 ATAATATTATAAAC
1 ATAATA-TATAAAC
24531 ATAATAATATAATA-
1 ATAAT-ATATAA-AC
24545 ATAATA-ATAAAC
1 ATAATATATAAAC
*
24557 ATAATA-ATAGAAT
1 ATAATATATA-AAC
24570 ATAATA-ATAATA-
1 ATAATATATAA-AC
24582 ATAATATAATAATA-
1 ATAATAT-ATAA-AC
24596 ATAATATATAA
1 ATAATATATAA
24607 TAATAGAGGT
Statistics
Matches: 68, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
11 1 0.01
12 20 0.29
13 17 0.25
14 28 0.41
15 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (13 bp):
ATAATATATAAAC
Found at i:24537 original size:3 final size:3
Alignment explanation
Indices: 24531--24611 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
24521 TATTATAAAC
*
24531 ATA ATA AT- ATA ATA ATA ATA ATA A-A CATA ATA AT- AGA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
24573 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
24612 GAGGTAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
2 8 0.12
3 57 0.83
4 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24538 original size:17 final size:17
Alignment explanation
Indices: 24516--24611 Score: 121
Period size: 17 Copynumber: 5.9 Consensus size: 17
24506 ATAAGATATA
*
24516 AATAATATTATAA-ACAT
1 AATAATATAATAATA-AT
24533 AATAATATAATAATAAT
1 AATAATATAATAATAAT
*
24550 AATAA-A-CATAATAAT
1 AATAATATAATAATAAT
*
24565 -AGAATATAATAATAAT
1 AATAATATAATAATAAT
24581 AATAATATAATAATAAT
1 AATAATATAATAATAAT
24598 AAT-ATATAATAATA
1 AATAATATAATAATA
24612 GAGGTAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
14 3 0.04
15 9 0.13
16 20 0.29
17 37 0.53
18 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:24540 original size:26 final size:26
Alignment explanation
Indices: 24511--24609 Score: 96
Period size: 26 Copynumber: 3.7 Consensus size: 26
24501 AAAAAATAAG
*
24511 ATATAAATAATATTATAAACATAATA
1 ATATAAATAATATAATAAACATAATA
24537 ATAT-AATAATAATAATAAACATAATA
1 ATATAAATAAT-ATAATAAACATAATA
* *
24563 ATAGAATATAATAATAATAATAATATAATA
1 ATATAA-ATAAT-ATAAT-A-AACATAATA
24593 ATA-ATAAT-ATATAATAA
1 ATATA-AATAATATAATAA
24610 TAGAGGTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
25 7 0.11
26 22 0.34
27 6 0.09
28 13 0.20
29 4 0.06
30 12 0.19
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (26 bp):
ATATAAATAATATAATAAACATAATA
Found at i:24571 original size:31 final size:31
Alignment explanation
Indices: 24531--24611 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
24521 TATTATAAAC
*
24531 ATAATAATATAATAATAATAATAAACATAATA
1 ATAAGAATATAATAATAATAAT-AACATAATA
*
24563 AT-AGAATATAATAATAATAATAATATAATA
1 ATAAGAATATAATAATAATAATAACATAATA
*
24593 ATAATAATAT-ATAATAATA
1 ATAAGAATATAATAATAATA
24612 GAGGTAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 19 0.42
31 24 0.53
32 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (31 bp):
ATAAGAATATAATAATAATAATAACATAATA
Found at i:24753 original size:22 final size:22
Alignment explanation
Indices: 24670--24755 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 22
24660 AGAAAAAACA
*
24670 AACAAAAAATAAAT-AATAAAT
1 AACAAAAAATAAATAAATGAAT
*
24691 -AGAAAAAATAAGA-ATAAT-AAT
1 AACAAAAAATAA-ATA-AATGAAT
*
24712 AACAAAAAA-AAACAAA-GAAT
1 AACAAAAAATAAATAAATGAAT
*
24732 AATAAAAAATAAATAAATGAAT
1 AACAAAAAATAAATAAATGAAT
24754 AA
1 AA
24756 AAATATGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
20 24 0.45
21 13 0.25
22 16 0.30
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (22 bp):
AACAAAAAATAAATAAATGAAT
Found at i:27710 original size:6 final size:6
Alignment explanation
Indices: 27699--27750 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
27689 CCCACCATAT
*
27699 TTTTTC TTTTTC TTTTTC TTTTTTCTC TTTTTT TTTGTTC ATTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC --TTTT-TC TTTTTC TTT-TTC -TTTTTC TTTTT
27751 TCAATTTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 21 0.54
7 9 0.23
8 7 0.18
9 2 0.05
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:27715 original size:7 final size:7
Alignment explanation
Indices: 27698--27752 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
27688 ACCCACCATA
27698 TTTTTTC
1 TTTTTTC
27705 -TTTTTC
1 TTTTTTC
27711 -TTTTTC
1 TTTTTTC
27717 TTTTTTC
1 TTTTTTC
27724 TCTTTTT-
1 T-TTTTTC
27731 TTTTGTTC
1 TTTT-TTC
*
27739 ATTTTTC
1 TTTTTTC
27746 TTTTTTC
1 TTTTTTC
27753 AATTTAGGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 15 0.36
7 19 0.45
8 8 0.19
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:41134 original size:41 final size:41
Alignment explanation
Indices: 41089--41171 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
41079 GAATTCTCGA
41089 ATAAGGATAGATACAAGATAGAGGCTTGCCTGGGATAGGGG
1 ATAAGGATAGATACAAGATAGAGGCTTGCCTGGGATAGGGG
*
41130 ATAAGGATAGATACAAGATAGAGGCTTGCTTGGGATAGGGG
1 ATAAGGATAGATACAAGATAGAGGCTTGCCTGGGATAGGGG
41171 A
1 A
41172 CATCAGAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.08, G:0.36, T:0.20
Consensus pattern (41 bp):
ATAAGGATAGATACAAGATAGAGGCTTGCCTGGGATAGGGG
Found at i:49348 original size:14 final size:14
Alignment explanation
Indices: 49329--49436 Score: 72
Period size: 14 Copynumber: 8.2 Consensus size: 14
49319 AATGGAAATT
49329 AATAAAATAAAGAA
1 AATAAAATAAAGAA
49343 AAT-AAATCAAAGAA
1 AATAAAAT-AAAGAA
* *
49357 AATAAAA-CAA-CA
1 AATAAAATAAAGAA
* *
49369 AATTAAATAAAGCA
1 AATAAAATAAAGAA
*
49383 AAGAAAATAAA-AA
1 AATAAAATAAAGAA
**
49396 AGATAAAA-AAAGTG
1 A-ATAAAATAAAGAA
49410 AATAAAAT----AA
1 AATAAAATAAAGAA
49420 AATAAAATAAAGAA
1 AATAAAATAAAGAA
49434 AAT
1 AAT
49437 GGAAAAAGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
10 8 0.11
12 7 0.10
13 19 0.27
14 34 0.48
15 3 0.04
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AATAAAATAAAGAA
Found at i:49611 original size:23 final size:23
Alignment explanation
Indices: 49574--49686 Score: 70
Period size: 21 Copynumber: 5.2 Consensus size: 23
49564 CATCAGGTGA
49574 AGAAAAAAAT-A-AATAATAAAT
1 AGAAAAAAATAAGAATAATAAAT
49595 AGAAAAAAATAAGAATAAT-AAT
1 AGAAAAAAATAAGAATAATAAAT
**
49617 A-ACAAACCA-AA-AATAA-AAAT
1 AGA-AAAAAATAAGAATAATAAAT
49637 AGTAAAAAAA-A-GAATAATAAA-
1 AG-AAAAAAATAAGAATAATAAAT
*
49658 A-AATAAAATAAACGAATAA-AAAT
1 AGAAAAAAAT-AA-GAATAATAAAT
49681 ATGAAA
1 A-GAAA
49687 TATATATATA
Statistics
Matches: 71, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
19 6 0.08
20 9 0.13
21 25 0.35
22 16 0.23
23 13 0.18
25 2 0.03
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (23 bp):
AGAAAAAAATAAGAATAATAAAT
Found at i:49652 original size:15 final size:14
Alignment explanation
Indices: 49625--49668 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
49615 ATAACAAACC
*
49625 AAAAATAAAAATAGT
1 AAAAA-AAAAATAAT
49640 AAAAAAAAGAATAAT
1 AAAAAAAA-AATAAT
49655 AAAAAATAAAATAA
1 AAAAAA-AAAATAA
49669 ACGAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAAAAAAAATAAT
Found at i:53298 original size:414 final size:413
Alignment explanation
Indices: 52517--53353 Score: 1191
Period size: 414 Copynumber: 2.0 Consensus size: 413
52507 TTGTTTTAAT
* *
52517 TATAGTGACAAAATATATTGTCACAAAGATTTTCTTCCATATTATTTTTGCGCCAAAAAAATTCA
1 TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCATATTATTTTTGCGCCAAAAAAATTCA
*
52582 TATATTAACAAATTTTGTAACTATAAGGGTTAATAATTATTACAAAAAAATTGCCACAAAAAATA
66 TATAATAACAAATTTTGTAACTATAAGGGTTAATAATTATTACAAAAAAATTGCCACAAAAAATA
* * *
52647 ATGATATTCACATTTTTATGACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGATAGCAT
131 ATGATATTCACATTTTTATGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATAACAT
* *
52712 ATATTGTCATAACTATTTTTTTCCACTTTTTTGTTTCAAAAGTTATATTGACAATTTTTATAATT
196 ATATTG--ATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGACAAGTTTTATAATT
* *
52777 ATAATTTATAGTTATTATTATATAAAAATTATCACATCAAATAATAAAATTTAAGTTTTTTATAA
259 ATAATTTATAGTTATTAGTATATAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTATAA
* * * *
52842 TTAATTATTTTTGTACTTATATATTTTAATTATTATAAAAATTTATACTATCAGAACCATTTCTC
324 TCAATTATTTTTGTACTTACATATTTTAATCATTATAAAAA-TTATACTATCAGAAACATTTCTC
*
52907 CCTA-TTTTTAGTGTCAAAAATGTTA
388 CCTATTTTTTAGTGCCAAAAATGTTA
* * * *
52932 TATAGTAACAAAATATATTGTCATAAAGATTTTCCTCCATATTTTTTTTGTGTCAAAAAAA-TCA
1 TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCATATTATTTTTGCGCCAAAAAAATTCA
* * * *
52996 TATAATAACAATTTTTGTAACTATAAGTGTTTATAATTATTACAAAAAACATTGTCACAAAAAA-
66 TATAATAACAAATTTTGTAACTATAAGGGTTAATAATTATTACAAAAAA-ATTGCCACAAAAAAT
* * * *
53060 AATGGTATTCATATTTTTTTGACAAATTATACTTGTAATTATAAATTTTAATTATAGTGATAACA
130 AATGATATTCACATTTTTATGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATAACA
* * * *
53125 TATATTG-TGA-TATTTTTCTCCATTTTTTTGTTTCAAAAAGTTATATTGATAAGTTTTGTAATT
195 TATATTGATAACTATTTTTCTCCACTTTTTTGTTTC-AAAAGTTATATTGACAAGTTTTATAATT
* * * *
53188 ATAATTTATAGTTATTGGTATA-AACATATTATCACATCAGATAATAAAATTCAAGTTTTTTTTG
259 ATAATTTATAGTTATTAGTATATAA-AAATTATCACATCAAATAATAAAATTCAAG--TTTTTTA
* *
53252 TAATCAATTATTTTTGTAGTTACATATTTTAATCATTATGAAAAATTATACTATCAGAAATATTT
321 TAATCAATTATTTTTGTACTTACATATTTTAATCATTAT-AAAAATTATACTATCAGAAACATTT
* * *
53317 TTGCCTATTTTTTAGTGCCAAAAATGTTG
385 CTCCCTATTTTTTAGTGCCAAAAATGTTA
53346 TATAGTAA
1 TATAGTAA
53354 AAGTTTTATA
Statistics
Matches: 375, Mismatches: 40, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
410 24 0.06
411 74 0.20
413 64 0.17
414 145 0.39
415 68 0.18
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (413 bp):
TATAGTAACAAAATATATTGTCACAAAGATTTTCCTCCATATTATTTTTGCGCCAAAAAAATTCA
TATAATAACAAATTTTGTAACTATAAGGGTTAATAATTATTACAAAAAAATTGCCACAAAAAATA
ATGATATTCACATTTTTATGACAAATTATACTTGTAATTATAAATTTTAACTATAGTGATAACAT
ATATTGATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGACAAGTTTTATAATTAT
AATTTATAGTTATTAGTATATAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTATAATC
AATTATTTTTGTACTTACATATTTTAATCATTATAAAAATTATACTATCAGAAACATTTCTCCCT
ATTTTTTAGTGCCAAAAATGTTA
Found at i:60218 original size:12 final size:12
Alignment explanation
Indices: 60201--60225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60191 TCCAACACTC
60201 CCTCGGAAGCCA
1 CCTCGGAAGCCA
60213 CCTCGGAAGCCA
1 CCTCGGAAGCCA
60225 C
1 C
60226 ATTGGCGCAA
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:0.24, C:0.44, G:0.24, T:0.08
Consensus pattern (12 bp):
CCTCGGAAGCCA
Found at i:65678 original size:3 final size:3
Alignment explanation
Indices: 65665--65737 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
65655 CCATTCTAAA
*
65665 ATT ATT A-T ATT ATT ATT ATT ATT A-T ATTT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
* *
65709 ACT ATT ATT ACT ATTT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
65738 AATAAATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.07
3 52 0.87
4 4 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:66136 original size:19 final size:19
Alignment explanation
Indices: 66112--66164 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
66102 CGTCCCATTC
*
66112 TTCGGTGAGTCACCACAGG
1 TTCGGTGACTCACCACAGG
66131 TTCGGTGACTCACCACAGG
1 TTCGGTGACTCACCACAGG
66150 TTCGGTGACTCACCA
1 TTCGGTGACTCACCA
66165 AAACTCATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (19 bp):
TTCGGTGACTCACCACAGG
Found at i:66216 original size:16 final size:16
Alignment explanation
Indices: 66195--66225 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66185 TCCGAGAGCA
66195 TCCTCGATGGTGGCTT
1 TCCTCGATGGTGGCTT
66211 TCCTCGATGGTGGCT
1 TCCTCGATGGTGGCT
66226 ATAAAAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.32, T:0.35
Consensus pattern (16 bp):
TCCTCGATGGTGGCTT
Found at i:67178 original size:12 final size:13
Alignment explanation
Indices: 67142--67184 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
67132 TTCTTTAAAT
67142 TTCAATATGTTTAA
1 TTCAATAT-TTTAA
67156 TTCAATATTTTAA
1 TTCAATATTTTAA
* *
67169 TT-ATTATTTTAT
1 TTCAATATTTTAA
67181 TTCA
1 TTCA
67185 GTCATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 10 0.38
13 8 0.31
14 8 0.31
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (13 bp):
TTCAATATTTTAA
Found at i:68882 original size:36 final size:36
Alignment explanation
Indices: 68834--68902 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
68824 CTATGCACAC
* *
68834 AAAGATCATGTTATATTAATACCAAAAGTATTCCAT
1 AAAGATCATGTTAGATTAATACCAAAAGCATTCCAT
* *
68870 AAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 AAAGATCATGTTAGATTAATACCAAAAGCATTC
68903 TACGACAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (36 bp):
AAAGATCATGTTAGATTAATACCAAAAGCATTCCAT
Found at i:69417 original size:43 final size:44
Alignment explanation
Indices: 69356--69442 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
69346 TGGCTTTAGA
* *
69356 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* *
69399 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
69443 TGATGCACGG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:69528 original size:6 final size:7
Alignment explanation
Indices: 69517--69557 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
69507 TTTTCAAACA
69517 TGCA-TT
1 TGCATTT
69523 TGCATTT
1 TGCATTT
*
69530 TGTATCTT
1 TGCAT-TT
69538 TGCATTT
1 TGCATTT
69545 T-CATTT
1 TGCATTT
69551 TGCATTT
1 TGCATTT
69558 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 10 0.33
7 14 0.47
8 6 0.20
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:73694 original size:21 final size:22
Alignment explanation
Indices: 73661--73701 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
73651 GGTTAAAATA
73661 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
73683 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
73702 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:74183 original size:12 final size:12
Alignment explanation
Indices: 74168--74197 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
74158 AAAAGTATGC
74168 GAAAAATAGAGA
1 GAAAAATAGAGA
*
74180 GAAAACTAGAGA
1 GAAAAATAGAGA
74192 GAAAAA
1 GAAAAA
74198 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:74417 original size:75 final size:76
Alignment explanation
Indices: 74350--74513 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 76
74340 AAAAAATAAT
* *
74350 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
74414 AAAATATAAAA
66 AAAATATAAAA
*
74425 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
74489 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
74501 ATATTATCCTAAA
1 ATAATATCCTAAA
74514 TTTGAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 32 0.40
76 48 0.60
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:81938 original size:21 final size:22
Alignment explanation
Indices: 81905--81945 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
81895 GGTTAAAATA
81905 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
81927 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
81946 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:82631 original size:19 final size:19
Alignment explanation
Indices: 82575--82637 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
82565 CTATTTAAAC
**
82575 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
82595 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
82615 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
82634 TAAA
1 TAAA
82638 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:86174 original size:54 final size:53
Alignment explanation
Indices: 86110--86264 Score: 175
Period size: 54 Copynumber: 2.9 Consensus size: 53
86100 GAAATCTGTG
* * *
86110 CAGAAACCACATAAAAGAATGAATGTGTTGTCAAATGCTTTACGAACATCTGGC
1 CAGAAGCCACA-AAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCCGGC
* * * *
86164 CAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGGG
1 CAGAAGCCACAA-AAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCCGGC
* * * * *
86218 CAGAAGCCACGAGAAAGGATGAATGTATTGTCACATGTTTTAAGAAC
1 CAGAAGCCAC-AAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
86265 TAGTGATTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 82 0.98
55 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (53 bp):
CAGAAGCCACAAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCCGGC
Found at i:86653 original size:22 final size:22
Alignment explanation
Indices: 86625--86708 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 22
86615 TATCTACATC
86625 TACATTCTTTAAAGATGATAGA
1 TACATTCTTTAAAGATGATAGA
*
86647 TACATTCTTCAAAGATGATAGA
1 TACATTCTTTAAAGATGATAGA
*
86669 TTC--TCTTTTCAAAGATGATAGA
1 TACATTC-TTT-AAAGATGATAGA
* * *
86691 TTCTTTTTTTAAAGATGA
1 TACATTCTTTAAAGATGA
86709 AAGCCTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.04
21 2 0.04
22 46 0.85
23 3 0.06
24 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TACATTCTTTAAAGATGATAGA
Found at i:87516 original size:76 final size:76
Alignment explanation
Indices: 87388--87606 Score: 327
Period size: 76 Copynumber: 2.9 Consensus size: 76
87378 CTTCAGTGCA
* * *
87388 TGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACATACAGTGCAGGATGTTTTCAAAAAGCCTT
87453 CGGGAGCTTTT
66 CGGGAGCTTTT
*
87464 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACATACAGTGCAGGTTGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACATACAGTGCAGGATGTTTTCAAAAAGCCTT
87529 CGGGAGCTTTT
66 CGGGAGCTTTT
* * * * *
87540 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTA-AGTGCATGATGTTTTC-AAAA-CCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAG-ACATACAGTGCAGGATGTTTTCAAAAAGCCT
87602 TCGGG
65 TCGGG
87607 TCATCTGTAA
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
74 8 0.06
75 4 0.03
76 117 0.89
77 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACATACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:87591 original size:45 final size:45
Alignment explanation
Indices: 87540--87903 Score: 561
Period size: 45 Copynumber: 8.1 Consensus size: 45
87530 GGGAGCTTTT
* *
87540 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTAAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
87585 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
**
87630 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTAAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
87675 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
87720 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
87765 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** *
87810 TGATGTTTTCAAAATATTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * * *
87855 TGAT-TTTTTAAAGCC-TCAAGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCA
*
87899 AGATG
1 TGATG
87904 ATAAGATCTC
Statistics
Matches: 295, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
43 2 0.01
44 34 0.12
45 259 0.88
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:88218 original size:3 final size:3
Alignment explanation
Indices: 88210--88291 Score: 96
Period size: 3 Copynumber: 27.3 Consensus size: 3
88200 CCATTCTAAA
* * *
88210 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATA ATT ATT ACT -TT ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
88256 ATT AAT ATT ATT ATTT ATT AATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT -ATT ATT ATT ATT ATT A
88292 AATAAATATA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
2 3 0.04
3 58 0.87
4 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:88240 original size:23 final size:23
Alignment explanation
Indices: 88210--88291 Score: 105
Period size: 23 Copynumber: 3.6 Consensus size: 23
88200 CCATTCTAAA
88210 ATTATTATTATTATTATATTATT
1 ATTATTATTATTATTATATTATT
* *
88233 ATTATTATAATTATTACT-TTATA
1 ATTATTATTATTATTA-TATTATT
*
88256 ATTAATATTATTATT-TATTAATT
1 ATTATTATTATTATTATATT-ATT
88279 ATTATTATTATTA
1 ATTATTATTATTA
88292 AATAAATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 46 0.92
24 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTATTATTATTATTATATTATT
Found at i:88290 original size:20 final size:20
Alignment explanation
Indices: 88213--88290 Score: 95
Period size: 20 Copynumber: 3.8 Consensus size: 20
88203 TTCTAAAATT
88213 ATTATTATTATTATATTATTA
1 ATTATTATTATTAT-TTATTA
*
88234 TTATTATAATTATTACTTTA-TA
1 --ATTATTATTATTA-TTTATTA
*
88256 ATTAATATTATTATTTATTA
1 ATTATTATTATTATTTATTA
88276 ATTATTATTATTATT
1 ATTATTATTATTATT
88291 AAATAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
19 4 0.08
20 27 0.55
22 2 0.04
23 15 0.31
24 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTATTATTATTTATTA
Found at i:88305 original size:20 final size:20
Alignment explanation
Indices: 88262--88305 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
88252 TATAATTAAT
* * * *
88262 ATTATTATTTATTAATTATT
1 ATTATTATTAAATAAATATA
88282 ATTATTATTAAATAAATATA
1 ATTATTATTAAATAAATATA
88302 ATTA
1 ATTA
88306 CAAATATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTATTAAATAAATATA
Found at i:91695 original size:18 final size:18
Alignment explanation
Indices: 91637--91708 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 18
91627 AAAGACCTCC
91637 AACAATAAA-A-AAAAATT
1 AACAATAAATATAAAAA-T
* *
91654 AAAAATAAAGATAAAAAT
1 AACAATAAATATAAAAAT
*
91672 -ACAATATATATAAAAAT
1 AACAATAAATATAAAAAT
*
91689 AATAATAAATA-AATAAAT
1 AACAATAAATATAA-AAAT
91707 AA
1 AA
91709 ATAGTTGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 24 0.53
18 16 0.36
19 5 0.11
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (18 bp):
AACAATAAATATAAAAAT
Found at i:94275 original size:31 final size:33
Alignment explanation
Indices: 94222--94321 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 33
94212 ATACAGACAT
*
94222 ACATGCATACATATAGTTAGTCATTTACATA-C
1 ACATACATACATATAGTTAGTCATTTACATACC
94254 ACATACATACATAT-GTTAGTCATTTACATACGTC
1 ACATACATACATATAGTTAGTCATTTACATAC--C
*
94288 ATATATGCATACATATAGTTAGTCATTATACATA
1 ACATA--CATACATATAGTTAGTCATT-TACATA
94322 AGAGAAATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
31 16 0.27
32 13 0.22
34 5 0.08
36 9 0.15
37 10 0.17
38 6 0.10
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (33 bp):
ACATACATACATATAGTTAGTCATTTACATACC
Done.