Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002086.1 Hibiscus syriacus cultivar Beakdansim tig00004258_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: 473624
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:208185 original size:22 final size:21
Alignment explanation
Indices: 208156--208206 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
208146 AACGCATTTG
208156 ATTTTTTTTCTTTT-TTTTCAC
1 ATTTTTTTTCTTTTGTTTTC-C
*
208177 ACTTTTTTTTGTTTTGTTTTCC
1 A-TTTTTTTTCTTTTGTTTTCC
208199 ATTTTTTT
1 ATTTTTTT
208207 CATGTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (21 bp):
ATTTTTTTTCTTTTGTTTTCC
Found at i:212096 original size:18 final size:18
Alignment explanation
Indices: 212050--212103 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
212040 GATTTTGGTA
*
212050 AAAAGATATTAAA-ATAAT
1 AAAAGAAATTAAATA-AAT
**
212068 AAAAGCGATTAAATAAAT
1 AAAAGAAATTAAATAAAT
212086 AAAAGAAATTAAAGTAAA
1 AAAAGAAATTAAA-TAAA
212104 AATAAGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (18 bp):
AAAAGAAATTAAATAAAT
Found at i:214899 original size:2 final size:2
Alignment explanation
Indices: 214892--214919 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
214882 TGTGCGCCCA
214892 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
214920 TTGTTATTAA
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:219430 original size:13 final size:12
Alignment explanation
Indices: 219418--219571 Score: 54
Period size: 13 Copynumber: 12.5 Consensus size: 12
219408 GAGGTTTTAT
*
219418 ATTTTAATTTTA
1 ATTTTAATATTA
*
219430 TATTATAGATATTA
1 -ATTTTA-ATATTA
219444 ATTTTAATATTA
1 ATTTTAATATTA
219456 ATTTTTTAA-A-TA
1 A--TTTTAATATTA
* *
219468 AATTAAATATT-
1 ATTTTAATATTA
219479 ATTTT--T-TTA
1 ATTTTAATATTA
*
219488 ATATT-ATATTATA
1 ATTTTAATA-T-TA
*
219501 GATATTAATATTA
1 -ATTTTAATATTA
*
219514 ATTTTTAA-AATA
1 A-TTTTAATATTA
* *
219526 AATTAAATATTA
1 ATTTTAATATTA
219538 ATTTTTAATATTA
1 A-TTTTAATATTA
*
219551 TATTATAGATATTTA
1 -ATTTTA-ATA-TTA
219566 ATTTTA
1 ATTTTA
219572 TATCATATAA
Statistics
Matches: 106, Mismatches: 17, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
8 2 0.02
9 5 0.05
10 5 0.05
11 8 0.08
12 21 0.20
13 33 0.31
14 26 0.25
15 6 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:219477 original size:24 final size:24
Alignment explanation
Indices: 219449--219543 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
219439 TATTAATTTT
219449 AATATTAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
* *
219473 AATATTATTTTTTTAATATTATATTA
1 AATATTAATTTTTTAA-A-TAAATTA
219499 TAGATATTAATATTAATTTTTAAAATAAATTA
1 -A-ATATT-A-A-T--TTTTT-AAATAAATTA
219531 AATATTAATTTTT
1 AATATTAATTTTT
219544 AATATTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
24 15 0.26
25 5 0.09
26 6 0.11
27 2 0.04
28 6 0.11
29 2 0.04
30 5 0.09
31 2 0.04
32 6 0.11
33 6 0.11
34 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:219499 original size:64 final size:63
Alignment explanation
Indices: 219419--219571 Score: 219
Period size: 58 Copynumber: 2.5 Consensus size: 63
219409 AGGTTTTATA
* * *
219419 TTTTAATTTTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTATTT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAAATAAATTAAATATTA-AT
219483 TTTTAATATTATATTATAG--A-T-A--TTAATATTAATTTTTAAAATAAATTAAATATTAAT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAAATAAATTAAATATTAAT
219540 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
219572 TATCATATAA
Statistics
Matches: 79, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
57 20 0.25
58 32 0.41
59 1 0.01
60 1 0.01
61 2 0.03
62 2 0.03
64 21 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (63 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAAATAAATTAAATATTAAT
Found at i:220014 original size:21 final size:21
Alignment explanation
Indices: 219990--220051 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
219980 TGATTCATTG
219990 ATTAATAATAGTTTAATGATA
1 ATTAATAATAGTTTAATGATA
* *
220011 A-T--TAAT-G-TTGAT--TG
1 ATTAATAATAGTTTAATGATA
220025 ATTAATAATAGTTTAATGATA
1 ATTAATAATAGTTTAATGATA
220046 ATTAAT
1 ATTAAT
220052 GTTGTTGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
14 2 0.07
15 1 0.03
16 4 0.13
17 5 0.17
18 5 0.17
19 4 0.13
20 1 0.03
21 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTAATAATAGTTTAATGATA
Found at i:220016 original size:18 final size:18
Alignment explanation
Indices: 219995--220051 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
219985 CATTGATTAA
219995 TAATAGTTTAATGATAAT
1 TAATAGTTTAATGATAAT
* *
220013 TAAT-GTTGATTGATTAA-
1 TAATAGTTTAATGA-TAAT
220030 TAATAGTTTAATGATAAT
1 TAATAGTTTAATGATAAT
220048 TAAT
1 TAAT
220052 GTTGTTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TAATAGTTTAATGATAAT
Found at i:220026 original size:17 final size:17
Alignment explanation
Indices: 220004--220055 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
219994 ATAATAGTTT
220004 AATGATAATTAATGTTG
1 AATGATAATTAATGTTG
* *
220021 ATTGATTAA-TAATAGTTT
1 AATGA-TAATTAAT-GTTG
220039 AATGATAATTAATGTTG
1 AATGATAATTAATGTTG
220056 TTGTGCCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (17 bp):
AATGATAATTAATGTTG
Found at i:220026 original size:35 final size:35
Alignment explanation
Indices: 219986--220055 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
219976 TGTATGATTC
219986 ATTGATTAATAATAGTTTAATGATAATTAATGTTG
1 ATTGATTAATAATAGTTTAATGATAATTAATGTTG
220021 ATTGATTAATAATAGTTTAATGATAATTAATGTTG
1 ATTGATTAATAATAGTTTAATGATAATTAATGTTG
220056 TTGTGCCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (35 bp):
ATTGATTAATAATAGTTTAATGATAATTAATGTTG
Found at i:220297 original size:31 final size:31
Alignment explanation
Indices: 220261--220320 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
220251 TAGTTGTATG
*
220261 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGTAAAACTAA
220292 AATTATTTAAATCTCAGTATTGTAAAACT
1 AATTATTTAAATCTCAGTATTGTAAAACT
220321 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGTAAAACTAA
Found at i:255639 original size:21 final size:21
Alignment explanation
Indices: 255613--255678 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
255603 TCTCCGCAGA
*
255613 GTTACATTCCTAGCCCTCAAG
1 GTTACATTCCTAGCCCGCAAG
* *
255634 GTTACATTCCTAGCTCGCCAG
1 GTTACATTCCTAGCCCGCAAG
* * *
255655 GTTACATGCTTAGCCCGCAGG
1 GTTACATTCCTAGCCCGCAAG
255676 GTT
1 GTT
255679 TTATGACACC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (21 bp):
GTTACATTCCTAGCCCGCAAG
Found at i:256516 original size:63 final size:64
Alignment explanation
Indices: 256417--256545 Score: 224
Period size: 63 Copynumber: 2.0 Consensus size: 64
256407 TTCATGCTCC
* *
256417 CAACCAACTTATCATTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCA-AA
1 CAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATAA
*
256480 CAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCATAA
1 CAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATAA
256544 CA
1 CA
256546 TTTTATCCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 58 0.94
64 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (64 bp):
CAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATAA
Found at i:256533 original size:23 final size:23
Alignment explanation
Indices: 256438--256560 Score: 107
Period size: 23 Copynumber: 5.6 Consensus size: 23
256428 TCATTTCACA
*
256438 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
* *
256461 TTTATCCAATATATTCA-AACA-
1 TTTATCCAATTTATCCATAACAT
* * * *
256482 ---A-CCAACTGATCACTTCACA-
1 TTTATCCAATTTATC-CATAACAT
*
256501 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
*
256524 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATCCATAACAT
256547 TTTATCCAATTTAT
1 TTTATCCAATTTAT
256561 TCAAACTTCA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 3 0.04
22 10 0.13
23 56 0.73
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (23 bp):
TTTATCCAATTTATCCATAACAT
Found at i:256561 original size:23 final size:23
Alignment explanation
Indices: 256501--256563 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
256491 TCACTTCACA
* *
256501 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATTCATAACAT
256524 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
256547 TTTATCCAATTTATTCA
1 TTTATCCAATTTATTCA
256564 AACTTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:256955 original size:138 final size:138
Alignment explanation
Indices: 256707--257371 Score: 1008
Period size: 138 Copynumber: 4.8 Consensus size: 138
256697 CAAGTCCCCT
*
256707 TAGGTACTGACATGAATAGTTCTTCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
1 TAGGTACTGACATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
* * * * *
256772 ATCTGACAAAATAATGGAAGGCACACCCCCGGGAACGCGCATTCACCACTTTTCCAAGTCCCCTC
66 CTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTC
*
256837 ATAAATAA
131 AGAAATAA
*
256845 TAGGTACTGATATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
1 TAGGTACTGACATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
* * *
256910 CTCTGACAAAATAATGGAAGGCGCGTCCCTGGGAACGTGCTTTCACCACTTTGCCAAGTCCCCTC
66 CTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTC
256975 AGAAATAA
131 AGAAATAA
* **
256983 TAGGTACTGACATGAATAGTTCTTCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATT
1 TAGGTACTGACATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
** * *
257048 CTCTGACAAAATAATGGAAGGCGCGCCCCTAGGAACGTGCCTTT-ACCACTTTGCCAAGTCTCCT
66 CTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCG-CTTTCACCACTTTGCCAAGTCCCCT
257112 CAGAAATAA
130 CAGAAATAA
* * * *
257121 TAGGTATTGATATGAATAGATCTCCGAGGGGACATAAGTGACATAATAGGGCAATGATAACATAT
1 TAGGTACTGACATGAATAGTTCTCCG-GGGGACATGAGTGACATAATAGGGCAATGATAACATAT
*
257186 TATCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCT
65 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCT
* *
257251 AAAAAATAA
130 CAGAAATAA
* * *
257260 TAGGTACTGACATAAATAGTTCTCCAGGGGACATGAGTGTCATAATAGGGCAATGATAACATATT
1 TAGGTACTGACATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
** * * *
257325 CTCTGACAAAATAATTAAAGGCGCACCCCCGAGAACGCGCCTTCACC
66 CTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACC
257372 TGAATAGTAC
Statistics
Matches: 479, Mismatches: 45, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
138 356 0.74
139 123 0.26
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (138 bp):
TAGGTACTGACATGAATAGTTCTCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATT
CTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTC
AGAAATAA
Found at i:257282 original size:277 final size:274
Alignment explanation
Indices: 256608--257371 Score: 1175
Period size: 277 Copynumber: 2.8 Consensus size: 274
256598 ATCCAATTTC
256608 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
*
256673 GGGAACGCTCTTTCACCACTTTGCCAAGTCCCC-----T--TAGGTACTGACATGAATAGTTCTT
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAATAATAGGTACTGACATGAATAGTTCTT
* * *
256731 CGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAATAATGGAAGGCAC
131 CAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
* * *
256796 ACCCCCGGGAACGCGCATTCACCACTTTTCCAAGTCCCCTCATAAATAATAGGTACTGATATGAA
196 ACCCCCAGGAACGCGCATTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGATATGAA
*
256861 TAGTTCTCCGGGGG
261 TAGATCTCCGGGGG
* *
256875 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGTCCCT
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
*
256940 GGGAACGTGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACATGAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCT-A-AAATAATAGGTACTGACATGAATAGTTC
*
257005 TTCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
129 TTCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
* * * * * * *
257070 GCGCCCCTAGGAACGTGCCTTTACCACTTTGCCAAGTCTCCTCAGAAATAATAGGTATTGATATG
194 GCACCCCCAGGAACGCGCATTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGATATG
257135 AATAGATCTCCGAGGGG
259 AATAGATCTCCG-GGGG
* *
257152 ACATAAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
*
257217 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAAAATAATAGGTACTGACATAAATAGTTC
66 GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCT--AAAATAATAGGTACTGACATGAATAGTTC
* * **
257282 TCCAGGGGACATGAGTGTCATAATAGGGCAATGATAACATATTCTCTGACAAAATAATTAAAGGC
129 TTCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGC
*
257347 GCACCCCC-GAGAACGCGCCTTCACC
194 GCACCCCCAG-GAACGCGCATTCACC
257372 TGAATAGTAC
Statistics
Matches: 450, Mismatches: 35, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
267 94 0.21
274 1 0.00
276 150 0.33
277 204 0.45
278 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (274 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
GGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTAAAATAATAGGTACTGACATGAATAGTTCTT
CAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC
ACCCCCAGGAACGCGCATTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGATATGAA
TAGATCTCCGGGGG
Found at i:260554 original size:21 final size:21
Alignment explanation
Indices: 260528--260569 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
260518 AATAATTAAT
*
260528 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
260549 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
260570 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:268701 original size:2 final size:2
Alignment explanation
Indices: 268694--268719 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
268684 TTGCTTTTTA
268694 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
268720 TAGAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269836 original size:29 final size:29
Alignment explanation
Indices: 269794--269906 Score: 100
Period size: 29 Copynumber: 3.9 Consensus size: 29
269784 CCCGAGACTC
*
269794 AAATTCGAATCTTGTAAACAGTATTACTA
1 AAATTCGAATCTTGTAAACAATATTACTA
* *
269823 AAATTCGAATCTTGTAAATAATATTATTA
1 AAATTCGAATCTTGTAAACAATATTACTA
* * * * * *
269852 AAAATAGAATATTATAAATAATATTATTA
1 AAATTCGAATCTTGTAAACAATATTACTA
* * * * *
269881 AAAATAGAATATTATAAATAATATTA
1 AAATTCGAATCTTGTAAACAATATTA
269907 TTGTAAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.37
Consensus pattern (29 bp):
AAATTCGAATCTTGTAAACAATATTACTA
Found at i:269864 original size:17 final size:17
Alignment explanation
Indices: 269842--269895 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
269832 TCTTGTAAAT
269842 AATATTATTAAAAATAG
1 AATATTATTAAAAATAG
269859 AATATTA-T--AAAT--
1 AATATTATTAAAAATAG
269871 AATATTATTAAAAATAG
1 AATATTATTAAAAATAG
269888 AATATTAT
1 AATATTAT
269896 AAATAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.22
13 1 0.03
14 4 0.12
15 4 0.12
16 1 0.03
17 15 0.47
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
AATATTATTAAAAATAG
Found at i:269870 original size:14 final size:14
Alignment explanation
Indices: 269847--269900 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
269837 TAAATAATAT
269847 TATTAAAAATAGAA
1 TATTAAAAATAGAA
*
269861 TATTATAAATA-ATA
1 TATTAAAAATAGA-A
269875 TTATTAAAAATAGAA
1 -TATTAAAAATAGAA
*
269890 TATTATAAATA
1 TATTAAAAATA
269901 ATATTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.03
14 21 0.62
15 11 0.32
16 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
TATTAAAAATAGAA
Found at i:269874 original size:12 final size:12
Alignment explanation
Indices: 269859--269907 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 12
269849 TTAAAAATAG
269859 AATATTATAAAT
1 AATATTATAAAT
269871 AATATTATTAAAAAT
1 AATATTA-T--AAAT
269886 AGAATATTATAAAT
1 --AATATTATAAAT
269900 AATATTAT
1 AATATTAT
269908 TGTAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 15 0.47
13 1 0.03
14 4 0.12
15 4 0.12
16 1 0.03
17 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
AATATTATAAAT
Found at i:269903 original size:17 final size:16
Alignment explanation
Indices: 269842--269903 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
269832 TCTTGTAAAT
269842 AATATTATTAAAAATAG
1 AATATTA-TAAAAATAG
269859 AATATTAT--AAAT--
1 AATATTATAAAAATAG
269871 AATATTATTAAAAATAG
1 AATATTA-TAAAAATAG
269888 AATATTATAAATAATA
1 AATATTATAAA-AATA
269904 TTATTGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.18
13 1 0.03
14 4 0.10
15 4 0.10
16 5 0.13
17 18 0.46
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AATATTATAAAAATAG
Found at i:269922 original size:29 final size:29
Alignment explanation
Indices: 269837--269908 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
269827 TCGAATCTTG
269837 TAAATAATATTATTAAAAATAGAATATTA
1 TAAATAATATTATTAAAAATAGAATATTA
269866 TAAATAATATTATTAAAAATAGAATATTA
1 TAAATAATATTATTAAAAATAGAATATTA
269895 TAAATAATATTATT
1 TAAATAATATTATT
269909 GTAAATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAATAATATTATTAAAAATAGAATATTA
Found at i:276050 original size:18 final size:18
Alignment explanation
Indices: 276027--276085 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
276017 CATAAACCAC
276027 CATTATCAACATCAATAT
1 CATTATCAACATCAATAT
** **
276045 CATTATCATGATCTCTAT
1 CATTATCAACATCAATAT
* *
276063 CATTATCAATATCATTAT
1 CATTATCAACATCAATAT
276081 CATTA
1 CATTA
276086 ACTCATTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (18 bp):
CATTATCAACATCAATAT
Found at i:276083 original size:6 final size:6
Alignment explanation
Indices: 276027--276085 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
276017 CATAAACCAC
** * * *
276027 CATTAT CAACAT CAATAT CATTAT CATGAT C-TCTAT CATTAT CAATAT
1 CATTAT CATTAT CATTAT CATTAT CATTAT CAT-TAT CATTAT CATTAT
276075 CATTAT CATTA
1 CATTAT CATTA
276086 ACTCATTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (6 bp):
CATTAT
Found at i:276463 original size:31 final size:31
Alignment explanation
Indices: 276425--276573 Score: 185
Period size: 31 Copynumber: 4.8 Consensus size: 31
276415 TAATAATATG
*
276425 TCCATATGTCCCG-AAGAACATAGATAAACTA
1 TCCATATGTCCCGAAAG-ACATAGGTAAACTA
* *
276456 TCCATATGTCTCGAAAGACATAGGTAAACTT
1 TCCATATGTCCCGAAAGACATAGGTAAACTA
* *
276487 TCCATATATCCCG-AAGAATATAGGTAAACTA
1 TCCATATGTCCCGAAAG-ACATAGGTAAACTA
* * *
276518 TCCATATGTCCCAAAAGACATAGGTAATCTTG
1 TCCATATGTCCCGAAAGACATAGGTAAAC-TA
276550 TCCATATGTCCCGAAAGACATAGG
1 TCCATATGTCCCGAAAGACATAGG
276574 CAACCCTCAA
Statistics
Matches: 101, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
30 3 0.03
31 68 0.67
32 30 0.30
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (31 bp):
TCCATATGTCCCGAAAGACATAGGTAAACTA
Found at i:276522 original size:62 final size:63
Alignment explanation
Indices: 276423--276572 Score: 223
Period size: 62 Copynumber: 2.4 Consensus size: 63
276413 TATAATAATA
* *
276423 TGTCCATATGTCCCGAAGAACATAGATAAACTATCCATATGTCTCGAAAGACATAGGTAAACT
1 TGTCCATATGTCCCGAAGAACATAGATAAACTATCCATATGTCCCAAAAGACATAGGTAAACT
* * * *
276486 T-TCCATATATCCCGAAGAATATAGGTAAACTATCCATATGTCCCAAAAGACATAGGTAATCT
1 TGTCCATATGTCCCGAAGAACATAGATAAACTATCCATATGTCCCAAAAGACATAGGTAAACT
276548 TGTCCATATGTCCCGAA-AGACATAG
1 TGTCCATATGTCCCGAAGA-ACATAG
276573 GCAACCCTCA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
62 57 0.74
63 20 0.26
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (63 bp):
TGTCCATATGTCCCGAAGAACATAGATAAACTATCCATATGTCCCAAAAGACATAGGTAAACT
Found at i:277946 original size:7 final size:7
Alignment explanation
Indices: 277928--277966 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
277918 TCCCACGTAT
277928 GAAGAA-
1 GAAGAAG
277934 GAAGAAG
1 GAAGAAG
277941 GAAGAAG
1 GAAGAAG
277948 GAAGAAG
1 GAAGAAG
277955 GAAGAAG
1 GAAGAAG
277962 GAAGA
1 GAAGA
277967 GATTTCTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAAGAAG
Found at i:280155 original size:3 final size:3
Alignment explanation
Indices: 280137--280172 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
280127 AATTAATATT
*
280137 TAA TAT TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
280173 GTAAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:282656 original size:50 final size:50
Alignment explanation
Indices: 282573--282667 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
282563 AGAGGAGCAG
* ** * *
282573 GAAGGGTCAAACGGTCGGACAAACGTGATGAGTCAATTAGTTTAAAAGAA
1 GAAGAGTCAAACAATCGGACAAACGTGACGAGTCAACTAGTTTAAAAGAA
* *
282623 GAAGAGTCAAACAATCGGTCAAATGTGACGAGTCAACTAGTTTAA
1 GAAGAGTCAAACAATCGGACAAACGTGACGAGTCAACTAGTTTAA
282668 TGTACCACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (50 bp):
GAAGAGTCAAACAATCGGACAAACGTGACGAGTCAACTAGTTTAAAAGAA
Found at i:291995 original size:170 final size:170
Alignment explanation
Indices: 291699--292038 Score: 509
Period size: 170 Copynumber: 2.0 Consensus size: 170
291689 TGGCATTTTT
* * * *
291699 TGGGTGCCAAACTGCTGTTACTTTTCTCTTATTTATTACATATCCAAAAGGTTGTGATCAAAGTT
1 TGGGTGCCAAACTACCGTCACTTTTCCCTTATTTATTACATATCCAAAAGGTTGTGATCAAAGTT
* * * * * **
291764 TACTACTGAATAGATGACTTTAGAGGAGCAAAAGAATGAATCATTGAACTCGGTGACATCGGAGA
66 TAATACCGAATAGATGACTCTAGAGGAGCAAAAGAATGAATCATTAAACTCAGCAACATCGGAGA
* * *
291829 GAGAGGTGAATGTTTCCATTGTACACAATAACGTTAGTTC
131 GAGAGGTGAATGTCTCCATTGCACACAATAACATTAGTTC
* **
291869 TGGGTGCCAAACTACCGTCACTTTTCCCTTATTTATTGCATATCCTGAAGGTTGTGATCAAAGTT
1 TGGGTGCCAAACTACCGTCACTTTTCCCTTATTTATTACATATCCAAAAGGTTGTGATCAAAGTT
*
291934 TAATACCGAATAGATGACTCTAGAGGAGCAGAAGAATGAATCATTAAACTCAGCAACATCGGAGA
66 TAATACCGAATAGATGACTCTAGAGGAGCAAAAGAATGAATCATTAAACTCAGCAACATCGGAGA
*
291999 GAGAGGTGAATGTCTCCATTGCACACGATAACATTAGTTC
131 GAGAGGTGAATGTCTCCATTGCACACAATAACATTAGTTC
292039 AAATAGATCT
Statistics
Matches: 151, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
170 151 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (170 bp):
TGGGTGCCAAACTACCGTCACTTTTCCCTTATTTATTACATATCCAAAAGGTTGTGATCAAAGTT
TAATACCGAATAGATGACTCTAGAGGAGCAAAAGAATGAATCATTAAACTCAGCAACATCGGAGA
GAGAGGTGAATGTCTCCATTGCACACAATAACATTAGTTC
Found at i:296223 original size:32 final size:32
Alignment explanation
Indices: 296183--296275 Score: 186
Period size: 32 Copynumber: 2.9 Consensus size: 32
296173 CATAAGTAAC
296183 TGTCCATATGTCCCGAAAGACATAGGTAATCA
1 TGTCCATATGTCCCGAAAGACATAGGTAATCA
296215 TGTCCATATGTCCCGAAAGACATAGGTAATCA
1 TGTCCATATGTCCCGAAAGACATAGGTAATCA
296247 TGTCCATATGTCCCGAAAGACATAGGTAA
1 TGTCCATATGTCCCGAAAGACATAGGTAA
296276 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATCA
Found at i:296383 original size:20 final size:21
Alignment explanation
Indices: 296347--296385 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
296337 TCTTTCATAT
296347 CATTTAACTTATTCATATGCA
1 CATTTAACTTATTCATATGCA
*
296368 CATTTCACTT-TTCATATG
1 CATTTAACTTATTCATATG
296386 ATTTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (21 bp):
CATTTAACTTATTCATATGCA
Found at i:299369 original size:20 final size:20
Alignment explanation
Indices: 299341--299383 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
299331 TATATTGGGC
* *
299341 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
299361 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
299381 TAT
1 TAT
299384 GGAATGGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:303152 original size:21 final size:21
Alignment explanation
Indices: 303127--303170 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
303117 AATTTAAAAT
*
303127 GTGTATCGATGCACTGATACA
1 GTGTACCGATGCACTGATACA
*
303148 GTGTACCGATGCACTGTTACA
1 GTGTACCGATGCACTGATACA
303169 GT
1 GT
303171 AATTTCAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTACCGATGCACTGATACA
Found at i:303866 original size:32 final size:32
Alignment explanation
Indices: 303828--303952 Score: 196
Period size: 32 Copynumber: 3.9 Consensus size: 32
303818 TAAGTAATTA
*
303828 TCCATATATCCCGAAAGACATAGGTAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
* * *
303860 TTCATATGTCCCGAAAGACATAGGTAATCCTA
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
*
303892 TCCATTTGTCCCGAAAGACATAGGTAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
*
303924 TCCATATGTCCCAAAAGACATAGGTAATC
1 TCCATATGTCCCGAAAGACATAGGTAATC
303953 CTCAACTCTT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATCATG
Found at i:303904 original size:64 final size:64
Alignment explanation
Indices: 303826--303954 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
303816 TATAAGTAAT
* *
303826 TATCCATATATCCCGAAAGACATAGGTAATCATGTTCATATGTCCCGAAAGACATAGGTAATCC
1 TATCCATATATCCCGAAAGACATAGGTAATCATGTCCATATGTCCCAAAAGACATAGGTAATCC
* *
303890 TATCCATTTGTCCCGAAAGACATAGGTAATCATGTCCATATGTCCCAAAAGACATAGGTAATCC
1 TATCCATATATCCCGAAAGACATAGGTAATCATGTCCATATGTCCCAAAAGACATAGGTAATCC
303954 T
1 T
303955 CAACTCTTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (64 bp):
TATCCATATATCCCGAAAGACATAGGTAATCATGTCCATATGTCCCAAAAGACATAGGTAATCC
Found at i:304254 original size:15 final size:15
Alignment explanation
Indices: 304236--304283 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
304226 CACATAAACC
304236 TATATCTTCTTATCA
1 TATATCTTCTTATCA
*
304251 TATAGCTTCTTAT--
1 TATATCTTCTTATCA
*
304264 TATATCATTCATATCA
1 TATATC-TTCTTATCA
304280 TATA
1 TATA
304284 ACTTATTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 12 0.44
16 4 0.15
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATCTTCTTATCA
Found at i:304713 original size:20 final size:20
Alignment explanation
Indices: 304688--304731 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
304678 TGCATCGATA
*
304688 CACCCCTTAATGTATCAATG
1 CACCCCTTAATATATCAATG
*
304708 CACCCCTTAATATATCGATG
1 CACCCCTTAATATATCAATG
304728 CACC
1 CACC
304732 TTCAAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.27
Consensus pattern (20 bp):
CACCCCTTAATATATCAATG
Found at i:308114 original size:29 final size:29
Alignment explanation
Indices: 308068--308132 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
308058 CGCCATAGGA
***
308068 CGCCATGCAATCCAGGCGACCTTGGAGGT
1 CGCCATGCAATCCAGGCGACCTCCAAGGT
*
308097 CGCCATGCAATCCGGGCGACCTCCAAGGT
1 CGCCATGCAATCCAGGCGACCTCCAAGGT
308126 CGCCATG
1 CGCCATG
308133 GCATTCGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.15
Consensus pattern (29 bp):
CGCCATGCAATCCAGGCGACCTCCAAGGT
Found at i:308236 original size:25 final size:25
Alignment explanation
Indices: 308208--308281 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
308198 CATGGGGGAG
308208 GGGATGCATGCTGTGCATGGGACGT
1 GGGATGCATGCTGTGCATGGGACGT
* *
308233 GGGA---A--CTGTGCAT-GGCCAT
1 GGGATGCATGCTGTGCATGGGACGT
*
308252 GCAGATGCATGCTGTGCATGGGACGT
1 G-GGATGCATGCTGTGCATGGGACGT
308278 GGGA
1 GGGA
308282 ACTGTGCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 5 0.14
20 10 0.28
22 1 0.03
23 1 0.03
25 14 0.39
26 5 0.14
ACGTcount: A:0.19, C:0.18, G:0.42, T:0.22
Consensus pattern (25 bp):
GGGATGCATGCTGTGCATGGGACGT
Found at i:308243 original size:20 final size:20
Alignment explanation
Indices: 308218--308292 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
308208 GGGATGCATG
308218 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
* * *
308238 CTGTGCATGGCCATGCAGAT-GCATG
1 CTGTGCATGG-GA--C-G-TGGGA-A
308263 CTGTGCATGGGACGTGGGAA
1 CTGTGCATGGGACGTGGGAA
308283 CTGTGCATGG
1 CTGTGCATGG
308293 CCATGCACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 21 0.50
21 4 0.10
22 1 0.02
23 1 0.02
24 4 0.10
25 11 0.26
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.23
Consensus pattern (20 bp):
CTGTGCATGGGACGTGGGAA
Found at i:308260 original size:45 final size:45
Alignment explanation
Indices: 308210--308299 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
308200 TGGGGGAGGG
308210 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
308255 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
1 GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
308300 CATTGAACGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (45 bp):
GATGCATGCTGTGCATGGGACGTGGGAACTGTGCATGGCCATGCA
Found at i:308809 original size:21 final size:21
Alignment explanation
Indices: 308784--308827 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
308774 AATCTAGTTA
308784 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
308805 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
308826 AT
1 AT
308828 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:308837 original size:28 final size:30
Alignment explanation
Indices: 308804--308866 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
308794 TAGTATAAAT
*
308804 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
308832 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
308862 TATTA
1 TATTA
308867 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:309400 original size:22 final size:22
Alignment explanation
Indices: 309365--309405 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
309355 TTTTAAAAAA
309365 TATTGTGTTTAAAAATATTTAG
1 TATTGTGTTTAAAAATATTTAG
309387 TATTGT-TTTAAAAATATTT
1 TATTGTGTTTAAAAATATTT
309406 TGTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (22 bp):
TATTGTGTTTAAAAATATTTAG
Found at i:309416 original size:20 final size:21
Alignment explanation
Indices: 309372--309416 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
309362 AAATATTGTG
**
309372 TTTAAAAATATTTAGTATTGT
1 TTTAAAAATATTTAGTATTAA
*
309393 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTATTAA
309413 TTTA
1 TTTA
309417 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTATTAA
Found at i:309706 original size:26 final size:25
Alignment explanation
Indices: 309677--309735 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
309667 AAATCATATT
*
309677 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
309703 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
309729 ATTATTA
1 ATTATTA
309736 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:310977 original size:15 final size:14
Alignment explanation
Indices: 310954--310984 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
310944 TACAACACTA
310954 AACTTTAATATAAT
1 AACTTTAATATAAT
310968 AACTTATAATATAAT
1 AACTT-TAATATAAT
310983 AA
1 AA
310985 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:310992 original size:16 final size:16
Alignment explanation
Indices: 310959--311005 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
310949 CACTAAACTT
*
310959 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
310974 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
310990 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
311006 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:311126 original size:32 final size:34
Alignment explanation
Indices: 311046--311127 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
311036 CTAAACCCTT
*
311046 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
311079 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
311112 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
311128 TACTAACTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:311244 original size:45 final size:45
Alignment explanation
Indices: 311167--311299 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
311157 TCAACAAACA
*
311167 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
311215 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
311259 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
311300 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:311327 original size:41 final size:40
Alignment explanation
Indices: 311239--311327 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
311229 TTAACAAAAC
* *
311239 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
311280 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
311321 AAACTAA
1 AAACTAA
311328 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:311441 original size:16 final size:18
Alignment explanation
Indices: 311401--311443 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
311391 CTAACAAATT
311401 AAAAATTTATAATAATAA
1 AAAAATTTATAATAATAA
**
311419 ACTAATTTA-AAT-ATAA
1 AAAAATTTATAATAATAA
311435 AAAAATTTA
1 AAAAATTTA
311444 CCTTATCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATTTATAATAATAA
Found at i:311492 original size:21 final size:21
Alignment explanation
Indices: 311462--311514 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
311452 CCCTTTCTTC
*
311462 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
311483 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
311504 TTCTTTCTTTC
1 TTCTTTCTTTC
311515 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:311505 original size:17 final size:16
Alignment explanation
Indices: 311485--311516 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
311475 TTCTCCCTTT
311485 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
311502 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
311517 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:311549 original size:23 final size:23
Alignment explanation
Indices: 311519--311564 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
311509 TCTTTCTCGG
311519 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
311542 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
311565 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:311711 original size:27 final size:27
Alignment explanation
Indices: 311676--311728 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
311666 GTACCAATAA
311676 TCAAATGGTTCACATGCATGCATTGGC
1 TCAAATGGTTCACATGCATGCATTGGC
311703 TCAAATGGTTCACATGCATGCATTGG
1 TCAAATGGTTCACATGCATGCATTGG
311729 GAGCTGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (27 bp):
TCAAATGGTTCACATGCATGCATTGGC
Found at i:311835 original size:29 final size:29
Alignment explanation
Indices: 311803--311882 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
311793 ATGGGAATGG
311803 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
311832 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
311861 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
311883 CTCTATTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:311927 original size:11 final size:11
Alignment explanation
Indices: 311913--311977 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
311903 CATTGGCTCG
311913 TATGGCTCGTA
1 TATGGCTCGTA
311924 TATGGCTCGT-
1 TATGGCTCGTA
**
311934 TGCAT-GCTCCCCA
1 T--ATGGCT-CGTA
311947 T-TGGCTCG--
1 TATGGCTCGTA
311955 TATGGCTCGTA
1 TATGGCTCGTA
311966 TATGGCTCGTA
1 TATGGCTCGTA
311977 T
1 T
311978 GTCACCCTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
8 1 0.02
9 7 0.16
10 3 0.07
11 28 0.65
12 3 0.07
13 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.26, T:0.35
Consensus pattern (11 bp):
TATGGCTCGTA
Found at i:311939 original size:42 final size:42
Alignment explanation
Indices: 311892--311975 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
311882 TCTCTATTCC
311892 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
311934 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
311976 ATGTCACCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.29, G:0.26, T:0.33
Consensus pattern (42 bp):
TGCATGCTCCCCATTGGCTCGTATGGCTCGTATATGGCTCGT
Found at i:312003 original size:12 final size:13
Alignment explanation
Indices: 311971--312005 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
311961 TCGTATATGG
311971 CTCGTATGTCACC
1 CTCGTATGTCACC
311984 CTCGTATGTCACC
1 CTCGTATGTCACC
311997 C-CGTATGTC
1 CTCGTATGTC
312006 GCCTGGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.31
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:323011 original size:21 final size:20
Alignment explanation
Indices: 322987--323026 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
322977 GTGGTATAGC
322987 TAAGAAAATAAAGATTTTGTA
1 TAAGAAAA-AAAGATTTTGTA
*
323008 TAAGAACAAAAGATTTTGT
1 TAAGAAAAAAAGATTTTGT
323027 TATTGTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (20 bp):
TAAGAAAAAAAGATTTTGTA
Found at i:328583 original size:23 final size:22
Alignment explanation
Indices: 328557--328620 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
328547 CAGCTCATAT
328557 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
328580 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
328603 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
328621 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:328764 original size:103 final size:103
Alignment explanation
Indices: 328636--328953 Score: 591
Period size: 103 Copynumber: 3.1 Consensus size: 103
328626 TAATGTCCAT
328636 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
328701 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
328739 AATGACCACATATCATTCCTTAAGAATCATATACATATTCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
328804 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
328842 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTATCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
328907 GACCTCACACATATTCCAAAGAATATATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
328945 AAGGACCAC
1 AAGGACCAC
328954 TTAGACCCTC
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:329440 original size:20 final size:20
Alignment explanation
Indices: 329417--329469 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
329407 TACTGGAGGT
329417 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
329437 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
329457 ATGCATCGATGCA
1 ATGCATCGATGCA
329470 TAAATCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGCACTACACC
Found at i:329570 original size:64 final size:62
Alignment explanation
Indices: 329437--329597 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 62
329427 GCACTACACC
*
329437 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGAGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGA-G
* * *
329502 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTT-TCTTTTGAAATTA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTGT-ATTT--AATGA
329566 -
62 G
* *
329566 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
329598 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
63 2 0.02
64 63 0.74
65 16 0.19
66 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTGTATTTAATGAG
Found at i:335777 original size:103 final size:103
Alignment explanation
Indices: 335653--335956 Score: 563
Period size: 103 Copynumber: 3.0 Consensus size: 103
335643 TAGAATTTCA
335653 CCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
1 CCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
*
335718 AAAGAATACATATATGTCCTGAAGGACCACATATCATT
66 AAAGAATACATATATGTCCCGAAGGACCACATATCATT
*
335756 CCTTAAGAATCATATACATATGCCAAGGATCGAGTATGTGTCTCACCAGACCTCACACATGTTCC
1 CCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
*
335821 AAAGAATACATATATGTCCCGAATGACCACATATCATT
66 AAAGAATACATATATGTCCCGAAGGACCACATATCATT
* *
335859 CCTTAATAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
1 CCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
335924 AAAGAATACATATATGTCCCGAAGGACCACATA
66 AAAGAATACATATATGTCCCGAAGGACCACATA
335957 GACCCTCTAC
Statistics
Matches: 194, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 194 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
CCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTCACACATGTTCC
AAAGAATACATATATGTCCCGAAGGACCACATATCATT
Found at i:336518 original size:64 final size:67
Alignment explanation
Indices: 336404--336531 Score: 201
Period size: 64 Copynumber: 2.0 Consensus size: 67
336394 ATTTTCATCT
*
336404 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGAATCGATGCATAAATCCTATTCGATGTTTG
336469 TA
66 TA
*
336471 TTTAAT-GAGG-ATGCATCGATGCACT-C-CTTATGAATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGAATCGATGCATAAATCCTATTCGATGTTT
336532 TCTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.55
65 15 0.26
66 4 0.07
67 6 0.10
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGAATCGATGCATAAATCCTATTCGATGTTTG
TA
Found at i:336572 original size:64 final size:63
Alignment explanation
Indices: 336416--336576 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
336406 TAATGGAGGT
* *
336416 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGAGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGA-G
* * * * *
336481 ATGCATCGATGCACTCCTTATGAATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAATTA-
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGAG
* *
336545 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
336577 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 56 0.67
65 23 0.28
66 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGAG
Found at i:351645 original size:19 final size:20
Alignment explanation
Indices: 351594--351647 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
351584 TGATGAGGTA
351594 ATTTAATTAATA-TTATTTT
1 ATTTAATTAATATTTATTTT
* *
351613 ATATT-TTTATTATTTA-TTT
1 AT-TTAATTAATATTTATTTT
351632 ATTTAATTAATATTTA
1 ATTTAATTAATATTTA
351648 AATAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 2 0.07
19 21 0.75
20 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTAATTAATATTTATTTT
Found at i:352354 original size:403 final size:403
Alignment explanation
Indices: 351607--352412 Score: 1531
Period size: 403 Copynumber: 2.0 Consensus size: 403
351597 TAATTAATAT
* *
351607 TATTTTATATTTTTATTATTTATTTATTTAATTAATATTTAAATAATTTTTCAATATTTATATTT
1 TATTTTATATTTTTATTATTTATTTAATTAATTAATATTTAAATAAATTTTCAATATTTATATTT
*
351672 TGTAGGGATATGAACGTGTATTAGAGTGTCATATAAATCGTGTGACACCGCTCGATGCAAATATT
66 CGTAGGGATATGAACGTGTATTAGAGTGTCATATAAATCGTGTGACACCGCTCGATGCAAATATT
351737 ATTGATTATTTTACATTTAGCGGGTTTCAGATATATCAGTAGTGTAACTGGTGAAGGTGTGAAGT
131 ATTGATTATTTTACATTTAGCGGGTTTCAGATATATCAGTAGTGTAACTGGTGAAGGTGTGAAGT
351802 TGCATCCTCCACTTATAAATGTGTTGATAGAAAGATGGAGAGTGGACACGCACACGTTTCATTTA
196 TGCATCCTCCACTTATAAATGTGTTGATAGAAAGATGGAGAGTGGACACGCACACGTTTCATTTA
351867 CCGCGTGGGGAGGCAACTATTACCTTGCAATATGTTACATTTCATCAGGGAATGCCTATTGATGG
261 CCGCGTGGGGAGGCAACTATTACCTTGCAATATGTTACATTTCATCAGGGAATGCCTATTGATGG
351932 AGTATCTATTACTGGTGTTGTCGGCGCCCCTAGAAATGTATGTGAGGTATTACTCGGAATTGATC
326 AGTATCTATTACTGGTGTTGTCGGCGCCCCTAGAAATGTATGTGAGGTATTACTCGGAATTGATC
351997 CGCCTGATGATGA
391 CGCCTGATGATGA
352010 TATTTTATATTTTTATTATTTATTTAATTAATTAATATTTAAATAAATTTTCAATATTTATATTT
1 TATTTTATATTTTTATTATTTATTTAATTAATTAATATTTAAATAAATTTTCAATATTTATATTT
*
352075 CGTAGGGATATGAACGTGTATTAGAGTGTCATATAAATTGTGTGACACCGCTCGATGCAAATATT
66 CGTAGGGATATGAACGTGTATTAGAGTGTCATATAAATCGTGTGACACCGCTCGATGCAAATATT
*
352140 ATTGATTATTTTACATTTAGCGGGTTTCAGTTATATCAGTAGTGTAACTGGTGAAGGTGTGAAGT
131 ATTGATTATTTTACATTTAGCGGGTTTCAGATATATCAGTAGTGTAACTGGTGAAGGTGTGAAGT
*
352205 TGCATCCTCCACTTATAAATGTGTTGGTAGAAAGATGGAGAGTGGACACGCACACGTTTCATTTA
196 TGCATCCTCCACTTATAAATGTGTTGATAGAAAGATGGAGAGTGGACACGCACACGTTTCATTTA
*
352270 CCGCGTGGGGAGGCAATTATTACCTTGCAATATGTTACATTTCATCAGGGAATGCCTATTGATGG
261 CCGCGTGGGGAGGCAACTATTACCTTGCAATATGTTACATTTCATCAGGGAATGCCTATTGATGG
*
352335 AGTATCTATTACTGGTGTTGTCGGCGCCCCTATAAATGTATGTGAGGTATTACTCGGAATTGATC
326 AGTATCTATTACTGGTGTTGTCGGCGCCCCTAGAAATGTATGTGAGGTATTACTCGGAATTGATC
*
352400 CTCCTGATGATGA
391 CGCCTGATGATGA
352413 ACGCGATGGT
Statistics
Matches: 394, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
403 394 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (403 bp):
TATTTTATATTTTTATTATTTATTTAATTAATTAATATTTAAATAAATTTTCAATATTTATATTT
CGTAGGGATATGAACGTGTATTAGAGTGTCATATAAATCGTGTGACACCGCTCGATGCAAATATT
ATTGATTATTTTACATTTAGCGGGTTTCAGATATATCAGTAGTGTAACTGGTGAAGGTGTGAAGT
TGCATCCTCCACTTATAAATGTGTTGATAGAAAGATGGAGAGTGGACACGCACACGTTTCATTTA
CCGCGTGGGGAGGCAACTATTACCTTGCAATATGTTACATTTCATCAGGGAATGCCTATTGATGG
AGTATCTATTACTGGTGTTGTCGGCGCCCCTAGAAATGTATGTGAGGTATTACTCGGAATTGATC
CGCCTGATGATGA
Found at i:353878 original size:23 final size:23
Alignment explanation
Indices: 353848--353901 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
353838 ACATCGGTTC
353848 CGATTCCAGTACTAGTGGTGGAT
1 CGATTCCAGTACTAGTGGTGGAT
353871 CGATTCCAGTACTAGTGGTGGAT
1 CGATTCCAGTACTAGTGGTGGAT
353894 CGATTCCA
1 CGATTCCA
353902 TATACAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
CGATTCCAGTACTAGTGGTGGAT
Found at i:356772 original size:216 final size:215
Alignment explanation
Indices: 356397--356834 Score: 815
Period size: 216 Copynumber: 2.0 Consensus size: 215
356387 TTCTGTATAT
356397 CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
1 CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
*
356462 TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCACTA
66 TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCAATAGAGGTTGTGCACTA
*
356527 ATGCTGTCACCACAGCTCGTATCATTGCACCAAAGTGCACGTAGAATTGCATCGTAGTGCCATAT
131 ATGCTGTCACCACAGCTCGTATCATTGCACCAAAGTGCACGTAGAATTGCACCGTAGTGCCATAT
356592 AATAATGTCCATAAGGACCA
196 AATAATGTCCATAAGGACCA
356612 CAATATCAC-TCATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATC
1 C-ATATCACAT-ATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATC
356676 TCTTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCAATAGAGGTTGTGCAC
64 TCTTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCAATAGAGGTTGTGCAC
*
356741 TAATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTGCACGTAGAATTGCACCGTAGTGCCAT
129 TAATGCTGTCACCACAGCTCGTATCATTGCACCAAAGTGCACGTAGAATTGCACCGTAGTGCCAT
*
356806 ATAATAATGTCTATAAGGACCA
194 ATAATAATGTCCATAAGGACCA
356828 CATATCA
1 CATATCA
356835 TTCCTTAAGG
Statistics
Matches: 217, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
215 8 0.04
216 209 0.96
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (215 bp):
CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCAATAGAGGTTGTGCACTA
ATGCTGTCACCACAGCTCGTATCATTGCACCAAAGTGCACGTAGAATTGCACCGTAGTGCCATAT
AATAATGTCCATAAGGACCA
Found at i:356845 original size:21 final size:21
Alignment explanation
Indices: 356819--356885 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
356809 ATAATGTCTA
356819 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
356840 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
356861 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
356882 TAAG
1 TAAG
356886 AATCATATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:361754 original size:216 final size:215
Alignment explanation
Indices: 361379--361816 Score: 842
Period size: 216 Copynumber: 2.0 Consensus size: 215
361369 TTCTGTATAT
361379 CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
1 CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
361444 TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCACTA
66 TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCACTA
361509 ATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTACACGTAGAATTGCACCGTAGTGCCATAT
131 ATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTACACGTAGAATTGCACCGTAGTGCCATAT
361574 AATAATGTCCATAAGGACCA
196 AATAATGTCCATAAGGACCA
361594 CAATATCAC-TCATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATC
1 C-ATATCACAT-ATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATC
361658 TCTTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCAC
64 TCTTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCAC
*
361723 TAATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTGCACGTAGAATTGCACCGTAGTGCCAT
129 TAATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTACACGTAGAATTGCACCGTAGTGCCAT
361788 ATAATAATGTCCATAAGGACCA
194 ATAATAATGTCCATAAGGACCA
361810 CATATCA
1 CATATCA
361817 TTACTTAAGG
Statistics
Matches: 220, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
215 8 0.04
216 212 0.96
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (215 bp):
CATATCACATATATATCATTTCACCAAAAGCATATACATTATATATATTGTATTTATGTTATCTC
TTTGATTAGCCCATGGTACACTTGTGAGAACTATCGATATGTGAGTCTATAGAGGTTGTGCACTA
ATGCTGTCACCACAGCTCGTATCATTGCACCGAAGTACACGTAGAATTGCACCGTAGTGCCATAT
AATAATGTCCATAAGGACCA
Found at i:361827 original size:21 final size:21
Alignment explanation
Indices: 361801--361867 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
361791 ATAATGTCCA
*
361801 TAAGGACCACATATCATTACT
1 TAAGGACCACATATCATTCCT
361822 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
361843 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
361864 TAAG
1 TAAG
361868 AATCATATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:365244 original size:2 final size:2
Alignment explanation
Indices: 365237--365302 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
365227 GCATCCAAAC
365237 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
365279 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
365303 CAGGTACATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:365633 original size:23 final size:23
Alignment explanation
Indices: 365599--365667 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
365589 CACCACAGCT
*
365599 CGTATAAATGCACC-AGAGTGCCA
1 CGTAGAAATGCACCGA-AGTGCCA
* *
365622 CGTAGAATTGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
365645 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
365668 TATAAGATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:366431 original size:2 final size:2
Alignment explanation
Indices: 366424--366461 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
366414 ACTTATAAAC
366424 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
366462 TACTTAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367259 original size:25 final size:23
Alignment explanation
Indices: 367207--367259 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
367197 CAATGCATTC
*
367207 TACA-GTGTATCGAAGCATCCTT
1 TACATGTGCATCGAAGCATCCTT
*
367229 TAACATGTGCATCGATGCACTCCTT
1 T-ACATGTGCATCGAAGCA-TCCTT
367254 ATACAT
1 -TACAT
367260 CGATGCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 11 0.44
25 9 0.36
26 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (23 bp):
TACATGTGCATCGAAGCATCCTT
Found at i:369849 original size:27 final size:28
Alignment explanation
Indices: 369794--369849 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
369784 TTTAATGTAT
* * * *
369794 ATATATGAATCTTATCTTTAATCACTTA
1 ATATATGAATATTATATTTAAACAATTA
369822 ATATAT-AATATTATATTTAAACAATTA
1 ATATATGAATATTATATTTAAACAATTA
369849 A
1 A
369850 AAAATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATATGAATATTATATTTAAACAATTA
Found at i:371041 original size:24 final size:24
Alignment explanation
Indices: 371014--371060 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
371004 TCCTTGGAGA
*
371014 TAATGCTTCATCATTGACTTGAGT
1 TAATGCTTCAACATTGACTTGAGT
371038 TAATGCTTCAACATTGACTTGAG
1 TAATGCTTCAACATTGACTTGAG
371061 AAATTCGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TAATGCTTCAACATTGACTTGAGT
Found at i:379406 original size:14 final size:14
Alignment explanation
Indices: 379389--379422 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
379379 AACGAACGTA
379389 AACGAACACAAATG
1 AACGAACACAAATG
*
379403 AACGAACATAAATG
1 AACGAACACAAATG
379417 AACGAA
1 AACGAA
379423 TGAGCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.18, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:380262 original size:37 final size:36
Alignment explanation
Indices: 380187--380262 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
380177 TTTTTATATT
*
380187 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
380223 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
380260 TTT
1 TTT
380263 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:380708 original size:14 final size:13
Alignment explanation
Indices: 380689--380718 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
380679 AAATAAATTC
380689 TTTTATCAATTCAA
1 TTTTATCAATT-AA
380703 TTTTATCAATTAA
1 TTTTATCAATTAA
380716 TTT
1 TTT
380719 CAATTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTATCAATTAA
Found at i:382207 original size:16 final size:17
Alignment explanation
Indices: 382183--382222 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
382173 TCTTATTCCC
* *
382183 TGCTTTTCAGTCTCAAT
1 TGCTTTTCAATCCCAAT
382200 TG-TTTTCAATCCCAAT
1 TGCTTTTCAATCCCAAT
382216 TGCTTTT
1 TGCTTTT
382223 GCTAGGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (17 bp):
TGCTTTTCAATCCCAAT
Found at i:399903 original size:36 final size:36
Alignment explanation
Indices: 399819--399934 Score: 182
Period size: 36 Copynumber: 3.3 Consensus size: 36
399809 GTGCGATACA
*
399819 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGAT-AC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
* *
399854 T-TTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
399889 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
*
399925 TCATTCCGTT
1 TCCTTCCGTT
399935 TTTTCTTTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 29 0.40
35 3 0.04
36 41 0.56
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCC
Found at i:404662 original size:31 final size:31
Alignment explanation
Indices: 404627--404690 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
404617 TGTAATATAA
*
404627 TCCCTCAACATTTAGTCCGTTTGCAATATGG
1 TCCCTCAACATTTAGTCAGTTTGCAATATGG
404658 TCCCTCAACATTTAGTCAGTTTGCAATATGG
1 TCCCTCAACATTTAGTCAGTTTGCAATATGG
404689 TC
1 TC
404691 TCTGACGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCAGTTTGCAATATGG
Found at i:405073 original size:8 final size:8
Alignment explanation
Indices: 405060--405096 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
405050 TATTTGAAAC
405060 AATTTAAT
1 AATTTAAT
405068 AATTTAAT
1 AATTTAAT
405076 -ATTTAAT
1 AATTTAAT
*
405083 -ATTTAAA
1 AATTTAAT
405090 AATTTAA
1 AATTTAA
405097 AAAGCTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATTTAAT
Found at i:405094 original size:15 final size:15
Alignment explanation
Indices: 405050--405096 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
405040 ATTTGATCTT
405050 TATTTGAAACAATTTAA
1 TATTT-AAA-AATTTAA
*
405067 TAATTT-AATATTTAA
1 T-ATTTAAAAATTTAA
405082 TATTTAAAAATTTAA
1 TATTTAAAAATTTAA
405097 AAAGCTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 15 0.58
16 2 0.08
17 1 0.04
18 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TATTTAAAAATTTAA
Found at i:406104 original size:15 final size:16
Alignment explanation
Indices: 406084--406113 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
406074 TTCTAAATTT
406084 TTTTTGAGTT-AAGTC
1 TTTTTGAGTTCAAGTC
406099 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
406114 TTCAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:414613 original size:28 final size:28
Alignment explanation
Indices: 414567--414632 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
414557 GTTCGGGTGC
414567 TGAAATGTTAAGAATATTTTGTTAAGTT
1 TGAAATGTTAAGAATATTTTGTTAAGTT
*
414595 TGAAATGTTAAGGAA-ATTTTGTTGAGTT
1 TGAAATGTTAA-GAATATTTTGTTAAGTT
414623 TGAAATGTTA
1 TGAAATGTTA
414633 TGTATTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.92
29 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (28 bp):
TGAAATGTTAAGAATATTTTGTTAAGTT
Found at i:418527 original size:16 final size:15
Alignment explanation
Indices: 418503--418565 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
418493 CGTATATACG
418503 TATTATTATATATTA
1 TATTATTATATATTA
* *
418518 TTTTACTTATATGTTA
1 TATTA-TTATATATTA
418534 TATTATATATATATATA
1 TATTAT-TATATAT-TA
418551 TATGTATATATATAT
1 TAT-TAT-TATATAT
418566 ATGTATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 5 0.12
16 19 0.47
17 5 0.12
18 11 0.28
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTATTATATATTA
Found at i:418542 original size:14 final size:13
Alignment explanation
Indices: 418495--418572 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 13
418485 TTTACACTCG
*
418495 TATATACGTATTAT
1 TATATATGTA-TAT
*
418509 TATATAT-TATTT
1 TATATATGTATAT
418521 TACTTATATGTTATAT
1 TA--TATATG-TATAT
418537 TATATA--TATA-
1 TATATATGTATAT
418547 TATATATGTATAT
1 TATATATGTATAT
418560 ATATATATGTATA
1 -TATATATGTATA
418573 CATTTGTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 6 0.11
11 4 0.08
12 8 0.15
13 2 0.04
14 27 0.51
16 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (13 bp):
TATATATGTATAT
Found at i:418544 original size:2 final size:2
Alignment explanation
Indices: 418532--418572 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
418522 ACTTATATGT
* *
418532 TA TA T- TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
418573 CATTTGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:418572 original size:12 final size:12
Alignment explanation
Indices: 418525--418565 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
418515 TTATTTTACT
418525 TATATGT-TATA
1 TATATGTATATA
*
418536 TTATATATATATA
1 -TATATGTATATA
418549 TATATGTATATA
1 TATATGTATATA
418561 TATAT
1 TATAT
418566 ATGTATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (12 bp):
TATATGTATATA
Found at i:418911 original size:17 final size:18
Alignment explanation
Indices: 418885--418920 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
418875 TATTTGATTA
418885 TAGTTATTTA-TTTTTTT
1 TAGTTATTTAGTTTTTTT
*
418902 TAGTTTTTTAGTTTTTTT
1 TAGTTATTTAGTTTTTTT
418920 T
1 T
418921 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (18 bp):
TAGTTATTTAGTTTTTTT
Found at i:418928 original size:17 final size:17
Alignment explanation
Indices: 418888--418958 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 17
418878 TTGATTATAG
418888 TTATTTATTTTTTTTAGT
1 TTATTTATTTTTTTTA-T
418906 TT-TTTAGTTTTTTTT-T
1 TTATTTA-TTTTTTTTAT
*
418922 TTATTTATTACTATTTATAT
1 TTATTTATT--T-TTTTTAT
*
418942 CT-TTTATTTTTTTTAT
1 TTATTTATTTTTTTTAT
418958 T
1 T
418959 GTTTATATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
16 11 0.26
17 9 0.21
18 11 0.26
19 10 0.23
20 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (17 bp):
TTATTTATTTTTTTTAT
Found at i:418946 original size:25 final size:25
Alignment explanation
Indices: 418918--418981 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
418908 TTTAGTTTTT
418918 TTTTTTATTTATTACTATTTATATC
1 TTTTTTATTTATTACTATTTATATC
* * *
418943 TTTTATT-TTTTTTATTGTTTATATC
1 TTTT-TTATTTATTACTATTTATATC
*
418968 TTTATTA-TTATTAC
1 TTTTTTATTTATTAC
418982 CATCATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 7 0.23
25 22 0.71
26 2 0.06
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTTTATTTATTACTATTTATATC
Found at i:418955 original size:9 final size:9
Alignment explanation
Indices: 418891--418958 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
418881 ATTATAGTTA
418891 TTTATTTTT
1 TTTATTTTT
*
418900 TTTA-GTTT
1 TTTATTTTT
*
418908 TTTAGTTTT
1 TTTATTTTT
*
418917 TTT-TTTTA
1 TTTATTTTT
* *
418925 TTTATTACTA
1 TTTATT-TTT
* *
418935 TTTATATCT
1 TTTATTTTT
418944 TTTATTTTT
1 TTTATTTTT
418953 TTTATT
1 TTTATT
418959 GTTTATATCT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
8 13 0.29
9 25 0.56
10 7 0.16
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTATTTTT
Found at i:429987 original size:13 final size:13
Alignment explanation
Indices: 429969--430003 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
429959 CATCTTCAAA
429969 AAAAAATAATAAT
1 AAAAAATAATAAT
*
429982 AAAAAAAAATAAT
1 AAAAAATAATAAT
429995 AAAAAATAA
1 AAAAAATAA
430004 AAAAATCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:429987 original size:16 final size:15
Alignment explanation
Indices: 429966--430006 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 15
429956 GAGCATCTTC
429966 AAAAAAAAATAATAA
1 AAAAAAAAATAATAA
429981 TAAAAAAAAATAATAA
1 -AAAAAAAAATAATAA
429997 AAAATAAAAA
1 AAAA-AAAAA
430007 AATCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATAATAA
Found at i:430374 original size:105 final size:105
Alignment explanation
Indices: 430192--430859 Score: 1207
Period size: 105 Copynumber: 6.4 Consensus size: 105
430182 AGGTTTTACC
*
430192 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
430257 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
430297 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
430362 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
430402 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
430467 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
430507 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
430572 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTC-ATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
430611 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
430676 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * *
430716 CAGAGCCAA-TTGATGCTTCACAACGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCAC
1 CAGAGCCAATTTCA-ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
430780 GACGAA-GGACCGCTGGTTTTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
430820 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
430860 GAAACAACAC
Statistics
Matches: 544, Mismatches: 16, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
104 172 0.32
105 372 0.68
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:430771 original size:209 final size:210
Alignment explanation
Indices: 430192--430859 Score: 1207
Period size: 209 Copynumber: 3.2 Consensus size: 210
430182 AGGTTTTACC
*
430192 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
430257 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
430322 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
430387 AACATTTCTCAATTT
196 AACATTTCTCAATTT
* *
430402 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
430467 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
* *
430532 AAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
430597 AACATTTCTC-ATTT
196 AACATTTCTCAATTT
430611 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
430676 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAA-TTGATGCTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCA-ACTTCACAAC
* * *
430740 GAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACGACGAA-GGACCGCTGGTTTTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
430804 AAACATTTCTCAATTT
195 AAACATTTCTCAATTT
430820 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
430860 GAAACAACAC
Statistics
Matches: 441, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
208 30 0.07
209 211 0.48
210 200 0.45
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAATTT
Found at i:432483 original size:2 final size:2
Alignment explanation
Indices: 432476--432509 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
432466 ACTTATATGT
* *
432476 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
432510 CATTTTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432491 original size:10 final size:10
Alignment explanation
Indices: 432469--432509 Score: 64
Period size: 10 Copynumber: 4.0 Consensus size: 10
432459 TTATTTTACT
432469 TATATGTTATA
1 TATATG-TATA
*
432480 TATATATATA
1 TATATGTATA
432490 TATATGTATA
1 TATATGTATA
432500 TATATGTATA
1 TATATGTATA
432510 CATTTTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 23 0.82
11 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (10 bp):
TATATGTATA
Found at i:432780 original size:4 final size:4
Alignment explanation
Indices: 432771--432899 Score: 70
Period size: 4 Copynumber: 31.8 Consensus size: 4
432761 TATTCATACC
* * **
432771 TTTA TTTA TTTTCA TTTA TTTA TTTA TTT- TTT- TTATT TTTA TTTG TACA
1 TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA
* * * * *
432820 TTTA TTTGA TTTA -TCA TTTA TTTA TTTT TTTA GTT- TTTA TTTT TTTT
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
432867 TTTA TTTA TTATA TTATA TATA TCTT- TTTA TTT
1 TTTA TTTA TT-TA TT-TA TTTA T-TTA TTTA TTT
432900 TTTTTATTGT
Statistics
Matches: 98, Mismatches: 17, Indels: 20
0.73 0.13 0.15
Matches are distributed among these distances:
3 11 0.11
4 65 0.66
5 21 0.21
6 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:432807 original size:9 final size:9
Alignment explanation
Indices: 432771--432907 Score: 79
Period size: 9 Copynumber: 15.1 Consensus size: 9
432761 TATTCATACC
432771 TTTATTTAT
1 TTTATTTAT
432780 TTTCATTTA-
1 TTT-ATTTAT
432789 TTTATTTAT
1 TTTATTTAT
*
432798 TTTTTTTATT
1 TTTATTTA-T
*
432808 TTTATTT-G
1 TTTATTTAT
**
432816 TACATTTAT
1 TTTATTTAT
*
432825 TTGATTTAT
1 TTTATTTAT
432834 CATTTATTTAT
1 --TTTATTTAT
432845 TTT-TTTAGTT
1 TTTATTTA--T
432855 TTTATTT-T
1 TTTATTTAT
*
432863 TTTTTTTA-
1 TTTATTTAT
432871 TTTATTATAT
1 TTTATT-TAT
* *
432881 TATATATAT
1 TTTATTTAT
*
432890 CTT-TTTAT
1 TTTATTTAT
*
432898 TTTTTTTAT
1 TTTATTTAT
432907 T
1 T
432908 GTTTATATCT
Statistics
Matches: 98, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
8 32 0.33
9 35 0.36
10 20 0.20
11 11 0.11
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:432907 original size:26 final size:26
Alignment explanation
Indices: 432865--432929 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
432855 TTTATTTTTT
432865 TTTTTATTTATTATATTATATATATC
1 TTTTTATTTATTATATTATATATATC
* * * *
432891 TTTTTATTTTTTTTATTGTTTATATC
1 TTTTTATTTATTATATTATATATATC
432917 TTTATTA-TTATTA
1 TTT-TTATTTATTA
432930 CCATCATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 29 0.91
27 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTTTATTTATTATATTATATATATC
Found at i:432949 original size:7 final size:7
Alignment explanation
Indices: 432937--432961 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
432927 TTACCATCAT
432937 TTTTATA
1 TTTTATA
432944 TTTTATA
1 TTTTATA
432951 TTTTATA
1 TTTTATA
432958 TTTT
1 TTTT
432962 CCTCATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:439165 original size:15 final size:15
Alignment explanation
Indices: 439147--439175 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
439137 TCTAGAGTTA
439147 ATATATATATGTTTG
1 ATATATATATGTTTG
439162 ATATATATATGTTT
1 ATATATATATGTTT
439176 TAATAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATATATATGTTTG
Found at i:439762 original size:71 final size:72
Alignment explanation
Indices: 439588--439821 Score: 258
Period size: 71 Copynumber: 3.2 Consensus size: 72
439578 GAGTCCCAAC
* * * *
439588 AACTCGAGATGGTTTTTCTTAAAACCAAATTCGTA-TTGTTTGAGATAGTTTTCGCTTGAAACAA
1 AACTCGAGATGGTTTTTCTTAAAACCAACTTCG-ACTCGCTTGAGATAATTTTC-CTTGAAACAA
*
439652 AATGTATCT
64 AATCTATCT
* * *
439661 CAGTTGAGATGGTTTTTCTTAAAACCAACTTCGACTCGCTTGAGATAATTTTCCTTGAAACAAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAACTTCGACTCGCTTGAGATAATTTTCCTTGAAACAAAA
*
439726 T-TTTCT
66 TCTATCT
* * * * * * * *
439732 AACTCGAGATGGTTTTTCTTAAAACTAACTTTGTCTCGCTTGATACAGCTTTCCCTCG-AACAAA
1 AACTCGAGATGGTTTTTCTTAAAACCAACTTCGACTCGCTTGAGATA-ATTTTCCTTGAAACAAA
439796 ATCTATCT
65 ATCTATCT
*
439804 CACTCGAGATGGTTTTTC
1 AACTCGAGATGGTTTTTC
439822 CCAAACCAGC
Statistics
Matches: 137, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
71 51 0.37
72 42 0.31
73 44 0.32
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (72 bp):
AACTCGAGATGGTTTTTCTTAAAACCAACTTCGACTCGCTTGAGATAATTTTCCTTGAAACAAAA
TCTATCT
Found at i:440405 original size:136 final size:134
Alignment explanation
Indices: 440158--440413 Score: 341
Period size: 136 Copynumber: 1.9 Consensus size: 134
440148 ATAACCGATC
* * *
440158 AACATTTCAAATGGAGAGTTCATAATGAAAGAACTCATCCGACAGAGAGAGAAGAGTTCATAATG
1 AACATTTCAAATGGAGAGTTCATAATGAAAGAAATCATCCAACAGAGAGAGAAAAGTTCATAATG
* **
440223 AGAAGATCTTGTTTAACCTATCACTCGATTCACAACATTTTGAATCAGTGACGCCTCGCTTGAGG
66 AGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCCTCGCTTGAGG
440288 GATT
131 GATT
** * * * *
440292 AACATTTCATTTGGAGAGTTTATAATGAGAATAAATCATCCAATAGATAGAGAATAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGA-AAGAAATCATCCAACAGAGAGAGAA-AAGTTCATAA
* * ***
440357 TGAGAAGATCTTGTTCGACCTATCACTCGATTTATGGCATTTCAAATCAGTGACGCC
64 TGAGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCC
440414 CCACCAGAGG
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
134 25 0.24
135 20 0.19
136 58 0.56
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (134 bp):
AACATTTCAAATGGAGAGTTCATAATGAAAGAAATCATCCAACAGAGAGAGAAAAGTTCATAATG
AGAAGATCTTGTTCAACCTATCACTCGATTCACAACATTTCAAATCAGTGACGCCTCGCTTGAGG
GATT
Found at i:440471 original size:59 final size:59
Alignment explanation
Indices: 440379--440524 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 59
440369 GTTCGACCTA
* * * * *
440379 TCACTCGATTTATGGCATTTCAAATCAGTGACGCCCCACCAGAGGGGTTAA-TATTTCCT
1 TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACT-TTTCCT
* *
440438 TCACTTGGTTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
1 TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
** * *
440497 TTGCTCGATTCATGACATTTTGAATCAA
1 TCACTCGATTCACGACATTTCGAATCAA
440525 AAATGCCTCG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 72 0.99
60 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (59 bp):
TCACTCGATTCACGACATTTCGAATCAATGACGCCCCACCAGAGGGGTTAACTTTTCCT
Found at i:442109 original size:14 final size:14
Alignment explanation
Indices: 442069--442114 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
442059 TGCATTTATT
* *
442069 TTTCAGCATTTACA
1 TTTCAGCTTTTAAA
*
442083 TTACAGTCTTTTAAA
1 TTTCAG-CTTTTAAA
442098 TTTCAGCTTTTAAA
1 TTTCAGCTTTTAAA
442112 TTT
1 TTT
442115 TGTACTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTCAGCTTTTAAA
Found at i:443872 original size:28 final size:28
Alignment explanation
Indices: 443841--443903 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
443831 CGATCCATTG
* * *
443841 CTTGAAACATTATGTCGTCGAGATAGTA
1 CTTGAAACATTATGTCATCAAGACAGTA
* *
443869 CTTGAAATATTATGTCATCAAGACAGTG
1 CTTGAAACATTATGTCATCAAGACAGTA
443897 CTTGAAA
1 CTTGAAA
443904 GCAATAACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (28 bp):
CTTGAAACATTATGTCATCAAGACAGTA
Found at i:447949 original size:13 final size:13
Alignment explanation
Indices: 447931--447963 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
447921 AGCTGAATAG
447931 ATCACCATCACAA
1 ATCACCATCACAA
447944 ATCACCATCACAA
1 ATCACCATCACAA
447957 ATCACCA
1 ATCACCA
447964 GTGAACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCATCACAA
Done.