Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 101 of 125
Found at i:30442519 original size:23 final size:23
Alignment explanation
Indices: 30442410--30442520 Score: 150
Period size: 23 Copynumber: 4.8 Consensus size: 23
30442400 ACTGAGGAAA
* *
30442410 CAGTAAGCACGCACATTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
30442433 CAGTAGGCACACACAATGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
30442456 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
30442479 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
30442502 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
30442521 TAAACAATAA
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:30442531 original size:23 final size:22
Alignment explanation
Indices: 30442407--30442532 Score: 135
Period size: 23 Copynumber: 5.5 Consensus size: 22
30442397 AGTACTGAGG
* *
30442407 AAACAGTAAGCACGCACATTGC
1 AAACAGTAAGCACACACAGTGC
* *
30442429 AAATCAGTAGGCACACACAATGC
1 AAA-CAGTAAGCACACACAGTGC
30442452 AAAACAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
* *
30442475 AAATCAGTAAGCACATATAGTGC
1 AAA-CAGTAAGCACACACAGTGC
*
30442498 GAATCAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
30442521 TAAACAATAAGC
1 -AAACAGTAAGC
30442533 GCGCTAATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
22 6 0.07
23 76 0.87
24 5 0.06
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:30445582 original size:19 final size:19
Alignment explanation
Indices: 30445543--30445582 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30445533 AATTGATCAC
* *
30445543 TTCATTCGTTCTGTTATGT
1 TTCATTCGTTCTATTAAGT
30445562 TTCATTCGTTCTATTAAGT
1 TTCATTCGTTCTATTAAGT
30445581 TT
1 TT
30445583 GTAACGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.57
Consensus pattern (19 bp):
TTCATTCGTTCTATTAAGT
Found at i:30449010 original size:3 final size:3
Alignment explanation
Indices: 30449002--30449027 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30448992 TGTGGGAGGT
30449002 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
30449028 GTTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30457748 original size:18 final size:18
Alignment explanation
Indices: 30457725--30457760 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30457715 TGTTTGTTGT
30457725 TATATATATGTGCATGTA
1 TATATATATGTGCATGTA
* *
30457743 TATATATGTGTGTATGTA
1 TATATATATGTGCATGTA
30457761 GGTATGTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (18 bp):
TATATATATGTGCATGTA
Found at i:30457756 original size:14 final size:15
Alignment explanation
Indices: 30457725--30457757 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30457715 TGTTTGTTGT
30457725 TATATATATGTGCATG
1 TATATATATGTG-ATG
30457741 TATATATATGTG-TG
1 TATATATATGTGATG
30457755 TAT
1 TAT
30457758 GTAGGTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
16 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (15 bp):
TATATATATGTGATG
Found at i:30463213 original size:2 final size:2
Alignment explanation
Indices: 30463206--30463270 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
30463196 TGCTACCTTT
30463206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30463248 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
30463271 TAAAGTGGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30467288 original size:19 final size:21
Alignment explanation
Indices: 30467264--30467309 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 21
30467254 GAATTACACA
30467264 AAAATTCAAAA-TA-ATTTTT
1 AAAATTCAAAATTATATTTTT
30467283 AAAATTCAAAATTTATATTTTT
1 AAAATTCAAAA-TTATATTTTT
30467305 AAAAT
1 AAAAT
30467310 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.46
21 2 0.08
22 11 0.46
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTCAAAATTATATTTTT
Found at i:30467346 original size:26 final size:27
Alignment explanation
Indices: 30467317--30467371 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
30467307 AATAATTTTA
30467317 AAAATTCTAAAAAATATATAAAA-AAT
1 AAAATTCTAAAAAATATATAAAACAAT
* * *
30467343 AAAATTTTAAAAAATTTCTAAAACAAT
1 AAAATTCTAAAAAATATATAAAACAAT
30467370 AA
1 AA
30467372 TTTTGAGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATTCTAAAAAATATATAAAACAAT
Found at i:30468749 original size:31 final size:32
Alignment explanation
Indices: 30468704--30468764 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
30468694 TTTTTAGTTA
* *
30468704 AATTTGACCCTCAACCTCTT-AAAAAGAGTAG
1 AATTTGACCATCAACATCTTGAAAAAGAGTAG
* *
30468735 AATTTGATCATCAACATTTTGAAAAAGAGT
1 AATTTGACCATCAACATCTTGAAAAAGAGT
30468765 TGAAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (32 bp):
AATTTGACCATCAACATCTTGAAAAAGAGTAG
Found at i:30468836 original size:11 final size:11
Alignment explanation
Indices: 30468817--30468845 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
30468807 TACTCCATGC
30468817 TAATTTTTTT-
1 TAATTTTTTTA
30468827 TAATTTTTTTA
1 TAATTTTTTTA
30468838 TAATTTTT
1 TAATTTTT
30468846 GAATTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:30475333 original size:22 final size:22
Alignment explanation
Indices: 30475282--30475361 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
30475272 AAGTACTTTA
*
30475282 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
30475304 CCAGTAGGCACACACAATGCAAT
1 -CAGTAGGCACACACAGTGCAAT
** * *
30475327 CAGTAGGCGTACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
30475350 CAGTAGGCACAC
1 CAGTAGGCACAC
30475362 GAAGTGCGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.30
23 33 0.70
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:30475389 original size:23 final size:23
Alignment explanation
Indices: 30475356--30475402 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
30475346 AAATCAGTAG
*
30475356 GCACACGAAGTGCGAAACAATAA
1 GCACACAAAGTGCGAAACAATAA
* *
30475379 GCACACAAAGTGTGAAACAGTAA
1 GCACACAAAGTGCGAAACAATAA
30475402 G
1 G
30475403 TGCGCTAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (23 bp):
GCACACAAAGTGCGAAACAATAA
Found at i:30478312 original size:18 final size:18
Alignment explanation
Indices: 30478291--30478327 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30478281 GTTGCTGACT
30478291 AGTTTGTGGTTTCTGAAA
1 AGTTTGTGGTTTCTGAAA
30478309 AGTTTGTGGTTTCTGAAA
1 AGTTTGTGGTTTCTGAAA
30478327 A
1 A
30478328 ATGTCTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.43
Consensus pattern (18 bp):
AGTTTGTGGTTTCTGAAA
Found at i:30483077 original size:95 final size:96
Alignment explanation
Indices: 30482909--30483094 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 96
30482899 TGGAAAAAGA
* ** * *
30482909 TATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCATAACT
1 TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAACTTTCATAACT
*
30482974 GAAGAT-AAAGAAACATTGCTTCGATTAACGG
66 GAAGATAAAAG-AACATTGCCTCGATTAACGG
*
30483005 TATTCGATTATTTCGATTCGAA-AAAAATTGCACCTAGTAAGTTAAGGCACAAACTTTCGA-AAC
1 TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAACTTTC-ATAAC
*
30483068 TCGAA-ATAAAAGAATATTGCCTCGATT
65 T-GAAGATAAAAGAACATTGCCTCGATT
30483095 TTAAAGTCTT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 51 0.65
96 28 0.35
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAACTTTCATAACT
GAAGATAAAAGAACATTGCCTCGATTAACGG
Found at i:30483541 original size:57 final size:56
Alignment explanation
Indices: 30483474--30483637 Score: 175
Period size: 57 Copynumber: 2.8 Consensus size: 56
30483464 GGATATCTAG
*
30483474 GGGTAAAATGGTAATTTTTGAAAGTTTTAAGGTCAAAATGAAGTTTTGGACATCCGA
1 GGGTAAAATGGTAATTTTT-AAAGTTTTGAGGTCAAAATGAAGTTTTGGACATCCGA
** * * * *
30483531 GGGTGGAATGGTAATTTTTAAAAGTTTCGAGGTTAAAAATAAAGTTTTTGGACATTCGA
1 GGGTAAAATGGTAATTTTT-AAAGTTTTGAGG-TCAAAATGAAG-TTTTGGACATCCGA
* * * * *
30483590 GGGTAAAATGATAAATTTTCAAGTTTTGGGGTCAAAATGGAATTTTTG
1 GGGTAAAATGGTAATTTTTAAAGTTTTGAGGTCAAAAT-GAAGTTTTG
30483638 TAAGTTTGAG
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
57 38 0.44
58 20 0.23
59 28 0.33
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (56 bp):
GGGTAAAATGGTAATTTTTAAAGTTTTGAGGTCAAAATGAAGTTTTGGACATCCGA
Found at i:30483649 original size:116 final size:116
Alignment explanation
Indices: 30483424--30483637 Score: 263
Period size: 116 Copynumber: 1.8 Consensus size: 116
30483414 GGGGTAAAAC
** * * * *
30483424 GGTAATTTTTAGAAAAATCGAGATTAAAAATGGAGTTTTTGGATATCTAGGGGTAAAATGGTAAT
1 GGTAATTTTTAGAAAAATCGAGATTAAAAATAAAGTTTTTGGACATCGAGGGGTAAAATGATAAA
30483489 TTTTGAAAGTTTTAAGGTCAAAATGAAGTTTTGGACATCCGAGGGTGGAAT
66 TTTTGAAAGTTTTAAGGTCAAAATGAAGTTTTGGACATCCGAGGGTGGAAT
** *
30483540 GGTAATTTTTA-AAAGTTTCGAGGTTAAAAATAAAGTTTTTGGACATTCGA-GGGTAAAATGATA
1 GGTAATTTTTAGAAA-AATCGAGATTAAAAATAAAGTTTTTGGACA-TCGAGGGGTAAAATGATA
* ** *
30483603 AATTTT-CAAGTTTTGGGGTCAAAATGGAATTTTTG
64 AATTTTGAAAGTTTTAAGGTCAAAAT-GAAGTTTTG
30483638 TAAGTTTGAG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
115 19 0.23
116 60 0.73
117 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (116 bp):
GGTAATTTTTAGAAAAATCGAGATTAAAAATAAAGTTTTTGGACATCGAGGGGTAAAATGATAAA
TTTTGAAAGTTTTAAGGTCAAAATGAAGTTTTGGACATCCGAGGGTGGAAT
Found at i:30483678 original size:29 final size:29
Alignment explanation
Indices: 30483623--30483678 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
30483613 TTTTGGGGTC
*
30483623 AAAATGGAATTTTTGTAAGTTTGAGGGCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGCA
*
30483652 AAAATGTAATTTTTGGACAGTTT-AGGG
1 AAAATGGAATTTTTGGA-AGTTTGAGGG
30483679 ACCTCTAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGCA
Found at i:30485594 original size:6 final size:6
Alignment explanation
Indices: 30485553--30485611 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
30485543 CTTTTTAATT
* * * *
30485553 AATTTT AATTTA AA-ATA AATTTT AATTTA AA-ATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
30485599 AA-GTA AATTTA AA
1 AATTTA AATTTA AA
30485612 CTCAAAAATG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
5 12 0.29
6 29 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:30485609 original size:17 final size:17
Alignment explanation
Indices: 30485553--30485633 Score: 99
Period size: 17 Copynumber: 4.7 Consensus size: 17
30485543 CTTTTTAATT
*
30485553 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
*
30485570 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
*
30485587 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
** *
30485604 AATTTAAACTCAAAAATG
1 AATTTAAA-TTTAAAATA
30485622 AATTTAAATTTA
1 AATTTAAATTTA
30485634 GAACAAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 42 0.76
18 13 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:30495269 original size:20 final size:19
Alignment explanation
Indices: 30495246--30495294 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
30495236 TCTGTTAAAT
*
30495246 TTTTTTGTATCCGTTATGAA
1 TTTTTTGTATCC-TTAGGAA
30495266 TTTTTGTGT-TCCTTAGGAA
1 TTTTT-TGTATCCTTAGGAA
*
30495285 ATTTTTGTAT
1 TTTTTTGTAT
30495295 TAGAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 11 0.44
20 8 0.32
21 3 0.12
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.57
Consensus pattern (19 bp):
TTTTTTGTATCCTTAGGAA
Found at i:30495269 original size:21 final size:20
Alignment explanation
Indices: 30495243--30495294 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
30495233 GTATCTGTTA
*
30495243 AATTTTTTTGTATCCGTTATG
1 AATTTTTTTGTATCC-TTAGG
*
30495264 AATTTTTGTGT-TCCTTAGG
1 AATTTTTTTGTATCCTTAGG
*
30495283 AA-ATTTTTGTAT
1 AATTTTTTTGTAT
30495295 TAGAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.23
19 7 0.27
20 3 0.12
21 10 0.38
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (20 bp):
AATTTTTTTGTATCCTTAGG
Found at i:30495670 original size:20 final size:20
Alignment explanation
Indices: 30495641--30495690 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
30495631 AATTTTAAAA
* * *
30495641 TAATATTTTTTTACAAATTT
1 TAATAATTTTTAACAAATTG
30495661 TAATAATTTTTAACAAATTG
1 TAATAATTTTTAACAAATTG
30495681 TAATAATTTT
1 TAATAATTTT
30495691 AAAATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATAATTTTTAACAAATTG
Found at i:30495695 original size:17 final size:17
Alignment explanation
Indices: 30495627--30495710 Score: 64
Period size: 17 Copynumber: 4.8 Consensus size: 17
30495617 CTAAAAAATC
**
30495627 TAATAATTTTAAAATAA
1 TAATAATTTTAAAATTT
**
30495644 T-ATTTTTTTACAAATTT
1 TAATAATTTTA-AAATTT
*
30495661 TAATAATTTTTAACAAATTG
1 TAATAA-TTTT-A-AAATTT
30495681 TAATAATTTTAAAATTAT
1 TAATAATTTTAAAATT-T
30495699 TAAT-ATTTTAAA
1 TAATAATTTTAAA
30495711 TAAAATTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.13
17 19 0.35
18 7 0.13
19 8 0.15
20 13 0.24
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (17 bp):
TAATAATTTTAAAATTT
Found at i:30497712 original size:14 final size:14
Alignment explanation
Indices: 30497693--30497723 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30497683 CTTGTTCTCT
30497693 TTGGCAAGGTTGAC
1 TTGGCAAGGTTGAC
30497707 TTGGCAAGGTTGAC
1 TTGGCAAGGTTGAC
30497721 TTG
1 TTG
30497724 TGCCAAGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.32
Consensus pattern (14 bp):
TTGGCAAGGTTGAC
Found at i:30499851 original size:3 final size:3
Alignment explanation
Indices: 30499843--30499867 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30499833 CATCAATTAT
30499843 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
30499868 AAGTATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:30500986 original size:33 final size:32
Alignment explanation
Indices: 30500922--30500987 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
30500912 TCAAAACTAT
*
30500922 AAACCTTAAACCTCAAATTCAAAATCCAAACCC
1 AAACCATAAACCTCAAATTCAAAAT-CAAACCC
*
30500955 AAACCATAAACCTTAAATCTCAAACAT-AAACCC
1 AAACCATAAACCTCAAAT-TCAAA-ATCAAACCC
30500988 TTAATATTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 22 0.76
34 5 0.17
35 2 0.07
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (32 bp):
AAACCATAAACCTCAAATTCAAAATCAAACCC
Found at i:30502514 original size:2 final size:2
Alignment explanation
Indices: 30502507--30502546 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30502497 AAATACAGAA
30502507 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
30502547 GCACACACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30503044 original size:20 final size:21
Alignment explanation
Indices: 30503000--30503044 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
30502990 TTAATTTTAA
*
30503000 AAATTTAGAGTTTAAATTATT
1 AAATTTAGAGTTCAAATTATT
30503021 -AATTTATGA-TTCAAATT-TT
1 AAATTTA-GAGTTCAAATTATT
30503040 AAATT
1 AAATT
30503045 CAAAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 2 0.10
20 17 0.81
21 2 0.10
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
AAATTTAGAGTTCAAATTATT
Found at i:30503125 original size:19 final size:18
Alignment explanation
Indices: 30503101--30503139 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
30503091 TAAAAAATTT
*
30503101 ATTAAAACATTATTAAATA
1 ATTAAAAAATTA-TAAATA
30503120 ATTAAAAAATTATAAATA
1 ATTAAAAAATTATAAATA
30503138 AT
1 AT
30503140 GAAATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAAATTATAAATA
Found at i:30503467 original size:27 final size:27
Alignment explanation
Indices: 30503432--30503506 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
30503422 TTTAAGAATT
*
30503432 TAAACTTTAAATTCAAAATTTTGAATCA
1 TAAA-TTTAAATTCAAAATTTCGAATCA
* *
30503460 TAAATTTAAATTC-AAATTACGAATCT
1 TAAATTTAAATTCAAAATTTCGAATCA
*
30503486 TAAATCTCAAATTCAAAATTT
1 TAAAT-TTAAATTCAAAATTT
30503507 AAATTTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.38
27 16 0.40
28 9 0.22
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.39
Consensus pattern (27 bp):
TAAATTTAAATTCAAAATTTCGAATCA
Found at i:30503508 original size:20 final size:19
Alignment explanation
Indices: 30503461--30503511 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
30503451 TTTGAATCAT
30503461 AAATTTAAATTCAAATTAC
1 AAATTTAAATTCAAATTAC
*
30503480 GAATCTTAAATCTCAAATT-C
1 AAAT-TTAAAT-TCAAATTAC
30503500 AAAATTTAAATT
1 -AAATTTAAATT
30503512 TTAACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATTTAAATTCAAATTAC
Found at i:30510134 original size:2 final size:2
Alignment explanation
Indices: 30510127--30510151 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30510117 AAAAGAGCAA
30510127 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30510152 AGATTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30526955 original size:89 final size:92
Alignment explanation
Indices: 30526851--30527023 Score: 282
Period size: 89 Copynumber: 1.9 Consensus size: 92
30526841 ACTTGTCCCA
*
30526851 ATGTACAATACGAATAGGAAGTGTCATTAGAGCATTTTCTTAACTT-GAAT-AA-TTTTTT-TTT
1 ATGTACAATACGAATAGGAAGTGTCACTAGAGCATTTTCTTAACTTCG-ATCAATTTTTTTCTTT
30526912 TATAATAACATTCATTTCACTCTTCTTG
65 TATAATAACATTCATTTCACTCTTCTTG
*
30526940 ATGTACAATACGAATAGGAGGTGTCACTAGAGCATTTTCTTAACTTCGATCAATTTTTTTTCTTT
1 ATGTACAATACGAATAGGAAGTGTCACTAGAGCATTTTCTTAACTTCGATCAA-TTTTTTTCTTT
30527005 TATAATAACATTCATTTCA
65 TATAATAACATTCATTTCA
30527024 AAATATAATA
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
89 46 0.60
90 3 0.04
92 6 0.08
93 22 0.29
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (92 bp):
ATGTACAATACGAATAGGAAGTGTCACTAGAGCATTTTCTTAACTTCGATCAATTTTTTTCTTTT
ATAATAACATTCATTTCACTCTTCTTG
Found at i:30532202 original size:21 final size:22
Alignment explanation
Indices: 30532176--30532226 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
30532166 TCCTACATAG
*
30532176 AAATTAATCAA-TTAAATGT-CA
1 AAATTAATAAAGTT-AATGTCCA
*
30532197 AAATTAATAAAGTTTATGTCCA
1 AAATTAATAAAGTTAATGTCCA
30532219 AAATTAAT
1 AAATTAAT
30532227 TAAAAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATTAATAAAGTTAATGTCCA
Found at i:30534109 original size:21 final size:21
Alignment explanation
Indices: 30534075--30534114 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30534065 CTGCAAAAAA
* *
30534075 AAGAAAATACAAAACAAAATG
1 AAGAAAAAACAAAAAAAAATG
*
30534096 AAGAAAAAAGAAAAAAAAA
1 AAGAAAAAACAAAAAAAAA
30534115 GGACGTGGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (21 bp):
AAGAAAAAACAAAAAAAAATG
Found at i:30546750 original size:6 final size:6
Alignment explanation
Indices: 30546739--30546764 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30546729 TCTAGCCATT
30546739 TCACCA TCACCA TCACCA TCACCA TC
1 TCACCA TCACCA TCACCA TCACCA TC
30546765 TCGCCACCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (6 bp):
TCACCA
Found at i:30548821 original size:20 final size:19
Alignment explanation
Indices: 30548766--30548829 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
30548756 TCAACAAAAA
30548766 TTATAAAATGATTCAAAATAAT
1 TTATAAAA--ATTCAAAAT-AT
*
30548788 TT-TTAAAATTCAAAATAT
1 TTATAAAAATTCAAAATAT
*
30548806 TTATAAAAATTTCAAAATCT
1 TTATAAAAA-TTCAAAATAT
30548826 TTAT
1 TTAT
30548830 TTTTTATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.11
19 14 0.38
20 13 0.35
21 4 0.11
22 2 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATAAAAATTCAAAATAT
Found at i:30554980 original size:24 final size:21
Alignment explanation
Indices: 30554931--30554980 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 21
30554921 TCCAAAATAA
* *
30554931 TAAAAATTTAATTTAATTTTT
1 TAAAAATTTAATTTAAATTAT
30554952 TAAAAATTATAATATATAAATTAT
1 TAAAAATT-TAAT-T-TAAATTAT
30554976 TAAAA
1 TAAAA
30554981 TGATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 4 0.17
23 1 0.04
24 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAAATTTAATTTAAATTAT
Found at i:30566563 original size:6 final size:6
Alignment explanation
Indices: 30566554--30566582 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30566544 TATCCGAATC
30566554 CAATTT CAATTT CAATTT CAATTT CAATT
1 CAATTT CAATTT CAATTT CAATTT CAATT
30566583 CATTATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
CAATTT
Found at i:30569826 original size:12 final size:12
Alignment explanation
Indices: 30569802--30569842 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
30569792 GTATAATTTT
*
30569802 TAAAAGTTAAAA
1 TAAAAATTAAAA
30569814 TTAAAAA-TAAAA
1 -TAAAAATTAAAA
30569826 TAAAAATTAAAA
1 TAAAAATTAAAA
30569838 -AAAAA
1 TAAAAA
30569843 AAGAGAGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.42
12 10 0.38
13 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:30570422 original size:22 final size:22
Alignment explanation
Indices: 30570380--30570422 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
30570370 AAAAAAATAT
* *
30570380 ATATTTATATTATTTTAATTTA
1 ATATTTATATAATTTAAATTTA
30570402 ATATTTA-ATAATTTAATATTT
1 ATATTTATATAATTTAA-ATTT
30570423 TTTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTATATAATTTAAATTTA
Found at i:30570430 original size:15 final size:15
Alignment explanation
Indices: 30570382--30570431 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
30570372 AAAAATATAT
30570382 ATTT-ATATTATTTTA
1 ATTTAATATT-TTTTA
**
30570397 ATTTAATATTTAATA
1 ATTTAATATTTTTTA
*
30570412 ATTTAATATTTTTTT
1 ATTTAATATTTTTTA
30570427 ATTTA
1 ATTTA
30570432 TTGAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATATTTTTTA
Found at i:30571970 original size:4 final size:4
Alignment explanation
Indices: 30571961--30571999 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
30571951 TTTCCCACTT
* * *
30571961 CATA CATA CATA CATA CATA CATG CATG CATG CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
30572000 CATTATAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:30572218 original size:16 final size:18
Alignment explanation
Indices: 30572180--30572219 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
30572170 AAAAAATATT
30572180 CTTTTAGTTTTTATTTAA
1 CTTTTAGTTTTTATTTAA
*
30572198 TTTTTAG-TTTT-TTTAA
1 CTTTTAGTTTTTATTTAA
30572214 CTTTTA
1 CTTTTA
30572220 AATTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.50
17 4 0.20
18 6 0.30
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
CTTTTAGTTTTTATTTAA
Found at i:30572317 original size:22 final size:21
Alignment explanation
Indices: 30572290--30572330 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
30572280 TGACATTTAA
*
30572290 ATTTTAAAATTTCAAAAAAACT
1 ATTTTAAAAATT-AAAAAAACT
30572312 ATTTTAAAAATTAAAAAAA
1 ATTTTAAAAATTAAAAAAA
30572331 TCATTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
ATTTTAAAAATTAAAAAAACT
Found at i:30575942 original size:2 final size:2
Alignment explanation
Indices: 30575935--30575967 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30575925 TCGTAGTTAC
30575935 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30575968 ATGTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30578452 original size:13 final size:13
Alignment explanation
Indices: 30578434--30578482 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
30578424 TATTTATTAA
30578434 ATAAAATA-AAATT
1 ATAAAATATAAA-T
30578447 ATAAAATATAAAT
1 ATAAAATATAAAT
30578460 ATAAAACTAATAAAAT
1 ATAAAA-T-AT-AAAT
30578476 ATAAAAT
1 ATAAAAT
30578483 TTGTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 15 0.47
14 4 0.12
15 3 0.09
16 10 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:30578902 original size:16 final size:16
Alignment explanation
Indices: 30578867--30578908 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30578857 TTGAATCAAT
*
30578867 TTTATCTATATTTTTAA
1 TTTATCAAT-TTTTTAA
30578884 TTT-TCAATTTTTATAA
1 TTTATCAATTTTT-TAA
30578900 TTTATCAAT
1 TTTATCAAT
30578909 AGTATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATCAATTTTTTAA
Found at i:30580866 original size:18 final size:18
Alignment explanation
Indices: 30580815--30580867 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
30580805 TGACATATAA
30580815 ATATCATATAT-AAAAAAT
1 ATAT-ATATATAAAAAAAT
* *
30580833 ATATATTTCCAAAAAAAAAT
1 ATATATAT--ATAAAAAAAT
30580853 ATATATATATAAAAA
1 ATATATATATAAAAA
30580868 TTAGTTGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 3 0.11
18 10 0.36
19 1 0.04
20 14 0.50
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAAAAAT
Found at i:30580866 original size:20 final size:20
Alignment explanation
Indices: 30580826--30580867 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30580816 TATCATATAT
* *
30580826 AAAAAATATATATTTCCAAA
1 AAAAAATATATATATACAAA
*
30580846 AAAAAATATATATATATAAA
1 AAAAAATATATATATACAAA
30580866 AA
1 AA
30580868 TTAGTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATATATATATACAAA
Found at i:30590242 original size:18 final size:18
Alignment explanation
Indices: 30590209--30590266 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
30590199 AAGGTTTTCT
30590209 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
30590224 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
* *
30590242 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
30590260 TATTGAT
1 TATTGAT
30590267 CGTGACCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
18 26 0.68
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:30595124 original size:43 final size:43
Alignment explanation
Indices: 30595065--30595147 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
30595055 TTAAATAATT
* * *
30595065 TTTTTTGAATAATTTAATAACTTAAATAAACACTTTCAAAGAA
1 TTTTTTAAATAATTTAATAACTTAAATAAAAACTATCAAAGAA
*
30595108 TTTTTTAAATAATTTAATAATTTAAATAAAAACTATCAAA
1 TTTTTTAAATAATTTAATAACTTAAATAAAAACTATCAAA
30595148 TAAATTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (43 bp):
TTTTTTAAATAATTTAATAACTTAAATAAAAACTATCAAAGAA
Found at i:30595916 original size:13 final size:13
Alignment explanation
Indices: 30595882--30595921 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
30595872 GGACTTTGAC
30595882 AAAATAATATATT
1 AAAATAATATATT
*
30595895 AAAGTAATA-ATT
1 AAAATAATATATT
30595907 AAAATAA-ATA-T
1 AAAATAATATATT
30595918 AAAA
1 AAAA
30595922 CATGTGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 6 0.25
12 10 0.42
13 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATAATATATT
Found at i:30600040 original size:19 final size:19
Alignment explanation
Indices: 30600009--30600080 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
30599999 AGAATTATAA
*
30600009 ATTTTAGAATTTTTATAAAT
1 ATTTTA-AATTTTTAAAAAT
*
30600029 ATTTTAAATTTTAAAAAAT
1 ATTTTAAATTTTTAAAAAT
*
30600048 ATTTT-GATATTTTAAAAATT
1 ATTTTAAAT-TTTTAAAAA-T
*
30600068 ATTTTGAATTTTT
1 ATTTTAAATTTTT
30600081 TTTTAGAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.05
19 24 0.55
20 16 0.36
21 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAAAT
Found at i:30606118 original size:18 final size:19
Alignment explanation
Indices: 30606097--30606134 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
30606087 AATTAACCAA
30606097 ATTAAATCAA-TTTAATCG
1 ATTAAATCAATTTTAATCG
*
30606115 ATTAATTCAATTTTAATCG
1 ATTAAATCAATTTTAATCG
30606134 A
1 A
30606135 AATTTGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTAAATCAATTTTAATCG
Found at i:30619404 original size:6 final size:6
Alignment explanation
Indices: 30619393--30619430 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
30619383 ACATCTATGA
30619393 CATTAG CATTAG CATTAG CATTAG CATTAG CATTAG CA
1 CATTAG CATTAG CATTAG CATTAG CATTAG CATTAG CA
30619431 ACCAAGAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (6 bp):
CATTAG
Found at i:30635396 original size:17 final size:17
Alignment explanation
Indices: 30635362--30635395 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30635352 TCTCAAATTA
30635362 TAAAAATAAATATATTT
1 TAAAAATAAATATATTT
*
30635379 TAAAATTAAATAT-TTT
1 TAAAAATAAATATATTT
30635395 T
1 T
30635396 TTGAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATAAATATATTT
Found at i:30638700 original size:19 final size:19
Alignment explanation
Indices: 30638673--30638721 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
30638663 AAATAAATAA
* * *
30638673 AATTGTAAACATCATAGAC
1 AATTTTAAAAATCATAAAC
*
30638692 AATTTTAAAAATTATAAAC
1 AATTTTAAAAATCATAAAC
*
30638711 AATATTAAAAA
1 AATTTTAAAAA
30638722 ATACACAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (19 bp):
AATTTTAAAAATCATAAAC
Found at i:30639910 original size:27 final size:26
Alignment explanation
Indices: 30639880--30639932 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
30639870 TTAAAATATG
*
30639880 AAATATAGAAAAATTAAATTCTTAAAA
1 AAATATAGAAAAACTAAATTC-TAAAA
*
30639907 AAATATATAAAAACTAAATTCTAAAA
1 AAATATAGAAAAACTAAATTCTAAAA
30639933 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATATAGAAAAACTAAATTCTAAAA
Found at i:30648424 original size:191 final size:191
Alignment explanation
Indices: 30648100--30648484 Score: 770
Period size: 191 Copynumber: 2.0 Consensus size: 191
30648090 AATGTGGATT
30648100 CTGATGTCATTGCTTGCGTTGCCGAACACCATTAAGCAGTTCATTTCTGGCCGCCAATACACTCG
1 CTGATGTCATTGCTTGCGTTGCCGAACACCATTAAGCAGTTCATTTCTGGCCGCCAATACACTCG
30648165 AAAACAGGGCATCCACTTGCTTTTCCAAAGCATCCATCTCCTTCTCGAAAACACCTAACTTTCCA
66 AAAACAGGGCATCCACTTGCTTTTCCAAAGCATCCATCTCCTTCTCGAAAACACCTAACTTTCCA
30648230 CCCAGATCCATGGCTGCATCACTGGTTTTCCCAGAAGGGATTGCTGATACTAGGGCATTTG
131 CCCAGATCCATGGCTGCATCACTGGTTTTCCCAGAAGGGATTGCTGATACTAGGGCATTTG
30648291 CTGATGTCATTGCTTGCGTTGCCGAACACCATTAAGCAGTTCATTTCTGGCCGCCAATACACTCG
1 CTGATGTCATTGCTTGCGTTGCCGAACACCATTAAGCAGTTCATTTCTGGCCGCCAATACACTCG
30648356 AAAACAGGGCATCCACTTGCTTTTCCAAAGCATCCATCTCCTTCTCGAAAACACCTAACTTTCCA
66 AAAACAGGGCATCCACTTGCTTTTCCAAAGCATCCATCTCCTTCTCGAAAACACCTAACTTTCCA
30648421 CCCAGATCCATGGCTGCATCACTGGTTTTCCCAGAAGGGATTGCTGATACTAGGGCATTTG
131 CCCAGATCCATGGCTGCATCACTGGTTTTCCCAGAAGGGATTGCTGATACTAGGGCATTTG
30648482 CTG
1 CTG
30648485 CACTGTTCAG
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 194 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (191 bp):
CTGATGTCATTGCTTGCGTTGCCGAACACCATTAAGCAGTTCATTTCTGGCCGCCAATACACTCG
AAAACAGGGCATCCACTTGCTTTTCCAAAGCATCCATCTCCTTCTCGAAAACACCTAACTTTCCA
CCCAGATCCATGGCTGCATCACTGGTTTTCCCAGAAGGGATTGCTGATACTAGGGCATTTG
Found at i:30658213 original size:13 final size:13
Alignment explanation
Indices: 30658195--30658221 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30658185 CCAGGATATC
30658195 TGAGCAACAAAGT
1 TGAGCAACAAAGT
30658208 TGAGCAACAAAGT
1 TGAGCAACAAAGT
30658221 T
1 T
30658222 AATCAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (13 bp):
TGAGCAACAAAGT
Found at i:30667833 original size:30 final size:30
Alignment explanation
Indices: 30667792--30667852 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
30667782 TTAAATTTTT
*
30667792 AATAATTAAATTAT-ATTTTAATTTTTTAAA
1 AATAATAAAATTATGA-TTTAATTTTTTAAA
*
30667822 AATAATAAAATTTTGATTTAATTTTTTAAA
1 AATAATAAAATTATGATTTAATTTTTTAAA
30667852 A
1 A
30667853 TTTACAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AATAATAAAATTATGATTTAATTTTTTAAA
Found at i:30667870 original size:17 final size:15
Alignment explanation
Indices: 30667848--30667907 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 15
30667838 TTTAATTTTT
30667848 TAAAATTTACAACAATA
1 TAAAATTTA-AA-AATA
30667865 TAAAATATTAAAAATAA
1 TAAAAT-TTAAAAAT-A
30667882 TAAAATTATAAAAATA
1 TAAAATT-TAAAAATA
*
30667898 TATAATTTAA
1 TAAAATTTAA
30667908 TTTTACGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 3 0.08
16 11 0.28
17 22 0.56
18 3 0.08
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATTTAAAAATA
Found at i:30669002 original size:18 final size:16
Alignment explanation
Indices: 30668968--30669016 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
30668958 TCGATTGTAA
*
30668968 TTAATTTAAAAATTTTAA
1 TTAA-TTAAAAA-TTTAT
30668986 TTAATT--AAATTTAT
1 TTAATTAAAAATTTAT
30669000 TTAATTAAAAATTTAT
1 TTAATTAAAAATTTAT
30669016 T
1 T
30669017 CTCATCCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 9 0.32
17 2 0.07
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTAAAAATTTAT
Found at i:30671049 original size:39 final size:41
Alignment explanation
Indices: 30670982--30671067 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 41
30670972 GCATTAAAAA
* * *
30670982 ATTAAAAAACACTATCATAAATATAATAAATGGTTTATTAT
1 ATTAAAAAACACTATAATAAATACAATAAATAGTTTATTAT
* *
30671023 ATTAAAAAACAC-A-AATAAATACAATAAATATTTTATTGT
1 ATTAAAAAACACTATAATAAATACAATAAATAGTTTATTAT
30671062 ATTAAA
1 ATTAAA
30671068 TATAATTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 27 0.68
40 1 0.03
41 12 0.30
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (41 bp):
ATTAAAAAACACTATAATAAATACAATAAATAGTTTATTAT
Found at i:30672082 original size:13 final size:14
Alignment explanation
Indices: 30672062--30672101 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
30672052 AAAATAGTAT
30672062 ATATTATTTATTTC
1 ATATTATTTATTTC
*
30672076 A-ATTATTTATTTT
1 ATATTATTTATTTC
*
30672089 ATTTTATTTATTT
1 ATATTATTTATTT
30672102 TTATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
ATATTATTTATTTC
Found at i:30672097 original size:14 final size:13
Alignment explanation
Indices: 30672064--30672107 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
30672054 AATAGTATAT
*
30672064 ATTATTTATTTCA
1 ATTATTTATTTTA
30672077 ATTATTTATTTTA
1 ATTATTTATTTTA
* *
30672090 TTTTATTTATTTTT
1 -ATTATTTATTTTA
30672104 ATTA
1 ATTA
30672108 AAAAAGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:30677844 original size:21 final size:21
Alignment explanation
Indices: 30677815--30677865 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
30677805 TTTCACTTTC
30677815 ATACTTTAATTTTTTTAAATTA
1 ATAC-TTAATTTTTTTAAATTA
* *
30677837 ATACTTAATTTTTTTAGATTG
1 ATACTTAATTTTTTTAAATTA
30677858 ATACTTAA
1 ATACTTAA
30677866 ATTAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (21 bp):
ATACTTAATTTTTTTAAATTA
Found at i:30677951 original size:13 final size:13
Alignment explanation
Indices: 30677935--30677968 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
30677925 GTTTTTTTAA
30677935 TTTTTTTTATTCT
1 TTTTTTTTATTCT
**
30677948 TTTTCATTATTCT
1 TTTTTTTTATTCT
30677961 TTTTTTTT
1 TTTTTTTT
30677969 TCTGGGCATG
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTATTCT
Found at i:30679720 original size:13 final size:13
Alignment explanation
Indices: 30679702--30679727 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30679692 ACCAGCTTTC
30679702 ATTCAAGCTAATA
1 ATTCAAGCTAATA
30679715 ATTCAAGCTAATA
1 ATTCAAGCTAATA
30679728 TTAATACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATTCAAGCTAATA
Found at i:30686574 original size:21 final size:20
Alignment explanation
Indices: 30686550--30686603 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 20
30686540 CCTCTTTCGC
30686550 CTTTTCTGCTGCTTCTTTCTT
1 CTTTTCT-CTGCTTCTTTCTT
30686571 C-TTTCTCT-CTTC-TTCTT
1 CTTTTCTCTGCTTCTTTCTT
*
30686588 -TTTTCTCAGCTTCTTT
1 CTTTTCTCTGCTTCTTT
30686604 TTGTTTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 8 0.28
19 4 0.14
20 5 0.17
21 1 0.03
ACGTcount: A:0.02, C:0.30, G:0.06, T:0.63
Consensus pattern (20 bp):
CTTTTCTCTGCTTCTTTCTT
Found at i:30686600 original size:18 final size:17
Alignment explanation
Indices: 30686560--30686611 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
30686550 CTTTTCTGCT
*
30686560 GCTTCTTTCTTCTTTCTC
1 GCTTC-TTCTTTTTTCTC
*
30686578 TCTTCTTCTTTTTTCTC
1 GCTTCTTCTTTTTTCTC
30686595 AGCTTCTT-TTTGTTTCT
1 -GCTTCTTCTTT-TTTCT
30686612 TGATTTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.02, C:0.27, G:0.06, T:0.65
Consensus pattern (17 bp):
GCTTCTTCTTTTTTCTC
Found at i:30689598 original size:56 final size:56
Alignment explanation
Indices: 30689512--30689626 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
30689502 AATAACAAGA
30689512 TATCAGATTTACCAGAAGAAAATAGTGTTATTCTACTAGCCCTGAGGTTGAGCTAC
1 TATCAGATTTACCAGAAGAAAATAGTGTTATTCTACTAGCCCTGAGGTTGAGCTAC
30689568 TATCAGATTTACCAGAAGAAAATAGTGTTATTCTACTAGCCCTGAGGTTGAGCTAC
1 TATCAGATTTACCAGAAGAAAATAGTGTTATTCTACTAGCCCTGAGGTTGAGCTAC
30689624 TAT
1 TAT
30689627 TATCTTCCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (56 bp):
TATCAGATTTACCAGAAGAAAATAGTGTTATTCTACTAGCCCTGAGGTTGAGCTAC
Found at i:30691621 original size:116 final size:118
Alignment explanation
Indices: 30691479--30692009 Score: 393
Period size: 123 Copynumber: 4.4 Consensus size: 118
30691469 AAAAAAAAAA
* * **
30691479 TTGGTTTTGGCCATGCAATGGTCGACACCCCCTTTTTTATCTGATAGGAAA-AAAATTTT-GTGT
1 TTGGTATTGGCCATGCAATGGCCGACA-CCCCTTTTTTATCTGATAAAAAATAAAATTTTGGTGT
* * * *
30691542 TAGCCAT-TGCATGGTTGACACCCCATTTTTTGTCAGAT-AAAAAA-TTT-AATTTT
65 TAGCCATGT-AATGGTCGACACCCC-CTTTTT-TCAGATAAAAAAATTTTAAACTTT
* *
30691595 TTGGTATTGGCCATGCAATGGCCGACACTCC-TATTTATCTGATAAAAAATTAAAATTTTGGGTG
1 TTGGTATTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATAAAAAA-TAAAATTTT-GGTG
*
30691659 TTGGCCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTTAAAACTTT
64 TTAGCCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTT-AAACTTT
* * * * *
30691715 TTGGTGTTGGCCATGCAATGGCCTACACCCCTTTTTT-GCAGATAAAAAAATTTTAAATTTTTTT
1 TTGGTATTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGAT-AAAAAA---TAAA--ATTTT
* ** * * *
30691779 TGTGTT-GACCATGCCATGGTCGACACCCTCTTTTTACAGATAAAAAAATTTTAAAATTT
60 GGTGTTAG-CCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTTAAACTTT
* * * * ** * * *
30691838 TTTGTGTTGGTCATGCCATGATCGACACCCCCTTTTTATTTGGTAAAAAATTTTAAAATTTTTTG
1 TTGGTATTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATAAAAAA---TAAAA--TTTTG
* ** * * *
30691903 GTGTTGGCCATGTAATGCCCAACA-CCCC-TTTTTCAGAT-AAAAAATTTCAAATTTTT
61 GTGTTAGCCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTTAAA-CTTT
* * * ** * * *
30691959 TTGGTGTTGGTCATGCCATGATCGACACCCCCTTTTTATTTGGTAAAAAAT
1 TTGGTATTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATAAAAAAT
30692010 TAATTTTTTT
Statistics
Matches: 347, Mismatches: 47, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
114 15 0.04
115 3 0.01
116 39 0.11
117 11 0.03
118 27 0.08
119 1 0.00
120 49 0.14
121 71 0.20
122 3 0.01
123 76 0.22
124 48 0.14
125 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (118 bp):
TTGGTATTGGCCATGCAATGGCCGACACCCCTTTTTTATCTGATAAAAAATAAAATTTTGGTGTT
AGCCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTTAAACTTT
Found at i:30691735 original size:62 final size:61
Alignment explanation
Indices: 30691479--30691995 Score: 460
Period size: 62 Copynumber: 8.6 Consensus size: 61
30691469 AAAAAAAAAA
* * **
30691479 TTGGTTTTGGCCATGCAATGGTCGACACCCCCTTTTTTATCTGATAGGAAA----AAAA--TT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCC-TTTTT-TCAGATAAAAAATTTTAAAATTTT
* * *
30691536 TT-GTGTTAGCCATTGC-ATGGTTGACACCCCATTTTTTGTCAGATAAAAAA-TTT--AATTTT
1 TTGGTGTTGGCCA-TGCAATGGTCGACACCCC-CTTTTT-TCAGATAAAAAATTTTAAAATTTT
* * * * *
30691595 TTGGTATTGGCCATGCAATGGCCGACA-CTCCTATTTATCTGATAAAAAA--TTAAAA-TTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCT-TTTTTCAGATAAAAAATTTTAAAATTTT
* * *
30691653 TGGGTGTTGGCCATGTAATGGTCGACACCCCCTTTTTTCAGATAAAAAAATTTTAAAACTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTTCAGAT-AAAAAATTTTAAAATTTT
* * *
30691715 TTGGTGTTGGCCATGCAATGGCCTACA-CCCCTTTTTTGCAGATAAAAAAATTTTAAATTTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTT-CAGAT-AAAAAATTTTAAAATTTT
* * * * *
30691777 TTTGTGTTGACCATGCCATGGTCGACACCCTCTTTTTACAGATAAAAAAATTTTAAAATTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTTCAGAT-AAAAAATTTTAAAATTTT
* * * ** *
30691839 TT-GTGTTGGTCATGCCATGATCGACACCCCCTTTTTATTTGGTAAAAAATTTTAAAATTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTT-TCAGATAAAAAATTTTAAAATTTT
* ** * * *
30691900 TTGGTGTTGGCCATGTAATGCCCAACA-CCCC-TTTTTCAGATAAAAAATTTCAAATTTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTTCAGATAAAAAATTTTAAAATTTT
* * *
30691959 TTGGTGTTGGTCATGCCATGATCGACACCCCCTTTTT
1 TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTT
30691996 ATTTGGTAAA
Statistics
Matches: 375, Mismatches: 62, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
56 35 0.09
57 9 0.02
58 46 0.12
59 64 0.17
60 24 0.06
61 74 0.20
62 115 0.31
63 8 0.02
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (61 bp):
TTGGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTTCAGATAAAAAATTTTAAAATTTT
Found at i:30691886 original size:123 final size:121
Alignment explanation
Indices: 30691569--30692010 Score: 456
Period size: 123 Copynumber: 3.7 Consensus size: 121
30691559 ACACCCCATT
* * * ** * *
30691569 TTTTGTCAGAT-AAAAAA-TTT--AATTTTTTGGTATTGGCCATGCAATGGCCGACA-CTCCTAT
1 TTTT-TCAGATAAAAAAATTTTAAAATTTTTT-GTGTTGGTCATGCCATGATCGACACCCCCTTT
* * *
30691629 TTATCTGATAAAAAA--TTAAAA-TTTTGGGTGTTGGCCATGTAATGGTCGACACCCCC
64 TTATTTGGTAAAAAATTTTAAAATTTTTTGGTGTTGGCCATGTAATGGTCGACA-CCCC
* * * ** *
30691685 TTTTTTCAGATAAAAAAATTTTAAAACTTTTTGGTGTTGGCCATGCAATGGCCTACA-CCCCTTT
1 -TTTTTCAGATAAAAAAATTTTAAAA-TTTTTTGTGTTGGTCATGCCATGATCGACACCCCCTTT
** * * * * **
30691749 TT-TGCAGATAAAAAAATTTTAAATTTTTTTTGTGTTGACCATGCCATGGTCGACACCCTC
64 TTAT-TTGGT-AAAAAATTTTAAAATTTTTTGGTGTTGGCCATGTAATGGTCGACACCC-C
30691809 TTTTTACAGATAAAAAAATTTTAAAATTTTTTGTGTTGGTCATGCCATGATCGACACCCCCTTTT
1 TTTTT-CAGATAAAAAAATTTTAAAATTTTTTGTGTTGGTCATGCCATGATCGACACCCCCTTTT
** *
30691874 TATTTGGTAAAAAATTTTAAAATTTTTTGGTGTTGGCCATGTAATGCCCAACACCCC
65 TATTTGGTAAAAAATTTTAAAATTTTTTGGTGTTGGCCATGTAATGGTCGACACCCC
* *
30691931 TTTTTCAGAT-AAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCCATGATCGACACCCCCTTTT
1 TTTTTCAGATAAAAAAATTTTAAAATTTTTT-GTGTTGGTCATGCCATGATCGACACCCCCTTTT
30691995 TATTTGGTAAAAAATT
65 TATTTGGTAAAAAATT
30692011 AATTTTTTTA
Statistics
Matches: 279, Mismatches: 31, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
116 6 0.02
117 10 0.04
118 3 0.01
119 1 0.00
120 53 0.19
121 65 0.23
122 6 0.02
123 77 0.28
124 57 0.20
125 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (121 bp):
TTTTTCAGATAAAAAAATTTTAAAATTTTTTGTGTTGGTCATGCCATGATCGACACCCCCTTTTT
ATTTGGTAAAAAATTTTAAAATTTTTTGGTGTTGGCCATGTAATGGTCGACACCCC
Found at i:30692822 original size:17 final size:17
Alignment explanation
Indices: 30692800--30692854 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
30692790 TTAAAAAAAT
30692800 AATTAGAATATACAAGA
1 AATTAGAATATACAAGA
*
30692817 AATTAGAA-A-A-TA-A
1 AATTAGAATATACAAGA
* *
30692830 AATTAAAATATACAGGA
1 AATTAGAATATACAAGA
30692847 AATTAGAA
1 AATTAGAA
30692855 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 8 0.28
14 2 0.07
15 2 0.07
16 1 0.03
17 16 0.55
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.24
Consensus pattern (17 bp):
AATTAGAATATACAAGA
Found at i:30692840 original size:30 final size:30
Alignment explanation
Indices: 30692787--30692897 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
30692777 AAGATGATAT
*
30692787 AAATTA-AAAA-AATAATTAGAATATACAAG
1 AAATTAGAAAATAA-AATTAAAATATACAAG
*
30692816 AAATTAGAAAATAAAATTAAAATATACAGG
1 AAATTAGAAAATAAAATTAAAATATACAAG
* * *
30692846 AAATTAGAAATTAAATTTAAAATA-AAAACG
1 AAATTAGAAAATAAAATTAAAATATACAA-G
* * *
30692876 AAATTACAAATTAAATTTAAAA
1 AAATTAGAAAATAAAATTAAAA
30692898 AGTAAACGGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.11
30 62 0.86
31 2 0.03
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (30 bp):
AAATTAGAAAATAAAATTAAAATATACAAG
Found at i:30693356 original size:12 final size:12
Alignment explanation
Indices: 30693341--30693371 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
30693331 TTGGAGATCG
30693341 GGTTGGTACTCC
1 GGTTGGTACTCC
*
30693353 GGTTGGTACTCG
1 GGTTGGTACTCC
30693365 GGTTGGT
1 GGTTGGT
30693372 CCTGAGCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.42, T:0.35
Consensus pattern (12 bp):
GGTTGGTACTCC
Found at i:30693404 original size:12 final size:12
Alignment explanation
Indices: 30693387--30693478 Score: 51
Period size: 12 Copynumber: 7.7 Consensus size: 12
30693377 GCCTCGTAAT
30693387 CGGGCTCATCAG
1 CGGGCTCATCAG
* *
30693399 CGGGCTCGTTAG
1 CGGGCTCATCAG
* *
30693411 TGGGCTCGTTC-G
1 CGGGCTC-ATCAG
30693423 CGGGCTCATCAG
1 CGGGCTCATCAG
** * *
30693435 TAGGCTCGTTAG
1 CGGGCTCATCAG
* *
30693447 CGGGCTCGTCAT
1 CGGGCTCATCAG
* **
30693459 TGGGCTCATCCT
1 CGGGCTCATCAG
30693471 CGGGCTCA
1 CGGGCTCA
30693479 AAATCTGAAC
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 2 0.03
12 56 0.95
13 1 0.02
ACGTcount: A:0.11, C:0.29, G:0.35, T:0.25
Consensus pattern (12 bp):
CGGGCTCATCAG
Found at i:30693415 original size:24 final size:24
Alignment explanation
Indices: 30693388--30693477 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
30693378 CCTCGTAATC
*
30693388 GGGCTCATCAGCGGGCTCGTTAGT
1 GGGCTCATCAGCGGGCTCGTCAGT
* *
30693412 GGGCTCGTTC-GCGGGCTCATCAGT
1 GGGCTC-ATCAGCGGGCTCGTCAGT
* * * *
30693436 AGGCTCGTTAGCGGGCTCGTCATT
1 GGGCTCATCAGCGGGCTCGTCAGT
**
30693460 GGGCTCATCCTCGGGCTC
1 GGGCTCATCAGCGGGCTC
30693478 AAAATCTGAA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 1 0.02
24 48 0.94
25 2 0.04
ACGTcount: A:0.10, C:0.29, G:0.36, T:0.26
Consensus pattern (24 bp):
GGGCTCATCAGCGGGCTCGTCAGT
Found at i:30693427 original size:36 final size:36
Alignment explanation
Indices: 30693387--30693455 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
30693377 GCCTCGTAAT
* *
30693387 CGGGCTCATCAGCGGGCTCGTTAGTGGGCTCGTTCG
1 CGGGCTCATCAGCAGGCTCGTTAGCGGGCTCGTTCG
*
30693423 CGGGCTCATCAGTAGGCTCGTTAGCGGGCTCGT
1 CGGGCTCATCAGCAGGCTCGTTAGCGGGCTCGT
30693456 CATTGGGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.25
Consensus pattern (36 bp):
CGGGCTCATCAGCAGGCTCGTTAGCGGGCTCGTTCG
Found at i:30693477 original size:36 final size:36
Alignment explanation
Indices: 30693379--30693477 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 36
30693369 GGTCCTGAGC
* *
30693379 CTCGTAATCGGGCTCATCAGCGGGCTCGTTAGTGGG
1 CTCGTCATCGGGCTCATCAGCGGGCTCGTTAGCGGG
* **
30693415 CTCGTTC-GCGGGCTCATCAGTAGGCTCGTTAGCGGG
1 CTCG-TCATCGGGCTCATCAGCGGGCTCGTTAGCGGG
* **
30693451 CTCGTCATTGGGCTCATCCTCGGGCTC
1 CTCGTCATCGGGCTCATCAGCGGGCTC
30693478 AAAATCTGAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
35 2 0.04
36 47 0.94
37 1 0.02
ACGTcount: A:0.11, C:0.29, G:0.33, T:0.26
Consensus pattern (36 bp):
CTCGTCATCGGGCTCATCAGCGGGCTCGTTAGCGGG
Found at i:30694154 original size:20 final size:21
Alignment explanation
Indices: 30694129--30694168 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30694119 TTTAAAAATC
*
30694129 CGAAAATA-TAAAAAATATTT
1 CGAAAATAGAAAAAAATATTT
30694149 CGAAAATAGAAAAAAATATT
1 CGAAAATAGAAAAAAATATT
30694169 ATTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (21 bp):
CGAAAATAGAAAAAAATATTT
Found at i:30695965 original size:84 final size:84
Alignment explanation
Indices: 30695325--30695957 Score: 1070
Period size: 84 Copynumber: 7.5 Consensus size: 84
30695315 TAAATTTAAA
* **
30695325 ATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATGAAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
30695390 ATTGTTAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
30695409 ATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
30695474 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
30695493 ATTTGATAAAAATTATAATATAATAATAATTTTTGATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
30695558 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
** *
30695577 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTT-GATAAATAATA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAG-TAAATAATG
30695641 TATTGTCAAATCAACACATT
65 TATTGTCAAATCAACACATT
* *
30695661 ATTTGATAAAAATTTTAATATAATAATATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
30695726 ATTGTCAAATCAATACATT
66 ATTGTCAAATCAACACATT
*
30695745 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
30695810 ATTGTCAAATCAACATATT
66 ATTGTCAAATCAACACATT
*
30695829 ATTTAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
30695894 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
30695913 ATTTGATAAAAATTGTAATATAATAATATTTTTTTATTTACATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAT
30695958 GAAAATTTGA
Statistics
Matches: 518, Mismatches: 29, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
83 1 0.00
84 516 1.00
85 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
ATTGTCAAATCAACACATT
Found at i:30696397 original size:118 final size:118
Alignment explanation
Indices: 30696213--30696465 Score: 343
Period size: 118 Copynumber: 2.1 Consensus size: 118
30696203 GAGAGTGTTG
* * *
30696213 CATGGCCAACACTAAAAAATTTTGAAATTTTTTTATCTGAAAAAGGGGCGTCGGCCATTGCATGG
1 CATGGCCAACACCAAAAAA-TTTGAAATTTTTTTATCTGAAAAAGGGACGTCGACCATTGCATGG
* *
30696278 TCAACATCGAAAAATTTGATTTTTTTATCAGA-TAAATAGGGGTGTCGACCATTA
65 TCAACACCGAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA-TA
*
30696332 CATGGCCAACACCAAAAAA-TTG-AA-TTTTTTATCTGACAAAAAAGGGATGTCGACCATTGCAT
1 CATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTG---AAAAAGGGACGTCGACCATTGCAT
* * *
30696394 GGTCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGGCCATG
63 GGTCAACACCGAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCATA
30696450 CAATGGCCAACACCAA
1 C-ATGGCCAACACCAA
30696466 TTTTTTTTTT
Statistics
Matches: 120, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
115 11 0.09
116 2 0.02
117 3 0.03
118 55 0.46
119 49 0.41
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (118 bp):
CATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGAAAAAGGGACGTCGACCATTGCATGGT
CAACACCGAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCATA
Found at i:30696443 original size:60 final size:60
Alignment explanation
Indices: 30696210--30696463 Score: 270
Period size: 59 Copynumber: 4.3 Consensus size: 60
30696200 AAAGAGAGTG
* * *
30696210 TTGCATGGCCAACA-CTAAAAAATTTTGAAATTTTTTTATC---TGAAAAAGGGGCGTCGGCCA
1 TTGCATGGCCAACACCT-AAAAA-TTTG--ATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA
* * * *
30696270 TTGCATGGTCAACATCGAAAAATTTGATTTTTTTATCAGA-TAAATAGGGGTGTCGACCA
1 TTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA
* * * * ** *
30696329 TTACATGGCCAACACC-AAAAAATTGAATTTTTTATCTGACAAAAAAGGGATGTCGACCA
1 TTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA
* *
30696388 TTGCATGGTCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGGCCA
1 TTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA
30696448 -TGCAATGGCCAACACC
1 TTGC-ATGGCCAACACC
30696464 AATTTTTTTT
Statistics
Matches: 162, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
57 11 0.07
58 20 0.12
59 65 0.40
60 65 0.40
61 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (60 bp):
TTGCATGGCCAACACCTAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGTCGACCA
Found at i:30698099 original size:108 final size:109
Alignment explanation
Indices: 30697909--30698126 Score: 321
Period size: 108 Copynumber: 2.0 Consensus size: 109
30697899 TGCCGAAATG
* *
30697909 AGAAAGGTGCATGTTGGCCAATTATTTCTAACCTTCCTCGTGTGAGGATAAATTATGTTGACATC
1 AGAAAGGTGCATATTGGCCAATTATTTCTAACCTTCATCGTGTGAGGATAAATTATGTTGACATC
* *
30697974 CTCTGAACAAGAACAAGCAGATTGCATTTCTAGATGGATAGCAA
66 CTCTGAACAAGAACAAGCAGATTGCATTGCTAGATGGACAGCAA
* * * ** *
30698018 AGAAAGGTGCATATTGGCCTATTATTTCTCACCTTCAT-TTGTGAGGATATGTTATGTTGATATC
1 AGAAAGGTGCATATTGGCCAATTATTTCTAACCTTCATCGTGTGAGGATAAATTATGTTGACATC
* *
30698082 TTCTGAACAAGCACAAGCAGATTGCATTGCTAGATGGACAGCAA
66 CTCTGAACAAGAACAAGCAGATTGCATTGCTAGATGGACAGCAA
30698126 A
1 A
30698127 AACCAATTGC
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 63 0.65
109 34 0.35
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (109 bp):
AGAAAGGTGCATATTGGCCAATTATTTCTAACCTTCATCGTGTGAGGATAAATTATGTTGACATC
CTCTGAACAAGAACAAGCAGATTGCATTGCTAGATGGACAGCAA
Found at i:30704552 original size:108 final size:108
Alignment explanation
Indices: 30704358--30704561 Score: 302
Period size: 108 Copynumber: 1.9 Consensus size: 108
30704348 AAATGAGAAA
* *
30704358 GGTGCATATTGGTCAATTATTTCTAACCTTCCTCGTGTGAGGATAAATTTTGTTGACATCCTCTG
1 GGTGCATATTGGCCAATTATTTCTAACCTTCCTC-TGTGAGGATAAATTATGTTGACATCCTCTG
* *
30704423 AACAAGAACAAGCAGATTGCATTTCTAGATGGATATCAATGAAT
65 AACAAGAACAAGCAGACTGCATTCCTAGATGGATATCAATGAAT
** * *
30704467 GGTGCATATTGGCCTCTTATTTCTCACCTTCACT-TGTGAGGATAAATTATGTTGACATCTTCTG
1 GGTGCATATTGGCCAATTATTTCTAACCTTC-CTCTGTGAGGATAAATTATGTTGACATCCTCTG
*
30704531 AACAAGCACAAGCAGACTGCATTCCTAGATG
65 AACAAGAACAAGCAGACTGCATTCCTAGATG
30704562 AACAGCAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 56 0.66
109 27 0.32
110 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (108 bp):
GGTGCATATTGGCCAATTATTTCTAACCTTCCTCTGTGAGGATAAATTATGTTGACATCCTCTGA
ACAAGAACAAGCAGACTGCATTCCTAGATGGATATCAATGAAT
Found at i:30707565 original size:11 final size:11
Alignment explanation
Indices: 30707549--30707573 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30707539 TTTATTTTGG
30707549 AATTTGGATAC
1 AATTTGGATAC
30707560 AATTTGGATAC
1 AATTTGGATAC
30707571 AAT
1 AAT
30707574 GAGATCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:30713330 original size:18 final size:18
Alignment explanation
Indices: 30713307--30713341 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30713297 GATCATTGAA
30713307 TCAAAAATAAT-TAAAAAT
1 TCAAAAA-AATCTAAAAAT
30713325 TCAAAAAAATCTAAAAA
1 TCAAAAAAATCTAAAAA
30713342 AAATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
TCAAAAAAATCTAAAAAT
Found at i:30714922 original size:24 final size:25
Alignment explanation
Indices: 30714876--30714930 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
30714866 GGCCTCAAAA
* *
30714876 TTATTATTTTAAAAAAATTAAATTT
1 TTATAATTTTAAAAAAATCAAATTT
30714901 TTATAATTTTAAAAAAA-CAAATTT
1 TTATAATTTTAAAAAAATCAAATTT
30714925 TATATA
1 T-TATA
30714931 TATATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATAATTTTAAAAAAATCAAATTT
Found at i:30719777 original size:7 final size:7
Alignment explanation
Indices: 30719765--30719806 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
30719755 TCTAATATGC
30719765 TCCAGAG
1 TCCAGAG
30719772 TCCAGAG
1 TCCAGAG
30719779 TCCAGAG
1 TCCAGAG
30719786 TCCAGAG
1 TCCAGAG
30719793 TCCAGAG
1 TCCAGAG
30719800 TCCAGAG
1 TCCAGAG
30719807 CCTGCCTAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
TCCAGAG
Found at i:30729237 original size:81 final size:81
Alignment explanation
Indices: 30729140--30729302 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
30729130 TGTGGCATTA
30729140 GATCATTTGCTTGTTCTCCCACGTCCTTGACAATTCACTTTCTCCTTATTTATTAAACATACATA
1 GATCATTTGCTTGTTCTCCCACGTCCTTGACAATTCACTTTCTCCTTATTTATTAAACATACATA
30729205 CATCCCTTTACTTTAT
66 CATCCCTTTACTTTAT
30729221 GATCATTTGCTTGTTCTCCCACGTCCTTGACAATTCACTTTCTCCTTATTTATTAAACATACATA
1 GATCATTTGCTTGTTCTCCCACGTCCTTGACAATTCACTTTCTCCTTATTTATTAAACATACATA
30729286 CATCCCTTTACTTTAT
66 CATCCCTTTACTTTAT
30729302 G
1 G
30729303 GCATTGGGTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (81 bp):
GATCATTTGCTTGTTCTCCCACGTCCTTGACAATTCACTTTCTCCTTATTTATTAAACATACATA
CATCCCTTTACTTTAT
Found at i:30731634 original size:14 final size:16
Alignment explanation
Indices: 30731595--30731629 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
30731585 TTGTGTTTTA
*
30731595 TTCTCAAATAACATTT
1 TTCTCAATTAACATTT
30731611 TTCTCAATTAACATTT
1 TTCTCAATTAACATTT
30731627 TTC
1 TTC
30731630 AATTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (16 bp):
TTCTCAATTAACATTT
Found at i:30732768 original size:80 final size:79
Alignment explanation
Indices: 30732635--30732789 Score: 229
Period size: 80 Copynumber: 1.9 Consensus size: 79
30732625 TTTAGGGTGG
* * **
30732635 AAGTTAAATTATAATTTTTATTATAGTATAAATATAATTTTTAAAGGATTAAATAAAAAATTTAT
1 AAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTAAATAAAAAATTTAT
30732700 CATTTTTAAGGAGCT
66 CA-TTTTAAGGAGCT
* * *
30732715 AAGTTAAATTATAATTTTTATGATAGTAAAAATGTAATTTTTAAAAAATTAAATCAAAATTTTAT
1 AAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTAAATAAAAAATTTAT
*
30732780 TATTTTAAGG
66 CATTTTAAGG
30732790 GCCTAAAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 8 0.12
80 59 0.88
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (79 bp):
AAGTTAAATTATAATTTTTATGATAGTAAAAATATAATTTTTAAAAAATTAAATAAAAAATTTAT
CATTTTAAGGAGCT
Found at i:30739510 original size:16 final size:17
Alignment explanation
Indices: 30739491--30739527 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
30739481 ATAATCAAAT
*
30739491 AAAATAAAAT-TTGTAA
1 AAAATAAAATATGGTAA
30739507 AAAATAAAATATGGTAA
1 AAAATAAAATATGGTAA
30739524 AAAA
1 AAAA
30739528 AAGTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AAAATAAAATATGGTAA
Found at i:30740361 original size:18 final size:19
Alignment explanation
Indices: 30740338--30740399 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
30740328 GGATAATTTT
30740338 ATTTTTATA-TAAAAATTA
1 ATTTTTATAGTAAAAATTA
*
30740356 ATTTTTA-AGTCAAAATTA
1 ATTTTTATAGTAAAAATTA
* *
30740374 ATATTATTATATTAATAA-TA
1 AT-TT-TTATAGTAAAAATTA
30740394 ATTTTT
1 ATTTTT
30740400 TATTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 19 0.53
19 4 0.11
20 7 0.19
21 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTTATAGTAAAAATTA
Found at i:30748417 original size:17 final size:17
Alignment explanation
Indices: 30748395--30748427 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30748385 TTATGATTAA
30748395 TTATATTAATTTTATTT
1 TTATATTAATTTTATTT
*
30748412 TTATATTATTTTTATT
1 TTATATTAATTTTATT
30748428 AGTTTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATATTAATTTTATTT
Found at i:30753125 original size:27 final size:26
Alignment explanation
Indices: 30753088--30753138 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
30753078 TACAAATAAT
30753088 TATGACATATTTTAATCTAGTATAAAAA
1 TATGACATATTTTAAT-TA-TATAAAAA
30753116 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTTAATTATATAAA
30753139 TATAAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 10 0.43
28 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
TATGACATATTTTAATTATATAAAAA
Found at i:30753229 original size:17 final size:17
Alignment explanation
Indices: 30753207--30753242 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30753197 ATGACATTGA
30753207 TTATTACAAAAAAAAAT
1 TTATTACAAAAAAAAAT
* *
30753224 TTATTATAAAATAAAAT
1 TTATTACAAAAAAAAAT
30753241 TT
1 TT
30753243 GATTGTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATTACAAAAAAAAAT
Found at i:30753590 original size:6 final size:6
Alignment explanation
Indices: 30753579--30753607 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30753569 TTGAACCATG
30753579 ACTTCT ACTTCT ACTTCT ACTTCT ACTTC
1 ACTTCT ACTTCT ACTTCT ACTTCT ACTTC
30753608 AAATCCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (6 bp):
ACTTCT
Found at i:30754081 original size:19 final size:19
Alignment explanation
Indices: 30754049--30754086 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
30754039 TTTTATTTAA
*
30754049 TTTATAATTAATTTTAATT
1 TTTATAATTAATTTAAATT
30754068 TTTATAATGT-ATTTAAATT
1 TTTATAAT-TAATTTAAATT
30754087 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATAATTAATTTAAATT
Found at i:30770573 original size:19 final size:18
Alignment explanation
Indices: 30770522--30770579 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
30770512 TATAAAACAC
*
30770522 TTAAATAATTTATAAAAAT
1 TTAAATAA-TTATTAAAAT
*
30770541 ATTAAA-AATCATTAAAAT
1 -TTAAATAATTATTAAAAT
30770559 TTATAATAATTATTAGAAAT
1 TTA-AATAATTATTA-AAAT
30770579 T
1 T
30770580 AACTAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.09
18 10 0.31
19 9 0.28
20 10 0.31
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAATAATTATTAAAAT
Found at i:30788358 original size:20 final size:18
Alignment explanation
Indices: 30788325--30788363 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
30788315 GGATTTGTCC
*
30788325 TTACTAATTAATTAGTAA
1 TTACTAATTAATTAATAA
30788343 TTACATAATGTAATTAATAA
1 TTAC-TAAT-TAATTAATAA
30788363 T
1 T
30788364 GATAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (18 bp):
TTACTAATTAATTAATAA
Found at i:30802592 original size:18 final size:17
Alignment explanation
Indices: 30802559--30802592 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30802549 ACAATTTTTA
*
30802559 TTAAATTATAATTATTT
1 TTAAATTATAAATATTT
30802576 TTAAATATATAAATATT
1 TTAAAT-TATAAATATT
30802593 ACAAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATAAATATTT
Found at i:30805432 original size:17 final size:16
Alignment explanation
Indices: 30805412--30805466 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
30805402 AAAATATTTA
*
30805412 TAAAAATATAAAAATT
1 TAAAAATATAAAAAAT
30805428 CTAAAAATATATAAAAAT
1 -TAAAAATATA-AAAAAT
30805446 TAAAAAT-TAAAAAAAT
1 TAAAAATAT-AAAAAAT
30805462 TAAAA
1 TAAAA
30805467 CAATAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 12 0.34
17 18 0.51
18 5 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATATAAAAAAT
Found at i:30805440 original size:27 final size:26
Alignment explanation
Indices: 30805396--30805458 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
30805386 AATAATTTTT
*
30805396 AAATTTAAAATATTTATAAAAATATAA
1 AAATTTAAAATATATATAAAAAT-TAA
30805423 AAATTCTAAAA-ATATATAAAAATTAA
1 AAATT-TAAAATATATATAAAAATTAA
*
30805449 AAATTAAAAA
1 AAATTTAAAA
30805459 AATTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 4 0.12
26 8 0.24
27 16 0.48
28 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
AAATTTAAAATATATATAAAAATTAA
Found at i:30805567 original size:16 final size:16
Alignment explanation
Indices: 30805546--30805576 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30805536 TATTGAATTT
30805546 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
30805562 TTTCAAATTTATATG
1 TTTCAAATATATATG
30805577 TTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:30805862 original size:2 final size:2
Alignment explanation
Indices: 30805855--30805879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30805845 TTATAAATAA
30805855 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30805880 AAGACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30806304 original size:15 final size:16
Alignment explanation
Indices: 30806273--30806306 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30806263 ACCACATTTA
*
30806273 TTTCTTGCTTTCCTTC
1 TTTCTTGCTTTCATTC
30806289 TTTCTT-CTTTCATTC
1 TTTCTTGCTTTCATTC
30806304 TTT
1 TTT
30806307 TGTGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTCTTGCTTTCATTC
Found at i:30807534 original size:22 final size:23
Alignment explanation
Indices: 30807504--30807546 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
30807494 ATAATCATTT
30807504 AATAATTTTTTA-AATTTTAAAA
1 AATAATTTTTTATAATTTTAAAA
*
30807526 AATATTTTTTTATAATTTTAA
1 AATAATTTTTTATAATTTTAA
30807547 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATAATTTTTTATAATTTTAAAA
Found at i:30807595 original size:39 final size:39
Alignment explanation
Indices: 30807501--30807582 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 39
30807491 TACATAATCA
* *
30807501 TTTAATAATTTTTTAAATTTTAAAAAATATTTTTTTATAAT
1 TTTAATAA-TTTTT-AATTTTTAAAAATATGTTTTTATAAT
30807542 TTTAATAATTTTTAATTTTTAAAAATA-GTTTTTATAAT
1 TTTAATAATTTTTAATTTTTAAAAATATGTTTTTATAAT
30807580 TTT
1 TTT
30807583 TTTATCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
38 13 0.33
39 13 0.33
40 5 0.13
41 8 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (39 bp):
TTTAATAATTTTTAATTTTTAAAAATATGTTTTTATAAT
Found at i:30807601 original size:39 final size:39
Alignment explanation
Indices: 30807501--30807608 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
30807491 TACATAATCA
*
30807501 TTTAATAATTTTTTAAATTTTAAAAAATATTTTTTTATAAT
1 TTTAATAA-TTTTTAAATTTT-AAAAATATGTTTTTATAAT
*
30807542 TTTAATAATTTTTAATTTTTAAAAATA-GTTTTTATAAT
1 TTTAATAATTTTTAAATTTTAAAAATATGTTTTTATAAT
* * *
30807580 TTT-TTTATCATTTTAAATTTTATAAATAT
1 TTTAATAAT--TTTTAAATTTTAAAAATAT
30807609 AATTAAATGT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.05
38 13 0.22
39 23 0.40
40 11 0.19
41 8 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (39 bp):
TTTAATAATTTTTAAATTTTAAAAATATGTTTTTATAAT
Found at i:30809706 original size:12 final size:12
Alignment explanation
Indices: 30809689--30809732 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
30809679 GGCACATATT
30809689 CTTGCATGTTTA
1 CTTGCATGTTTA
*
30809701 CTTGCATGCTTA
1 CTTGCATGTTTA
*
30809713 ATAGTGCATGTTTA
1 CT--TGCATGTTTA
30809727 CTTGCA
1 CTTGCA
30809733 GTAAACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (12 bp):
CTTGCATGTTTA
Found at i:30811090 original size:58 final size:58
Alignment explanation
Indices: 30811003--30811148 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 58
30810993 ATATATTATA
* * *
30811003 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
* *
30811063 A-TTTTATTAAATTTTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
30811120 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
30811149 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
57 19 0.25
58 45 0.58
59 8 0.10
60 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:30811339 original size:16 final size:16
Alignment explanation
Indices: 30811318--30811357 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
30811308 TAAATTACTG
*
30811318 ATTACAG-TCCTATTGC
1 ATTACAGCT-CTATTCC
30811334 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
30811350 ATTACAGC
1 ATTACAGC
30811358 GAACCAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:30811595 original size:16 final size:16
Alignment explanation
Indices: 30811574--30811609 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
30811564 CGTTTGGTTC
30811574 GCTGTAATGAAATAGA
1 GCTGTAATGAAATAGA
*
30811590 GCTGTAATGGAATAGA
1 GCTGTAATGAAATAGA
30811606 GCTG
1 GCTG
30811610 CAATCAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.25
Consensus pattern (16 bp):
GCTGTAATGAAATAGA
Found at i:30811686 original size:44 final size:46
Alignment explanation
Indices: 30811595--30811688 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
30811585 ATAGAGCTGT
* *
30811595 AATGGAATAGAGCTGCAATCAGTAATTCAATTGTTTGGTTGATTGG
1 AATGGAATAGAGCTGCAATCAATAATTCAATTGTTTGGTTGAATGG
* *
30811641 AATGGAATAGAGCTGTAAT-AAT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGCAATCAATAATTCAAT-TGTTTGGTTGAATGG
30811685 AATG
1 AATG
30811689 ATGCTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 2 0.05
46 18 0.42
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (46 bp):
AATGGAATAGAGCTGCAATCAATAATTCAATTGTTTGGTTGAATGG
Done.