Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 12 of 147
Found at i:2486688 original size:19 final size:19
Alignment explanation
Indices: 2486664--2486700 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2486654 TGAAAATGGA
2486664 GTTGAATTTGACCATAAAC
1 GTTGAATTTGACCATAAAC
*
2486683 GTTGAATTTGATCATAAA
1 GTTGAATTTGACCATAAA
2486701 TGCAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
GTTGAATTTGACCATAAAC
Found at i:2487584 original size:2 final size:2
Alignment explanation
Indices: 2487577--2487619 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2487567 TTTCTAATTT
2487577 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
2487619 T
1 T
2487620 CTCTTTGGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2487697 original size:151 final size:151
Alignment explanation
Indices: 2487444--2487726 Score: 503
Period size: 151 Copynumber: 1.9 Consensus size: 151
2487434 AACAATTGAG
* * *
2487444 TATATATATATATATATTTATTTATTTATTTGGAGTTGGGAGAGGTTAGCCCCAAGAGATCTCTC
1 TATATATATATATATATATATATATCTATTTGGAGTTGGGAGAGGTTAGCCCCAAGAGATCTCTC
* *
2487509 GTTTTGTTCATCGAAAAAAGTTGTAATGAAAACGACCTTCTTGGAAGCTGCCCCTGCATTTCTAA
66 GTTTCGTGCATCGAAAAAAGTTGTAATGAAAACGACCTTCTTGGAAGCTGCCCCTGCATTTCTAA
2487574 TTTTATATATATATATATATA
131 TTTTATATATATATATATATA
*
2487595 TATATATATATATATATATATATATCTCTTTGGAGTTGGGAGAGGTTAGCCCCAAGAGATCTCTC
1 TATATATATATATATATATATATATCTATTTGGAGTTGGGAGAGGTTAGCCCCAAGAGATCTCTC
*
2487660 GTTTCGTGCATCGAAAAAAGTTGTAATGAAACCGACCTTCTTGGAAGCTGCCCCTGCATTTCTAA
66 GTTTCGTGCATCGAAAAAAGTTGTAATGAAAACGACCTTCTTGGAAGCTGCCCCTGCATTTCTAA
2487725 TT
131 TT
2487727 AATTACAATA
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 125 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (151 bp):
TATATATATATATATATATATATATCTATTTGGAGTTGGGAGAGGTTAGCCCCAAGAGATCTCTC
GTTTCGTGCATCGAAAAAAGTTGTAATGAAAACGACCTTCTTGGAAGCTGCCCCTGCATTTCTAA
TTTTATATATATATATATATA
Found at i:2488068 original size:17 final size:17
Alignment explanation
Indices: 2488043--2488075 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2488033 AATGCCCGTC
*
2488043 AAATCAATATTTATAAG
1 AAATAAATATTTATAAG
2488060 AAATAAATATTTATAA
1 AAATAAATATTTATAA
2488076 AATTATATTT
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:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATAAATATTTATAAG
Found at i:2495422 original size:3 final size:3
Alignment explanation
Indices: 2495414--2495448 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2495404 GGATAATTTT
2495414 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2495449 GATGATGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2496003 original size:35 final size:35
Alignment explanation
Indices: 2495958--2496025 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
2495948 ATAAGGATAA
2495958 TAAAAATAAAATAAATAAA-AATATTATATAAATAT
1 TAAAAATAAAA-AAATAAATAATATTATATAAATAT
* * * *
2495993 TAAAATTAAAAATATAAATAGTATTTTATAAAT
1 TAAAAATAAAAAAATAAATAATATTATATAAAT
2496026 TGTGATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (35 bp):
TAAAAATAAAAAAATAAATAATATTATATAAATAT
Found at i:2498934 original size:15 final size:15
Alignment explanation
Indices: 2498914--2498948 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2498904 AAAGTTCTTC
*
2498914 AAAAAAATAAAAAAT
1 AAAAAAAGAAAAAAT
*
2498929 AAAAAAAGCAAAAAT
1 AAAAAAAGAAAAAAT
2498944 AAAAA
1 AAAAA
2498949 GAATGTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAAAAGAAAAAAT
Found at i:2516029 original size:28 final size:30
Alignment explanation
Indices: 2515978--2516049 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 30
2515968 AGGAATTATT
2515978 TTTAAATTATAATAAAATATTTAATAGAATA
1 TTTAAATTATAA-AAAATATTTAATAGAATA
**
2516009 TTTAAATT-TAAAAAAT-TTTAATATTATA
1 TTTAAATTATAAAAAATATTTAATAGAATA
2516037 TTTAAATTATAAA
1 TTTAAATTATAAA
2516050 TTTATTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 18 0.47
29 9 0.24
30 3 0.08
31 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
TTTAAATTATAAAAAATATTTAATAGAATA
Found at i:2516546 original size:29 final size:29
Alignment explanation
Indices: 2516470--2516555 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 29
2516460 TAATAAAATC
* *
2516470 ATAATTTAAATATCATATTAAA-ATTTTTTT
1 ATAATTTAAGTATC--ATTAAACATTTTATT
* *
2516500 A-AATTTATGTACCCCATTAAACATTTTATT
1 ATAATTTAAGTA--TCATTAAACATTTTATT
2516530 ATAATTTAAGTATCATTCATAACATT
1 ATAATTTAAGTATCATT-A-AACATT
2516556 AACCTTTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
29 18 0.41
30 10 0.23
31 16 0.36
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (29 bp):
ATAATTTAAGTATCATTAAACATTTTATT
Found at i:2516622 original size:12 final size:12
Alignment explanation
Indices: 2516605--2516641 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2516595 CTCGACAATG
2516605 AAATTAAAAAAA
1 AAATTAAAAAAA
* *
2516617 AAATTACAAAGA
1 AAATTAAAAAAA
2516629 AAATTAAAAAAA
1 AAATTAAAAAAA
2516641 A
1 A
2516642 TTATACATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (12 bp):
AAATTAAAAAAA
Found at i:2516688 original size:17 final size:17
Alignment explanation
Indices: 2516666--2516698 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2516656 TAAGATATAT
2516666 TTAAAAATAA-AAAATAA
1 TTAAAAA-AATAAAATAA
2516683 TTAAAAAAATAAAATA
1 TTAAAAAAATAAAATA
2516699 TATCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAAAAATAAAATAA
Found at i:2519025 original size:59 final size:59
Alignment explanation
Indices: 2518957--2519075 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
2518947 ATGAGGATAC
2518957 AATGGATAAATATGTACTAAAAAATATAAAAGACAAGATCACTGCAGAA-AGTTCAGTGA
1 AATGGATAAATATGTACTAAAAAATATAAAAGACAAGATCACTGCA-AAGAGTTCAGTGA
*
2519016 AATGGATAAATATGTACTCAAAAATATAAAAGACAAGATCACTGCAAAGAGTTCAGTGA
1 AATGGATAAATATGTACTAAAAAATATAAAAGACAAGATCACTGCAAAGAGTTCAGTGA
2519075 A
1 A
2519076 GGCCAAGACC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 2 0.03
59 56 0.97
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (59 bp):
AATGGATAAATATGTACTAAAAAATATAAAAGACAAGATCACTGCAAAGAGTTCAGTGA
Found at i:2520258 original size:16 final size:15
Alignment explanation
Indices: 2520210--2520258 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
2520200 TTATATTAAA
2520210 TATTAAAATT-TATT
1 TATTAAAATTATATT
* *
2520224 TATTAATATTATGTTT
1 TATTAAAATTAT-ATT
2520240 TATTAAAATTATATAT
1 TATTAAAATTATAT-T
2520256 TAT
1 TAT
2520259 AATTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 17 0.61
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTAAAATTATATT
Found at i:2523259 original size:18 final size:20
Alignment explanation
Indices: 2523217--2523262 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
2523207 ATCAATGTTG
2523217 AATTTTA-TAAATGTATTTT
1 AATTTTATTAAATGTATTTT
2523236 AATTTTATTAAAT-T-TTTT
1 AATTTTATTAAATGTATTTT
*
2523254 ATTTTTATT
1 AATTTTATT
2523263 TTTGTGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 12 0.48
19 8 0.32
20 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTATTAAATGTATTTT
Found at i:2529288 original size:6 final size:6
Alignment explanation
Indices: 2529277--2529336 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
2529267 TTTGGAAATA
* * * *
2529277 AGTTTT AGTTTT GGTTTC GGTTTT AGTTTT AGTTTT AATTTT AGTTTT
1 AGTTTT AGTTTT AGTTTT AGTTTT AGTTTT AGTTTT AGTTTT AGTTTT
*
2529325 AGATTT AGTTTT
1 AGTTTT AGTTTT
2529337 TTTTCTTTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.02, G:0.18, T:0.63
Consensus pattern (6 bp):
AGTTTT
Found at i:2529673 original size:67 final size:67
Alignment explanation
Indices: 2529475--2529710 Score: 189
Period size: 67 Copynumber: 3.5 Consensus size: 67
2529465 GATAATCTAT
** * * * * **
2529475 TAAGGCGTTTCCTTTTTACAAACGCCTTATTTGATAAATGATCTTCTAGAATCTTTATAAAAGCA
1 TAAGGCGTTTCCTTTGAACAAACGCCTTATTTGATAGACGATCTTTTAGAATCTTTACAAATTCA
2529540 AA
66 AA
* * * * * *
2529542 TAAAGCGTTT-CTGTGAATAAATGCCTTATTTGAT-G-C--T-TTTCCCA-ACATATTTACAAAG
1 TAAGGCGTTTCCTTTGAACAAACGCCTTATTTGATAGACGATCTTT--TAGA-ATCTTTAC-AA-
2529600 GCATTCAAA
61 --ATTCAAA
* **
2529609 TAAGGCGTTTCTTTTTTACAAACGCCTTATTTGATAGACGATCTTTTAGAATCTTTACAAATTCA
1 TAAGGCGTTTCCTTTGAACAAACGCCTTATTTGATAGACGATCTTTTAGAATCTTTACAAATTCA
2529674 AA
66 AA
* *
2529676 TAAGGCATTTCCTTTGAACAAACACCTTATTTGAT
1 TAAGGCGTTTCCTTTGAACAAACGCCTTATTTGAT
2529711 GCTTTTTCCA
Statistics
Matches: 127, Mismatches: 28, Indels: 28
0.69 0.15 0.15
Matches are distributed among these distances:
61 2 0.02
62 2 0.02
63 7 0.06
64 2 0.02
66 19 0.15
67 60 0.47
68 18 0.14
69 1 0.01
70 3 0.02
71 8 0.06
72 2 0.02
73 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (67 bp):
TAAGGCGTTTCCTTTGAACAAACGCCTTATTTGATAGACGATCTTTTAGAATCTTTACAAATTCA
AA
Found at i:2531479 original size:15 final size:18
Alignment explanation
Indices: 2531459--2531496 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2531449 GATTTTCAGG
2531459 AGAAGC-TAA-AA-GAGA
1 AGAAGCATAAGAAGGAGA
2531474 AGAAGCATAAGAAGGAGA
1 AGAAGCATAAGAAGGAGA
2531492 AGAAG
1 AGAAG
2531497 GACAAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 2 0.10
18 9 0.45
ACGTcount: A:0.58, C:0.05, G:0.32, T:0.05
Consensus pattern (18 bp):
AGAAGCATAAGAAGGAGA
Found at i:2531604 original size:24 final size:23
Alignment explanation
Indices: 2531572--2531616 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2531562 GAAAGACAAA
2531572 AAGGAAAAACACAAAGACAAAAAG
1 AAGGAAAAACACAAAGA-AAAAAG
*
2531596 AAGGAAAAAGACAAAGAAAAA
1 AAGGAAAAACACAAAGAAAAA
2531617 GATAGAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (23 bp):
AAGGAAAAACACAAAGAAAAAAG
Found at i:2531615 original size:21 final size:20
Alignment explanation
Indices: 2531563--2531616 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 20
2531553 TAAGGATAAG
2531563 AAAGACAAAAAGGAAAAACAC
1 AAAGA-AAAAAGGAAAAACAC
*
2531584 AAAGACAAAAAGAAGGAAAAAGAC
1 AAAG---AAAA-AAGGAAAAACAC
2531608 AAAGAAAAA
1 AAAGAAAAA
2531617 GATAGAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
23 3 0.11
24 16 0.57
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAGGAAAAACAC
Found at i:2534671 original size:16 final size:17
Alignment explanation
Indices: 2534650--2534681 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2534640 AACATTAAAT
2534650 TAAAATTTAT-ATATAA
1 TAAAATTTATAATATAA
2534666 TAAAATTTATAATATA
1 TAAAATTTATAATATA
2534682 TTTGGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATAATATAA
Found at i:2534762 original size:24 final size:24
Alignment explanation
Indices: 2534715--2534762 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2534705 AAAATTGATT
*
2534715 ATTTATTATTTATTTATTATTTTA
1 ATTTATTATTTATTTATTAATTTA
2534739 ATTTATTATTTA-TTAGTTAATTTA
1 ATTTATTATTTATTTA-TTAATTTA
2534763 TTAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTATTATTTATTTATTAATTTA
Found at i:2534772 original size:31 final size:31
Alignment explanation
Indices: 2534690--2534772 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
2534680 TATTTGGTAT
*
2534690 TTATAAATTTA-TAGTAA-AATTGATTATTTA
1 TTATTAATTTATTA-TAATAATTGATTATTTA
* ** *
2534720 TTATTTATTTATTATTTTAATTTATTATTTA
1 TTATTAATTTATTATAATAATTGATTATTTA
2534751 TTAGTTAATTTATTA-AATAATT
1 TTA-TTAATTTATTATAATAATT
2534773 ATATAAATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 10 0.24
31 22 0.52
32 10 0.24
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (31 bp):
TTATTAATTTATTATAATAATTGATTATTTA
Found at i:2538300 original size:59 final size:60
Alignment explanation
Indices: 2538192--2538309 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
2538182 ATAATCCCTT
* * *
2538192 ATAAAAAATTGAATGGAGTTATTCAAAGCGCGTTTCTGGTAAAAAATATCTTTAATAATA
1 ATAAAAAAATGAAAGGAGTTATTCAAAGCGCGTTTCTGGTAAAAAATATCTGTAATAATA
** * *
2538252 ATAAAAAAATGAAAGGAGATTATT-AAAG-GTTTTTTTGGTTAAAAATATCTGTAATAAT
1 ATAAAAAAATGAAAGGAG-TTATTCAAAGCGCGTTTCTGGTAAAAAATATCTGTAATAAT
2538310 CTCTTACAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 25 0.50
60 20 0.40
61 5 0.10
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (60 bp):
ATAAAAAAATGAAAGGAGTTATTCAAAGCGCGTTTCTGGTAAAAAATATCTGTAATAATA
Found at i:2544212 original size:24 final size:23
Alignment explanation
Indices: 2544166--2544212 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2544156 AACAAATAAC
**
2544166 CAAAAACCAAAGAAAAAGGAAAG
1 CAAAAACCAAAGAAAAAAAAAAG
*
2544189 CAAAAACTCATAGAAAAAAAAAAG
1 CAAAAAC-CAAAGAAAAAAAAAAG
2544213 GATACCTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.70, C:0.13, G:0.13, T:0.04
Consensus pattern (23 bp):
CAAAAACCAAAGAAAAAAAAAAG
Found at i:2552087 original size:13 final size:13
Alignment explanation
Indices: 2552069--2552095 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2552059 ATTTGAATTG
2552069 AATTTTAAATAAT
1 AATTTTAAATAAT
2552082 AATTTTAAATAAT
1 AATTTTAAATAAT
2552095 A
1 A
2552096 TTCAAACTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTTAAATAAT
Found at i:2553000 original size:19 final size:19
Alignment explanation
Indices: 2552968--2553005 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2552958 TATTTTAATT
*
2552968 GAAAAATTATAGAA-ATAA
1 GAAAAATTAAAGAAGATAA
2552986 GAAAATATTAAAGAAGATAA
1 GAAAA-ATTAAAGAAGATAA
2553006 TAATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (19 bp):
GAAAAATTAAAGAAGATAA
Found at i:2560350 original size:2 final size:2
Alignment explanation
Indices: 2560343--2560367 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2560333 AATTTTCATG
2560343 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2560368 GGTTTATTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2567831 original size:16 final size:15
Alignment explanation
Indices: 2567806--2567835 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2567796 TTGAATCTAA
2567806 AATTAAATTAATTTG
1 AATTAAATTAATTTG
2567821 AATTCAAATTAATTT
1 AATT-AAATTAATTT
2567836 AAATACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTAAATTAATTTG
Found at i:2567837 original size:21 final size:21
Alignment explanation
Indices: 2567788--2567837 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2567778 ATAAATAATC
2567788 TTAATTT-ATTGAATCTAAAA
1 TTAATTTAATTGAATCTAAAA
* *
2567808 TTAAATTAATTTGAAT-TCAAA
1 TTAATTTAA-TTGAATCTAAAA
2567829 TTAATTTAA
1 TTAATTTAA
2567838 ATACAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.24
21 13 0.52
22 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAATTTAATTGAATCTAAAA
Found at i:2567844 original size:16 final size:16
Alignment explanation
Indices: 2567810--2567844 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2567800 ATCTAAAATT
* *
2567810 AAATTAATTTGAATTC
1 AAATTAATTTAAATAC
2567826 AAATTAATTTAAATAC
1 AAATTAATTTAAATAC
2567842 AAA
1 AAA
2567845 ATATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (16 bp):
AAATTAATTTAAATAC
Found at i:2573826 original size:12 final size:11
Alignment explanation
Indices: 2573808--2573850 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2573798 AATTTTTAAT
2573808 ATAAATATATA
1 ATAAATATATA
2573819 ACTAAATATATA
1 A-TAAATATATA
*
2573831 TATAAATATAAA
1 -ATAAATATATA
2573843 ATTAAATA
1 A-TAAATA
2573851 ATTAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 25 0.89
13 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAATATATA
Found at i:2573860 original size:24 final size:24
Alignment explanation
Indices: 2573784--2573860 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
2573774 TATTTTAAAA
* *
2573784 AAATATAAAATATTAATTTTTAATAT
1 AAATAT-AAA-ATTAAATATTAATAT
* *
2573810 AAATATATAACTAAATA-TATATAT
1 AAATATAAAATTAAATATTA-ATAT
2573834 AAATATAAAATTAAATAATTAAT-T
1 AAATATAAAATTAAAT-ATTAATAT
2573858 AAA
1 AAA
2573861 AAATAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.05
24 27 0.64
25 5 0.12
26 8 0.19
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATATAAAATTAAATATTAATAT
Found at i:2575815 original size:20 final size:20
Alignment explanation
Indices: 2575790--2575828 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2575780 GCCTCCCTTC
*
2575790 AACACCGTAGACGTACATAG
1 AACACCGTAGACGAACATAG
2575810 AACACCGTAGACGAACATA
1 AACACCGTAGACGAACATA
2575829 AAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
AACACCGTAGACGAACATAG
Found at i:2578891 original size:23 final size:23
Alignment explanation
Indices: 2578865--2578946 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 23
2578855 ATATATTTGG
2578865 TATATATATTTTTTATTAAATAA
1 TATATATATTTTTTATTAAATAA
* *
2578888 TATAAATTATTATTTTATGGTAATTAA
1 TATATA-TATT-TTTTAT--TAAATAA
* *
2578915 AAT-TAATATATTTTTATTGAAAAAA
1 TATAT-ATAT-TTTTTATT-AAATAA
2578940 TATATAT
1 TATATAT
2578947 TAATATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
23 5 0.11
24 5 0.11
25 14 0.32
26 10 0.23
27 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TATATATATTTTTTATTAAATAA
Found at i:2579353 original size:26 final size:26
Alignment explanation
Indices: 2579306--2579375 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 26
2579296 TATTATAACT
*
2579306 ATTAAAATAT-TAAAAATTATTTATA
1 ATTAAAATATATTAAAATTATTTATA
* *
2579331 ATTAAAGTATATTAAAATTATTTATT
1 ATTAAAATATATTAAAATTATTTATA
*
2579357 ATTAAAAT-TATTAATATTA
1 ATTAAAATATATTAAAATTA
2579376 AAAAAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
ATTAAAATATATTAAAATTATTTATA
Found at i:2579359 original size:16 final size:16
Alignment explanation
Indices: 2579340--2579423 Score: 66
Period size: 16 Copynumber: 5.1 Consensus size: 16
2579330 AATTAAAGTA
2579340 TATTAAAATTATTTAT
1 TATTAAAATTATTTAT
*
2579356 TATTAAAATTA-TTAA
1 TATTAAAATTATTTAT
**
2579371 TATTAAAAAAATTATAT
1 TATTAAAATTATT-TAT
*
2579388 T-TTAATAATAATATTTAA
1 TATTAA-AAT--TATTTAT
2579406 TATTAAAA-TATTATAT
1 TATTAAAATTATT-TAT
2579422 TA
1 TA
2579424 ATATAAAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
15 16 0.30
16 20 0.38
17 5 0.09
18 5 0.09
19 7 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTAAAATTATTTAT
Found at i:2579384 original size:50 final size:48
Alignment explanation
Indices: 2579330--2579424 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 48
2579320 AATTATTTAT
* *
2579330 AATTAAAGTATATTAA-AATTATTTATTATTAAAATTATTAATATTAAAAA
1 AATTAAAGTATAATAATAA-TATTTAATATTAAAA-TATT-ATATTAAAAA
* * *
2579380 AATTATATTTTAATAATAATATTTAATATTAAAATATTATATTAA
1 AATTAAAGTATAATAATAATATTTAATATTAAAATATTATATTAA
2579425 TATAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 7 0.18
49 4 0.10
50 26 0.67
51 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (48 bp):
AATTAAAGTATAATAATAATATTTAATATTAAAATATTATATTAAAAA
Found at i:2579424 original size:19 final size:18
Alignment explanation
Indices: 2579339--2579434 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
2579329 TAATTAAAGT
2579339 ATATTAAAAT-TAT-TTA
1 ATATTAAAATATATATTA
*
2579355 TTATT-AAA-AT-TATTA
1 ATATTAAAATATATATTA
2579370 ATATTAAAA-A-A-ATTA
1 ATATTAAAATATATATTA
*
2579385 TATTTTAATAATA-ATATTTA
1 -ATATTAA-AATATATA-TTA
2579405 ATATTAAAATATTATATTA
1 ATATTAAAATA-TATATTA
*
2579424 ATATAAAAATA
1 ATATTAAAATA
2579435 CTTAAAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
14 1 0.02
15 15 0.23
16 14 0.22
17 2 0.03
18 6 0.09
19 20 0.31
20 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTAAAATATATATTA
Found at i:2579518 original size:26 final size:24
Alignment explanation
Indices: 2579454--2579518 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 24
2579444 AAACTATTTT
2579454 TATA-TTATTAATAATATAATATAA
1 TATATTTATTAATAAT-TAATATAA
*
2579478 TATATTTGTT--T-ATTAATATAA
1 TATATTTATTAATAATTAATATAA
2579499 TACTATTTATTAATAGATTA
1 TA-TATTTATTAATA-ATTA
2579519 TAATATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 10 0.30
22 9 0.27
23 1 0.03
24 5 0.15
25 4 0.12
26 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (24 bp):
TATATTTATTAATAATTAATATAA
Found at i:2579725 original size:13 final size:13
Alignment explanation
Indices: 2579707--2579732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2579697 TTAAAAAGAA
2579707 AAAATTATTTTTC
1 AAAATTATTTTTC
2579720 AAAATTATTTTTC
1 AAAATTATTTTTC
2579733 GTAAAACAAA
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTATTTTTC
Found at i:2587710 original size:29 final size:29
Alignment explanation
Indices: 2587672--2587746 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
2587662 CACATTAGTT
* *
2587672 AATATGTTTATAATTCATATATCACACTA
1 AATATTTTTATAATTCAAATATCACACTA
* * * *
2587701 GATATTTTTAAAATTCAAATATTACGCTA
1 AATATTTTTATAATTCAAATATCACACTA
2587730 AATATTTTACTATAATT
1 AATATTTT--TATAATT
2587747 TAGAGATAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 30 0.83
31 6 0.17
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (29 bp):
AATATTTTTATAATTCAAATATCACACTA
Found at i:2599131 original size:300 final size:300
Alignment explanation
Indices: 2598589--2599188 Score: 1137
Period size: 300 Copynumber: 2.0 Consensus size: 300
2598579 ACCCATAGTC
*
2598589 CAGCTGCATTCTGAACATAACCCATGCTATGCAGTGTAGGAGCCCCTAGAACACTATATGGGTCA
1 CAGCTGCATTCTGAACATAACCCATGCTATGCAGTGTAGGAGCCCCTAGAACACTAAATGGGTCA
2598654 TTGAATACCATCTGCTTGTCTCCTCTGGTATTCACCTCCAAATGCCTCAAAAGGTTACTTATTGC
66 TTGAATACCATCTGCTTGTCTCCTCTGGTATTCACCTCCAAATGCCTCAAAAGGTTACTTATTGC
*
2598719 ATACCCATATACCAAAGTAGAATCTTTATTTTGAACTATCTTCATCATATCATGAAAAATGAAGT
131 ATACCCATATACCAAAGCAGAATCTTTATTTTGAACTATCTTCATCATATCATGAAAAATGAAGT
2598784 GCACCAAATTTGGTTTCTGTCTATTCTTAATCTTATACATCCACCAATAATCTTGCTTCCTAATG
196 GCACCAAATTTGGTTTCTGTCTATTCTTAATCTTATACATCCACCAATAATCTTGCTTCCTAATG
2598849 ATGGAGTATTGTGTCCCAAAAGGTACTAGAACATGAGTAA
261 ATGGAGTATTGTGTCCCAAAAGGTACTAGAACATGAGTAA
2598889 CAGCTGCATTCTGAACATAACCCATGCTATGCAGTGTAGGAGCCCCTAGAACACTAAATGGGTCA
1 CAGCTGCATTCTGAACATAACCCATGCTATGCAGTGTAGGAGCCCCTAGAACACTAAATGGGTCA
*
2598954 TTGAATACCATCTGCTTGTCTCCTCTGGTATTCACCTCCAAATTCCTCAAAAGGTTACTTATTGC
66 TTGAATACCATCTGCTTGTCTCCTCTGGTATTCACCTCCAAATGCCTCAAAAGGTTACTTATTGC
*
2599019 ATGCCCATATACCAAAGCAGAATCTTTATTTTGAACTATCTTCATCATATCATGAAAAATGAAGT
131 ATACCCATATACCAAAGCAGAATCTTTATTTTGAACTATCTTCATCATATCATGAAAAATGAAGT
*
2599084 GCACCAAATTTGGTTTCTGTCTATTCTTAATCTTATACATCCACCAATAATCTTGTTTCCTAATG
196 GCACCAAATTTGGTTTCTGTCTATTCTTAATCTTATACATCCACCAATAATCTTGCTTCCTAATG
* *
2599149 GTGGAGTATTGTGTCCCAAAAGGTGCTAGAACATGAGTAA
261 ATGGAGTATTGTGTCCCAAAAGGTACTAGAACATGAGTAA
2599189 GAATGAGATG
Statistics
Matches: 293, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
300 293 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (300 bp):
CAGCTGCATTCTGAACATAACCCATGCTATGCAGTGTAGGAGCCCCTAGAACACTAAATGGGTCA
TTGAATACCATCTGCTTGTCTCCTCTGGTATTCACCTCCAAATGCCTCAAAAGGTTACTTATTGC
ATACCCATATACCAAAGCAGAATCTTTATTTTGAACTATCTTCATCATATCATGAAAAATGAAGT
GCACCAAATTTGGTTTCTGTCTATTCTTAATCTTATACATCCACCAATAATCTTGCTTCCTAATG
ATGGAGTATTGTGTCCCAAAAGGTACTAGAACATGAGTAA
Found at i:2602297 original size:18 final size:18
Alignment explanation
Indices: 2602271--2602305 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2602261 TAATCCGTGA
*
2602271 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
2602289 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
2602306 CAAAGAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:2602794 original size:22 final size:22
Alignment explanation
Indices: 2602766--2602809 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2602756 TTTTTTGTCC
**
2602766 TTAATTTTAGGGATACAAATAT
1 TTAATTTTAGAAATACAAATAT
2602788 TTAATTTTAGAAATACAAATAT
1 TTAATTTTAGAAATACAAATAT
2602810 AAATATACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
TTAATTTTAGAAATACAAATAT
Found at i:2611133 original size:2 final size:2
Alignment explanation
Indices: 2611126--2611164 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2611116 GCGTCCACTA
2611126 AT AT AT 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 AT AT AT A
2611165 ATTTGTGTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2615846 original size:23 final size:25
Alignment explanation
Indices: 2615820--2615867 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2615810 CATATGTTAG
*
2615820 TTAAATATAT-CAAAT-AAGCACAA
1 TTAAACATATGCAAATCAAGCACAA
*
2615843 TTAAACATATGCATATCAAGCACAA
1 TTAAACATATGCAAATCAAGCACAA
2615868 GCAAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (25 bp):
TTAAACATATGCAAATCAAGCACAA
Found at i:2620512 original size:21 final size:21
Alignment explanation
Indices: 2620486--2620540 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2620476 CATAACTAAC
2620486 TCATCAAAGGTATCTTGCAAT
1 TCATCAAAGGTATCTTGCAAT
*
2620507 TTATCAAAGGTATCTTGCAAT
1 TCATCAAAGGTATCTTGCAAT
2620528 TCATCAAAGGTAT
1 TCATCAAAGGTAT
2620541 ATGAGTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (21 bp):
TCATCAAAGGTATCTTGCAAT
Found at i:2623975 original size:2 final size:2
Alignment explanation
Indices: 2623970--2623995 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2623960 CCCATATGAA
2623970 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
2623996 GCATTTGAAG
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:2635884 original size:12 final size:12
Alignment explanation
Indices: 2635861--2635895 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2635851 GTGTTCACTT
2635861 AAAATATATAAAC
1 AAAAT-TATAAAC
2635874 AAAATTATAAAC
1 AAAATTATAAAC
2635886 AAAATT-TAAA
1 AAAATTATAAA
2635896 ATAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 13 0.59
13 5 0.23
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATTATAAAC
Found at i:2637515 original size:44 final size:42
Alignment explanation
Indices: 2637456--2637538 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 42
2637446 ATTTTATATA
* * *
2637456 TTTATATAAGATTAATGATACGTTATAATGTTAGAATTTTGTT
1 TTTATATAAAATTAATGATACATTATAATATTAG-ATTTTGTT
*
2637499 TTTATTATAAAATTAATTATACATTATAATATTAGATTTT
1 TTTA-TATAAAATTAATGATACATTATAATATTAGATTTT
2637539 ATATATACAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 9 0.26
44 26 0.74
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (42 bp):
TTTATATAAAATTAATGATACATTATAATATTAGATTTTGTT
Found at i:2638828 original size:24 final size:24
Alignment explanation
Indices: 2638801--2638847 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2638791 AAAATAACTC
* **
2638801 GGCCTAAAAGCTTGGACTCAGCTT
1 GGCCAAAAAGCTCAGACTCAGCTT
2638825 GGCCAAAAAGCTCAGACTCAGCT
1 GGCCAAAAAGCTCAGACTCAGCT
2638848 CGGTCAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (24 bp):
GGCCAAAAAGCTCAGACTCAGCTT
Found at i:2641501 original size:34 final size:33
Alignment explanation
Indices: 2641434--2641553 Score: 152
Period size: 33 Copynumber: 3.6 Consensus size: 33
2641424 GTGGTGTAAA
* * *
2641434 AGTGGTTTTCATATCATGCCACTGGTTATGAAT
1 AGTGGTTTTCATACCATGCCACCGGTTAAGAAT
2641467 AGTGGTTTTCATACCATGCCACCGGGTTAAGAAT
1 AGTGGTTTTCATACCATGCCACC-GGTTAAGAAT
* **
2641501 AGTGG-TTTCGTACTGTGCCACCGGTTAAGAAT
1 AGTGGTTTTCATACCATGCCACCGGTTAAGAAT
* *
2641533 AGTGATTTTCGTACCATGCCA
1 AGTGGTTTTCATACCATGCCA
2641554 ACAGTTTCAG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 14 0.18
33 48 0.63
34 14 0.18
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (33 bp):
AGTGGTTTTCATACCATGCCACCGGTTAAGAAT
Found at i:2649578 original size:20 final size:22
Alignment explanation
Indices: 2649536--2649580 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
2649526 TAAATGAAAG
2649536 AAATAAATTAACAAATGAACCAAC
1 AAATAAATTAACAAAT--ACCAAC
2649560 AAAT-AATTAACAAAT-CCAAC
1 AAATAAATTAACAAATACCAAC
2649580 A
1 A
2649581 TAAAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.62, C:0.18, G:0.02, T:0.18
Consensus pattern (22 bp):
AAATAAATTAACAAATACCAAC
Found at i:2649587 original size:20 final size:20
Alignment explanation
Indices: 2649540--2649587 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 20
2649530 TGAAAGAAAT
2649540 AAATTAACAAATGAACCAACAA
1 AAATTAACAAAT--ACCAACAA
2649562 ATAATTAACAAAT-CCAACATA
1 A-AATTAACAAATACCAACA-A
2649583 AAATT
1 AAATT
2649588 CAATCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 10 0.42
21 2 0.08
22 1 0.04
23 11 0.46
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (20 bp):
AAATTAACAAATACCAACAA
Found at i:2652652 original size:2 final size:2
Alignment explanation
Indices: 2652645--2652671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2652635 TTGACTGTGC
2652645 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2652672 TTCTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2656289 original size:85 final size:83
Alignment explanation
Indices: 2656159--2656470 Score: 277
Period size: 85 Copynumber: 3.7 Consensus size: 83
2656149 AGTTCAGCCA
* ** ** ** * *
2656159 AAGAGCTTAGACTCAACTTAACCAAAAGAACTGGGATATACAAAATGCTTTCATAAAGATCAAAT
1 AAGAGCTTAGACTCAACTTGATTAAAAGAGTTTAGATCTAGAAAATGCTTTCATAAAG-TC-AAT
2656224 TCAACAAAATAACTTGACCT
64 TCAACAAAATAACTTGACCT
* *
2656244 AAGAGCTTAGACTCAATTTGATTAAAAGAGTTTAGATCTAGAAAATGCTTTCATAAAAGCTCAAC
1 AAGAGCTTAGACTCAACTTGATTAAAAGAGTTTAGATCTAGAAAATGCTTTCAT-AAAG-TCAAT
* *
2656309 TCAACAAAACAA-TTCGGCCT
64 TCAACAAAATAACTT-GACCT
** * * *
2656329 AAGAGCTTAGACTCAACTCAATTAAAAGAGTTTAGATCTATAAAATGTTTTCACAAAGTCTCAAT
1 AAGAGCTTAGACTCAACTTGATTAAAAGAGTTTAGATCTAGAAAATGCTTTCATAAAG--TCAAT
** * *
2656394 TTGACAAAATAACTTGATCA
64 TCAACAAAATAACTTGACCT
* * ** * * *
2656414 AATAGTTTAGACTCAACTTGACCAAAAGAGTTCAAATAT-GTAAAATGCTTTCATAAA
1 AAGAGCTTAGACTCAACTTGATTAAAAGAGTTTAGATCTAG-AAAATGCTTTCATAAA
2656471 AACCTAATTT
Statistics
Matches: 183, Mismatches: 39, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
84 6 0.03
85 169 0.92
86 8 0.04
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (83 bp):
AAGAGCTTAGACTCAACTTGATTAAAAGAGTTTAGATCTAGAAAATGCTTTCATAAAGTCAATTC
AACAAAATAACTTGACCT
Found at i:2665727 original size:2 final size:2
Alignment explanation
Indices: 2665715--2665746 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2665705 GTCCTATGTA
*
2665715 AT AT AT GT 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
2665747 CTTTGTTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2667744 original size:42 final size:41
Alignment explanation
Indices: 2667616--2667745 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 41
2667606 TTTCTCATGA
* * ** * *
2667616 AAGGTCAAGATCCAAATCAAAATCACCCCTTAGTTATCGGAG
1 AAGGTCAAG-TCCAAGTCAAGATCACCAATCAGTTATCGGCG
* * * * * *
2667658 AAGGTCAAAATCAAAGTCTAGATCACCAATCAGGTACCGACG
1 AAGGTC-AAGTCCAAGTCAAGATCACCAATCAGTTATCGGCG
*
2667700 AAGGTCAATGTCCAAGTCAAGATCACCAATCAGTTATAGGCG
1 AAGGTCAA-GTCCAAGTCAAGATCACCAATCAGTTATCGGCG
2667742 AAGG
1 AAGG
2667746 AGGTCTCGCT
Statistics
Matches: 67, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
41 2 0.03
42 63 0.94
43 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
AAGGTCAAGTCCAAGTCAAGATCACCAATCAGTTATCGGCG
Found at i:2671565 original size:2 final size:2
Alignment explanation
Indices: 2671558--2671586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2671548 ACAATAAACC
2671558 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 A
2671587 CATGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2675148 original size:14 final size:14
Alignment explanation
Indices: 2675126--2675156 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2675116 AATTTGTCCC
2675126 AATCATTAACTCTA
1 AATCATTAACTCTA
*
2675140 AATCGTTAACTCTA
1 AATCATTAACTCTA
2675154 AAT
1 AAT
2675157 AATGACATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.35
Consensus pattern (14 bp):
AATCATTAACTCTA
Found at i:2678018 original size:18 final size:18
Alignment explanation
Indices: 2677995--2678029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2677985 AGATATTATT
2677995 ATTGATAATAATTAATTC
1 ATTGATAATAATTAATTC
* *
2678013 ATTGATGATTATTAATT
1 ATTGATAATAATTAATT
2678030 ATTAATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (18 bp):
ATTGATAATAATTAATTC
Found at i:2678956 original size:14 final size:14
Alignment explanation
Indices: 2678937--2678964 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2678927 TAAGTTTGAA
2678937 TATTATTTAAAATT
1 TATTATTTAAAATT
2678951 TATTATTTAAAATT
1 TATTATTTAAAATT
2678965 CAATTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTATTTAAAATT
Found at i:2679197 original size:19 final size:20
Alignment explanation
Indices: 2679139--2679197 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
2679129 TTTATATAGG
*
2679139 TAAAATAAT-AATTTTTAAT
1 TAAAATAATAAAATTTTAAT
* *
2679158 TAAAATAATAAAAATAT-AT
1 TAAAATAATAAAATTTTAAT
*
2679177 TAAAAT-TTAAAATTTTAAT
1 TAAAATAATAAAATTTTAAT
2679196 TA
1 TA
2679198 CTTTTGTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.22
19 21 0.66
20 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATAATAAAATTTTAAT
Found at i:2684281 original size:13 final size:14
Alignment explanation
Indices: 2684260--2684289 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2684250 TTACTCTTAA
2684260 AATTTTTTTCTTTC
1 AATTTTTTTCTTTC
2684274 AATTTTTTTCTTTC
1 AATTTTTTTCTTTC
2684288 AA
1 AA
2684290 ATAACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTTTTTCTTTC
Found at i:2686571 original size:17 final size:17
Alignment explanation
Indices: 2686545--2686577 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2686535 CTCTTTACTC
2686545 TTAAAGTTTTTTATTTT
1 TTAAAGTTTTTTATTTT
*
2686562 TTAAATTTTTTTATTT
1 TTAAAGTTTTTTATTT
2686578 ATCAAATAAT
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:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTAAAGTTTTTTATTTT
Found at i:2686584 original size:17 final size:17
Alignment explanation
Indices: 2686551--2686584 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2686541 ACTCTTAAAG
* *
2686551 TTTTTTATTTTTTAAAT
1 TTTTTTATTTATCAAAT
2686568 TTTTTTATTTATCAAAT
1 TTTTTTATTTATCAAAT
2686585 AATATATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTATTTATCAAAT
Found at i:2687220 original size:19 final size:20
Alignment explanation
Indices: 2687198--2687236 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2687188 GATAAAAAAA
2687198 AATTAGAG-AATTTTCTTAT
1 AATTAGAGAAATTTTCTTAT
* *
2687217 AATTTGAGAAATTTTTTTAT
1 AATTAGAGAAATTTTCTTAT
2687237 TATACCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
AATTAGAGAAATTTTCTTAT
Found at i:2691350 original size:65 final size:65
Alignment explanation
Indices: 2691276--2691415 Score: 235
Period size: 65 Copynumber: 2.2 Consensus size: 65
2691266 GGCACTTGCG
*
2691276 TGCAGCAACAATAATTTCAAGCATGACCTCCAAAAAATGCTTATAAAAAATGTAACGTATATGAT
1 TGCAGCAACAATAATTTCAAGCATGACCTCAAAAAAATGCTTATAAAAAATGTAACGTATATGAT
* * * *
2691341 TGCAACAACAATAATTTCAAGTATGACTTCAAAAAAATGCTTATAAAAAATGTAATGTATATGAT
1 TGCAGCAACAATAATTTCAAGCATGACCTCAAAAAAATGCTTATAAAAAATGTAACGTATATGAT
2691406 TGCAGCAACA
1 TGCAGCAACA
2691416 GTTATCTCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (65 bp):
TGCAGCAACAATAATTTCAAGCATGACCTCAAAAAAATGCTTATAAAAAATGTAACGTATATGAT
Found at i:2693587 original size:36 final size:36
Alignment explanation
Indices: 2693540--2693611 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2693530 CAGTGGCCAT
*
2693540 CCTAAAGCATCTAAGACACGTGGCAACTTCCTTTAC
1 CCTAAAGCATCTAAGACAAGTGGCAACTTCCTTTAC
*
2693576 CCTAAAGCATCTAAGGCAAGTGGCAACTTCCTTTAC
1 CCTAAAGCATCTAAGACAAGTGGCAACTTCCTTTAC
2693612 AAACTAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (36 bp):
CCTAAAGCATCTAAGACAAGTGGCAACTTCCTTTAC
Found at i:2697050 original size:42 final size:42
Alignment explanation
Indices: 2696990--2697070 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
2696980 TCCTTTATAC
*
2696990 TTAATATTGGCATGATGCAAATGTTTCAATCTTTTTGCCCAA
1 TTAATATTGGCATGATGCAAATGTTTCAATCTCTTTGCCCAA
*
2697032 TTAATCTTGGC-TGCATGCAAATGTTTCAATCTCTTTGCC
1 TTAATATTGGCATG-ATGCAAATGTTTCAATCTCTTTGCC
2697071 AGATTGCTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (42 bp):
TTAATATTGGCATGATGCAAATGTTTCAATCTCTTTGCCCAA
Found at i:2697334 original size:18 final size:18
Alignment explanation
Indices: 2697311--2697366 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
2697301 ATTATTAAAA
2697311 AATAAATAAAAATATATT
1 AATAAATAAAAATATATT
*
2697329 AAT-AA-AAAAATATATA
1 AATAAATAAAAATATATT
*
2697345 AAGTCAAATCAAAATA-ATT
1 AA-T-AAATAAAAATATATT
2697364 AAT
1 AAT
2697367 CGTAGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 12 0.39
17 3 0.10
18 4 0.13
19 6 0.19
20 6 0.19
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAATAAAAATATATT
Found at i:2700852 original size:24 final size:23
Alignment explanation
Indices: 2700819--2700874 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
2700809 AACTTTTTCC
**
2700819 TTTTTGAAAAATATTTAATATATA
1 TTTTT-AAAAATATAAAATATATA
*
2700843 TTTTCTAAAATTATAAAATATATA
1 TTTT-TAAAAATATAAAATATATA
2700867 TTTTTAAA
1 TTTTTAAA
2700875 GGTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 23 0.82
25 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTTAAAAATATAAAATATATA
Found at i:2701041 original size:110 final size:113
Alignment explanation
Indices: 2700819--2701018 Score: 259
Period size: 110 Copynumber: 1.8 Consensus size: 113
2700809 AACTTTTTCC
* * * *
2700819 TTTTTGAAAAATATTTAATATATATTTTCTAAAATTATAAAATATATATTTTTAAAGGTTTTATT
1 TTTTTAAAAAATATTTAATATATATTTTCTAAAATTAGAAAAAATATATTTTTAAAGATTTTATT
* * * **
2700884 TTTTATGTGTAGGACTCTTTTATATCTAACTTTTTTTCATTTCTTTTTA
66 TTTCATGTATAGGACCCACTTATATCTAACTTTTTTT-ATTTCTTTTTA
2700933 TTTTTAAAAAATATTTAATA-AT-TTTT-T-AAATTAGAAAAAATATATTTTTAAAGATTTT-TT
1 TTTTTAAAAAATATTTAATATATATTTTCTAAAATTAGAAAAAATATATTTTTAAAGATTTTATT
2700993 TTTCATGTAT-GTGACCCACTTATATC
66 TTTCATGTATAG-GACCCACTTATATC
2701019 CTGCCTTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
108 1 0.01
109 21 0.28
110 28 0.37
111 1 0.01
112 4 0.05
113 2 0.03
114 19 0.25
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.53
Consensus pattern (113 bp):
TTTTTAAAAAATATTTAATATATATTTTCTAAAATTAGAAAAAATATATTTTTAAAGATTTTATT
TTTCATGTATAGGACCCACTTATATCTAACTTTTTTTATTTCTTTTTA
Found at i:2701704 original size:17 final size:16
Alignment explanation
Indices: 2701654--2701706 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2701644 AAAAGCTTTC
* *
2701654 TTTTTCCTTTTTTTAT
1 TTTTTCCTTTATATAT
* *
2701670 TTTTTTCTTTA-ATTT
1 TTTTTCCTTTATATAT
2701685 TTTTTCCTATTATATAT
1 TTTTTCCT-TTATATAT
2701702 TTTTT
1 TTTTT
2701707 TAATAAAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 9 0.31
16 12 0.41
17 8 0.28
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCCTTTATATAT
Found at i:2704545 original size:20 final size:21
Alignment explanation
Indices: 2704499--2704543 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2704489 AAATAATAAA
* * *
2704499 AAAAAATTTGTTTTTCACTTT
1 AAAACATTTGTTTTTCAATCT
2704520 AAAACATTTGTTTTTCAATCT
1 AAAACATTTGTTTTTCAATCT
2704541 AAA
1 AAA
2704544 CAAAAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (21 bp):
AAAACATTTGTTTTTCAATCT
Found at i:2705623 original size:19 final size:20
Alignment explanation
Indices: 2705599--2705636 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2705589 CTAATCGAGC
2705599 TTTTA-TATTTAAATTTTTT
1 TTTTATTATTTAAATTTTTT
*
2705618 TTTTATTTTTTAAATTTTT
1 TTTTATTATTTAAATTTTT
2705637 AAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTATTTAAATTTTTT
Found at i:2707162 original size:153 final size:152
Alignment explanation
Indices: 2706989--2707289 Score: 557
Period size: 153 Copynumber: 2.0 Consensus size: 152
2706979 TCAGTTGAAT
2706989 TAGATTTTTTTTTCTTCAAGATGTTGTCCCAAAATTGTGTCGAAAGTCAAGATTCCATGCTGCCA
1 TAGATTTTTTTTTCTTCAAGATGTTGTCCCAAAATTGTGTCGAAAGTCAAGATTCCATGCTGCCA
*
2707054 ATTGCTTTCTTGTCTCTTATTCTTTCCTTATCATGTTCATCAATCTGTCTCATCAACAAGCTTGT
66 ATTGCTTTCTTGTCTCTTATTCTTTCCTTATCATGTCCATCAATCTGTCTCATCAACAAGCTTGT
*
2707119 ATATAAGAAACTTGCAATGTTG
131 ATATAAGAAACGTGCAATGTTG
* *
2707141 TAGATTTTTTTTTTCTTCAAGATGTTGTCCCAGAATTGTGTTGAAAGTCAAGATTCCATGCTGCC
1 TAGA-TTTTTTTTTCTTCAAGATGTTGTCCCAAAATTGTGTCGAAAGTCAAGATTCCATGCTGCC
2707206 AATTGCTTTCTTGTCTCTTATTCTTTCCTTATCATGTCCATCAATCTGTCTCATCAACAAGCTTG
65 AATTGCTTTCTTGTCTCTTATTCTTTCCTTATCATGTCCATCAATCTGTCTCATCAACAAGCTTG
2707271 TATATAAGAAACGTGCAAT
130 TATATAAGAAACGTGCAAT
2707290 TTTCTAGGGT
Statistics
Matches: 144, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
152 4 0.03
153 140 0.97
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (152 bp):
TAGATTTTTTTTTCTTCAAGATGTTGTCCCAAAATTGTGTCGAAAGTCAAGATTCCATGCTGCCA
ATTGCTTTCTTGTCTCTTATTCTTTCCTTATCATGTCCATCAATCTGTCTCATCAACAAGCTTGT
ATATAAGAAACGTGCAATGTTG
Found at i:2712515 original size:26 final size:27
Alignment explanation
Indices: 2712478--2712528 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2712468 GAGACACATG
* *
2712478 AAAATAATTAATTTTTAATTTTTTATT
1 AAAATAATTAATTGTTAATTATTTATT
2712505 AAAA-AATTAATTGTTAATTATTTA
1 AAAATAATTAATTGTTAATTATTTA
2712529 AGATGGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
AAAATAATTAATTGTTAATTATTTATT
Found at i:2712755 original size:59 final size:59
Alignment explanation
Indices: 2712675--2712795 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
2712665 ATACGTACAA
2712675 ATTATAAGGGTATTTGTATTGAGAATATTGACTCAAACATTAAAAAAATATAATAAGAG
1 ATTATAAGGGTATTTGTATTGAGAATATTGACTCAAACATTAAAAAAATATAATAAGAG
2712734 ATTATAAGGGTATTTGTATTGAGAATATTGACTCAAACATTAAAAAAATATAATAAGAG
1 ATTATAAGGGTATTTGTATTGAGAATATTGACTCAAACATTAAAAAAATATAATAAGAG
2712793 ATT
1 ATT
2712796 TGTTTGAGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (59 bp):
ATTATAAGGGTATTTGTATTGAGAATATTGACTCAAACATTAAAAAAATATAATAAGAG
Found at i:2714226 original size:10 final size:10
Alignment explanation
Indices: 2714211--2714249 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2714201 TAATATTAAT
2714211 AAAGGAAAAG
1 AAAGGAAAAG
**
2714221 AAAGGAATGG
1 AAAGGAAAAG
*
2714231 AAAGGAAATG
1 AAAGGAAAAG
2714241 AAAGGAAAA
1 AAAGGAAAA
2714250 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (10 bp):
AAAGGAAAAG
Found at i:2714238 original size:15 final size:15
Alignment explanation
Indices: 2714211--2714249 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2714201 TAATATTAAT
2714211 AAAGGAAAAGAAAGG
1 AAAGGAAAAGAAAGG
* * *
2714226 AATGGAAAGGAAATG
1 AAAGGAAAAGAAAGG
2714241 AAAGGAAAA
1 AAAGGAAAA
2714250 TAAATTTTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (15 bp):
AAAGGAAAAGAAAGG
Found at i:2717442 original size:255 final size:255
Alignment explanation
Indices: 2716976--2717505 Score: 845
Period size: 255 Copynumber: 2.1 Consensus size: 255
2716966 CAACCAATTA
2716976 GCAAACTCCTCCTTTTCAATTGAAAGCAACAACAAAAGCTTTACTATTCCCCAATTAGATTATCT
1 GCAAACTCCTCCTTTTCAATTGAAAGCAACAACAAAAGCTTTACTATTCCCCAATTAGATTATCT
2717041 TAACCTAGAGTCTTGCAACCTTACAGAATTTCCAGAATTCATCAAAACACAAAACAAGTTGACTA
66 TAACCTAGAGTCTTGCAACCTTACAGAATTTCCAGAATTCATCAAAACACAAAACAAGTTGACTA
* *
2717106 CCCTATATCTTTCTAACAACAAAATCCATGGTTTTGTGCCTAATTGGTTGTGGAAGACCACTCTT
131 CCCTATATCTTTCCAACAACAAAATCCATGGTTTAGTGCCTAATTGGTTGTGGAAGACCACTCTT
* * ** * *
2717171 TTATCGTTAGACCTTTCTTTCAATGCCATT-AATTTTTCAAAAGAGTTT-CCTTTCGGTGAT
196 CTAACGTTAGACCTTTCTTTCAATGCCATTGAA-TTCCCAAAACAATTTCCCTTT-GGTGAT
* *
2717231 GCAAACTCCTCCTTTTCAATTGAAAGCAACAACAAAAGCTTTGCTATTCCCCAATTAGGTTATCT
1 GCAAACTCCTCCTTTTCAATTGAAAGCAACAACAAAAGCTTTACTATTCCCCAATTAGATTATCT
*
2717296 TAACCTACGA-TCTTGCAACCTTACAGAATTTCCAGAATTCATCAAAACACAAGACAAGTTGACT
66 TAACCTA-GAGTCTTGCAACCTTACAGAATTTCCAGAATTCATCAAAACACAAAACAAGTTGACT
*
2717360 ACCCTATATCTTTCCAACAACCAAATCCATGGTTTAGTGCCTAATTGGTTGTGGAAGACCACTCT
130 ACCCTATATCTTTCCAACAACAAAATCCATGGTTTAGTGCCTAATTGGTTGTGGAAGACCACTCT
*
2717425 TCTAGAC-TT-GTACCTTTCTTTCAATGCTATTGAATTCCCAAAACAATTTCCCTTTGGTGAT
195 TCTA-ACGTTAG-ACCTTTCTTTCAATGCCATTGAATTCCCAAAACAATTTCCCTTTGGTGAT
* *
2717486 GCAAACTCTTCCTTTCCAAT
1 GCAAACTCCTCCTTTTCAAT
2717506 GCTGAGGGGG
Statistics
Matches: 255, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
254 1 0.00
255 244 0.96
256 10 0.04
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (255 bp):
GCAAACTCCTCCTTTTCAATTGAAAGCAACAACAAAAGCTTTACTATTCCCCAATTAGATTATCT
TAACCTAGAGTCTTGCAACCTTACAGAATTTCCAGAATTCATCAAAACACAAAACAAGTTGACTA
CCCTATATCTTTCCAACAACAAAATCCATGGTTTAGTGCCTAATTGGTTGTGGAAGACCACTCTT
CTAACGTTAGACCTTTCTTTCAATGCCATTGAATTCCCAAAACAATTTCCCTTTGGTGAT
Found at i:2725957 original size:27 final size:27
Alignment explanation
Indices: 2725887--2725975 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
2725877 ACATGAATTA
2725887 TTTTAATTT-TTAAAATAAA-TTTTAT
1 TTTTAATTTATTAAAATAAATTTTTAT
* *
2725912 ATTTTCATTATATTCAAATAAATTTTTAT
1 -TTTTAATT-TATTAAAATAAATTTTTAT
2725941 TTTTAATTTATCT-AAAT-AATTCTTTAT
1 TTTTAATTTAT-TAAAATAAATT-TTTAT
*
2725968 TTTAAATT
1 TTTTAATT
2725976 AAATAATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 11 0.20
27 20 0.37
28 17 0.31
29 6 0.11
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTAATTTATTAAAATAAATTTTTAT
Found at i:2726046 original size:30 final size:30
Alignment explanation
Indices: 2726012--2726114 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
2726002 TATAAATGAC
2726012 TTATTTAGATATAAATTAAAAGTTAAAAAT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
* * * **
2726042 TTATTTATATAAAAATTAAAGGTTAATGAT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
* * *
2726072 TTATTTAG-TACAAATTAAAATTTAAAAGT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
*
2726101 TTATTTAAATATAA
1 TTATTTAGATATAA
2726115 TAAAATATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.38
30 36 0.62
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.43
Consensus pattern (30 bp):
TTATTTAGATATAAATTAAAAGTTAAAAAT
Found at i:2726129 original size:28 final size:28
Alignment explanation
Indices: 2726087--2726159 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
2726077 TAGTACAAAT
* * *
2726087 TAAAATTTAAAAGTTTATTTAAATATAA
1 TAAAATATAAAAGTTTATCTAAATAAAA
* *
2726115 TAAAATATAAGAGTTTATCTAATTAAAA
1 TAAAATATAAAAGTTTATCTAAATAAAA
2726143 TAAAATGATAAAA-TTTA
1 TAAAAT-ATAAAAGTTTA
2726160 GAGTTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (28 bp):
TAAAATATAAAAGTTTATCTAAATAAAA
Found at i:2732124 original size:2 final size:2
Alignment explanation
Indices: 2732111--2732154 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2732101 CCATGTGTTG
* * *
2732111 AT AT AG AT AT AT AT AT AC AT AC 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
2732153 AT
1 AT
2732155 CTAGAAAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2737177 original size:156 final size:156
Alignment explanation
Indices: 2736886--2737177 Score: 408
Period size: 156 Copynumber: 1.9 Consensus size: 156
2736876 AACCTTGGAT
* * *
2736886 TTGGTTGTGAGAAAGATCTAGAACAGTCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAG
1 TTGGTTGTAAGAAAGATCTAGAAAAGCCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAG
* * * *
2736951 TAAAGTTGCAAGATCGTAGGTTAAGATAATCTAATTGAGGAATAGTAAAGCTTTTGTTGTGGCTT
66 TAAAGTTGCAAGACCGTAGGCTAAGATAATCCAATTGAGGAATAGTAAAGCTTTTGTTGTCGCTT
*
2737016 TCAATTGAAAAGGAGGAGTTTGCTAA
131 CCAATTGAAAAGGAGGAGTTTGCTAA
2737042 TTGGTTGTAAGAAAGATCTAGAAAAGCCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAG
1 TTGGTTGTAAGAAAGATCTAGAAAAGCCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAG
* * * * ** * *
2737107 TAAGGTTGCATGACCTTAGGGCTAA-CTCCTCCAATTGGGGAAATA-TAAGGCTTTTGTTGTCGC
66 TAAAGTTGCAAGACCGTA-GGCTAAGATAATCCAATTGAGG-AATAGTAAAGCTTTTGTTGTCGC
2737170 TTCCAATT
129 TTCCAATT
2737178 AACAAGCTCA
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
156 109 0.92
157 9 0.08
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (156 bp):
TTGGTTGTAAGAAAGATCTAGAAAAGCCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAG
TAAAGTTGCAAGACCGTAGGCTAAGATAATCCAATTGAGGAATAGTAAAGCTTTTGTTGTCGCTT
CCAATTGAAAAGGAGGAGTTTGCTAA
Found at i:2740038 original size:13 final size:14
Alignment explanation
Indices: 2740017--2740046 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2740007 TTACTCTTAA
2740017 AATTTTTTTCTTTC
1 AATTTTTTTCTTTC
2740031 AATTTTTTTCTTTC
1 AATTTTTTTCTTTC
2740045 AA
1 AA
2740047 ATAACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTTTTTCTTTC
Found at i:2742329 original size:17 final size:17
Alignment explanation
Indices: 2742303--2742335 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2742293 CTCTTTACTC
2742303 TTAAAGTTTTTTATTTT
1 TTAAAGTTTTTTATTTT
*
2742320 TTAAATTTTTTTATTT
1 TTAAAGTTTTTTATTT
2742336 ATCAAATAAT
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:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTAAAGTTTTTTATTTT
Found at i:2742342 original size:17 final size:17
Alignment explanation
Indices: 2742309--2742342 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2742299 ACTCTTAAAG
* *
2742309 TTTTTTATTTTTTAAAT
1 TTTTTTATTTATCAAAT
2742326 TTTTTTATTTATCAAAT
1 TTTTTTATTTATCAAAT
2742343 AATATATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTATTTATCAAAT
Found at i:2742976 original size:19 final size:20
Alignment explanation
Indices: 2742954--2742992 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2742944 GATAAAAAAA
2742954 AATTAGAG-AATTTTCTTAT
1 AATTAGAGAAATTTTCTTAT
* *
2742973 AATTTGAGAAATTTTTTTAT
1 AATTAGAGAAATTTTCTTAT
2742993 TATACCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
AATTAGAGAAATTTTCTTAT
Found at i:2749842 original size:27 final size:27
Alignment explanation
Indices: 2749772--2749860 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
2749762 ACATGAATTA
2749772 TTTTAATTT-TTAAAATAAA-TTTTAT
1 TTTTAATTTATTAAAATAAATTTTTAT
* *
2749797 ATTTTCATTATATTCAAATAAATTTTTAT
1 -TTTTAATT-TATTAAAATAAATTTTTAT
2749826 TTTTAATTTATCT-AAAT-AATTCTTTAT
1 TTTTAATTTAT-TAAAATAAATT-TTTAT
*
2749853 TTTAAATT
1 TTTTAATT
2749861 AAATAATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 11 0.20
27 20 0.37
28 17 0.31
29 6 0.11
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTAATTTATTAAAATAAATTTTTAT
Found at i:2749931 original size:30 final size:30
Alignment explanation
Indices: 2749897--2749999 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
2749887 TATAAATGAC
2749897 TTATTTAGATATAAATTAAAAGTTAAAAAT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
* * * **
2749927 TTATTTATATAAAAATTAAAGGTTAATGAT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
* * *
2749957 TTATTTAG-TACAAATTAAAATTTAAAAGT
1 TTATTTAGATATAAATTAAAAGTTAAAAAT
*
2749986 TTATTTAAATATAA
1 TTATTTAGATATAA
2750000 TAAAAATATA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.38
30 36 0.62
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.43
Consensus pattern (30 bp):
TTATTTAGATATAAATTAAAAGTTAAAAAT
Found at i:2750005 original size:29 final size:29
Alignment explanation
Indices: 2749968--2750045 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
2749958 TATTTAGTAC
* * *
2749968 AAATTAAAATTTAAAAGTTTATTTAAATA
1 AAATAAAAATATAAAAGTTTATCTAAATA
* * *
2749997 TAATAAAAATATAAGAGTTTATCTAATTA
1 AAATAAAAATATAAAAGTTTATCTAAATA
2750026 AAAT-AAAATGATAAAA-TTTA
1 AAATAAAAAT-ATAAAAGTTTA
2750046 GAGTTTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 9 0.22
29 31 0.77
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.37
Consensus pattern (29 bp):
AAATAAAAATATAAAAGTTTATCTAAATA
Found at i:2765690 original size:21 final size:22
Alignment explanation
Indices: 2765647--2765695 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2765637 ACCAATAGAT
* *
2765647 AATTAAA-CAAATTCAACATAA
1 AATTAAATCAAACTCAACAAAA
2765668 AATTAAATCAAACTC-ACAAAA
1 AATTAAATCAAACTCAACAAAA
2765689 AA-TAAAT
1 AATTAAAT
2765696 AAGACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 14 0.56
22 6 0.24
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.22
Consensus pattern (22 bp):
AATTAAATCAAACTCAACAAAA
Found at i:2767085 original size:14 final size:14
Alignment explanation
Indices: 2767068--2767097 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2767058 TTACTCTTAA
2767068 AATTTTTGTCTTTC
1 AATTTTTGTCTTTC
*
2767082 AATTTTTTTCTTTC
1 AATTTTTGTCTTTC
2767096 AA
1 AA
2767098 ATAACATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.03, T:0.63
Consensus pattern (14 bp):
AATTTTTGTCTTTC
Found at i:2771039 original size:13 final size:13
Alignment explanation
Indices: 2771023--2771051 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2771013 CACTTTATCT
2771023 TATCACTATTAAA
1 TATCACTATTAAA
2771036 TATCACTATTAAA
1 TATCACTATTAAA
2771049 TAT
1 TAT
2771052 TTGTTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TATCACTATTAAA
Found at i:2786488 original size:255 final size:255
Alignment explanation
Indices: 2786008--2786509 Score: 679
Period size: 255 Copynumber: 2.0 Consensus size: 255
2785998 CCCCCACAGC
* * * * **
2786008 ATTGGAAAGGAAGAGTTTGCATCACCAAAGGGAAATTGTTTTGGGAAATCAATGGCGTTGAAAGA
1 ATTGAAAAGGAAGAGTTTGCATCACCAAAGGGAAACTCTCTTGAAAAATCAATGGCGTTGAAAGA
* * *
2786073 AAGGTCTAAATATAGAAGAGTGGTCTTCCACAGCCAATTAGGCACAAAACCATGGATTTGGTTGT
66 AAGGTCTAAAGACAGAAGAGTGGTCTTCCACAACCAATTAGGCACAAAACCATGGATTTGGTTGT
* * * *
2786138 TAGAAAGATATAGGGCAACCAACTTGTCTTGTGTTTTGATGAATTCAGGAAATTCTGTAAGGTTG
131 TAGAAAGATATAGAGCAACCAACTTGCCTTGTGTTTTGATGAATTCAGGAAATCCAGTAAGGTTG
* * *
2786203 CAAGATCGTAGGCTAAGATAATATAATTGGGGAAA-AGTAAAGTTTTTGTTGTTGCTTTCA
196 CAAGACCGTAGGCTAAGATAATACAATTGGGGAAATA-TAAAGCTTTTGTTGTTGCTTTCA
* *
2786263 ATTGAAAAGGAGGAGTTTGCATCACCGAAA-GGAAACTCTCTTGAAAAATTAATGG-GATTGAAA
1 ATTGAAAAGGAAGAGTTTGCATCACC-AAAGGGAAACTCTCTTGAAAAATCAATGGCG-TTGAAA
2786326 GAAAGGTCTAAAGACAGAAGAGTGGTCTTCCACAACCAATTAGGCACAAAACCATGGATTTGGTT
64 GAAAGGTCTAAAGACAGAAGAGTGGTCTTCCACAACCAATTAGGCACAAAACCATGGATTTGGTT
* * * *
2786391 GTTAGAAAGATCTAGATCAGCCAACTTGCCTTGTGTTTTGATGAATTCTGGAAATCCAGTAAGGT
129 GTTAGAAAGATATAGAGCAACCAACTTGCCTTGTGTTTTGATGAATTCAGGAAATCCAGTAAGGT
* * * ** * *
2786456 TGCATGACCTTAGGGCTAA-CTCCTCCAATTGGGGAAATATAAGGCTTTTGTTGT
194 TGCAAGACCGTA-GGCTAAGATAATACAATTGGGGAAATATAAAGCTTTTGTTGT
2786510 CGCTCCCAAT
Statistics
Matches: 214, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
254 1 0.00
255 203 0.95
256 10 0.05
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (255 bp):
ATTGAAAAGGAAGAGTTTGCATCACCAAAGGGAAACTCTCTTGAAAAATCAATGGCGTTGAAAGA
AAGGTCTAAAGACAGAAGAGTGGTCTTCCACAACCAATTAGGCACAAAACCATGGATTTGGTTGT
TAGAAAGATATAGAGCAACCAACTTGCCTTGTGTTTTGATGAATTCAGGAAATCCAGTAAGGTTG
CAAGACCGTAGGCTAAGATAATACAATTGGGGAAATATAAAGCTTTTGTTGTTGCTTTCA
Found at i:2789790 original size:67 final size:68
Alignment explanation
Indices: 2789708--2789836 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 68
2789698 AAAATAGGAT
*
2789708 GAAAGAAAAACTTGAGAATTTGAAAATT-ATTTTTGTTTTCAAAGT-CTTTGAACCAATTGACAT
1 GAAAGAAAAACTTGAGAATTTAAAAATTCATTTTTGTTTTCAAAGTAC-TTGAACCAATTGACAT
2789771 GGTA
65 GGTA
* * * * *
2789775 GAAATAAAACCTTGAGAATTTAAAAATTGCTTTTTTTTTTTCAAAGTACTTGAACCTATTGA
1 GAAAGAAAAACTTGAGAATTTAAAAATT-CATTTTTGTTTTCAAAGTACTTGAACCAATTGA
2789837 AACAATAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 25 0.47
69 27 0.51
70 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (68 bp):
GAAAGAAAAACTTGAGAATTTAAAAATTCATTTTTGTTTTCAAAGTACTTGAACCAATTGACATG
GTA
Found at i:2789846 original size:69 final size:67
Alignment explanation
Indices: 2789708--2789863 Score: 163
Period size: 69 Copynumber: 2.3 Consensus size: 67
2789698 AAAATAGGAT
* * * ***
2789708 GAAAGAAAAACTTGAGAATTTGAAAATTATTTTTGTTTTCAAAGTCTTTGAACCAATTGACATGG
1 GAAAAAAAAACTTGAGAATTTAAAAATTATTTTTGTTTTCAAAGTCTTTGAACCAATTGAAACAA
2789773 TA
66 TA
* * * * *
2789775 GAAATAAAACCTTGAGAATTTAAAAATTGCTTTTTTTTTTTCAAAGTAC-TTGAACCTATTGAAA
1 GAAAAAAAAACTTGAGAATTTAAAAATT--ATTTTTGTTTTCAAAGT-CTTTGAACCAATTGAAA
2789839 CAATA
63 CAATA
*
2789844 GAAAAAAAAA-TAGAGAATTT
1 GAAAAAAAAACTTGAGAATTT
2789864 TCTTAGAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
67 25 0.34
68 9 0.12
69 38 0.52
70 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (67 bp):
GAAAAAAAAACTTGAGAATTTAAAAATTATTTTTGTTTTCAAAGTCTTTGAACCAATTGAAACAA
TA
Found at i:2801201 original size:27 final size:28
Alignment explanation
Indices: 2801126--2801210 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
2801116 ACATGAATTA
*
2801126 TTTTAATTT-T-TAAAATATTTTTTATAT
1 TTTTAATTTATCTAAAATAATTTTTAT-T
*
2801153 TTTT-A-TTATACTCAAATAAATTTTTATT
1 TTTTAATTTAT-CTAAAAT-AATTTTTATT
2801181 TTTTAATTTATCT-AAATAATTCTTTATT
1 TTTTAATTTATCTAAAATAATT-TTTATT
2801209 TT
1 TT
2801211 AAATGAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 8 0.16
28 22 0.45
29 11 0.22
30 4 0.08
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTAATTTATCTAAAATAATTTTTATT
Found at i:2801273 original size:30 final size:30
Alignment explanation
Indices: 2801239--2801334 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
2801229 TATAAAAAAC
*
2801239 TTATTGACATATAAATTAAAAGTTAAAATT
1 TTATTTACATATAAATTAAAAGTTAAAATT
* * ***
2801269 TTATTTACATAAAAATTAAAGGTTAATGGT
1 TTATTTACATATAAATTAAAAGTTAAAATT
*
2801299 TTATTTA-ATATAAATTAAAATTTAATAA-T
1 TTATTTACATATAAATTAAAAGTTAA-AATT
2801328 TTATTTA
1 TTATTTA
2801335 AATGTAATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
29 23 0.43
30 31 0.57
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (30 bp):
TTATTTACATATAAATTAAAAGTTAAAATT
Found at i:2801314 original size:29 final size:29
Alignment explanation
Indices: 2801247--2801335 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 29
2801237 ACTTATTGAC
2801247 ATATAAATTAAAAGTTAA-AATTTTATTTA
1 ATATAAATTAAAAGTTAATAA-TTTATTTA
* * **
2801276 CATAAAAATTAAAGGTTAATGGTTTATTTA
1 -ATATAAATTAAAAGTTAATAATTTATTTA
*
2801306 ATATAAATTAAAATTTAATAATTTATTTA
1 ATATAAATTAAAAGTTAATAATTTATTTA
2801335 A
1 A
2801336 ATGTAATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 25 0.51
30 24 0.49
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (29 bp):
ATATAAATTAAAAGTTAATAATTTATTTA
Found at i:2801347 original size:29 final size:29
Alignment explanation
Indices: 2801298--2801372 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
2801288 AGGTTAATGG
* * *
2801298 TTTATTTAATATAAATTAAAATTTAATAA
1 TTTATTTAATATAAATAAAAATATAAGAA
*
2801327 TTTATTTAA-ATGTAATAAAAATATAAGAA
1 TTTATTTAATAT-AAATAAAAATATAAGAA
*
2801356 TTTA-CTAATAATAAATA
1 TTTATTTAAT-ATAAATA
2801373 CATATGTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 5 0.14
29 30 0.81
30 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTATTTAATATAAATAAAAATATAAGAA
Found at i:2801837 original size:18 final size:18
Alignment explanation
Indices: 2801816--2801857 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2801806 CAATACTTTA
2801816 AAATATA-ATTTTACTTAT
1 AAATATATATTTTA-TTAT
2801834 AAATA-ATATTTTATTAT
1 AAATATATATTTTATTAT
2801851 -AATATAT
1 AAATATAT
2801858 TAGTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATATATTTTATTAT
Found at i:2801864 original size:28 final size:29
Alignment explanation
Indices: 2801832--2801907 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 29
2801822 AATTTTACTT
*
2801832 ATAAATAATATT-TTATTATAATATATTA
1 ATAAATAATATTATTATTATAATATATCA
* *
2801860 GTAAATAATATGTTATTAATATAATATATCA
1 ATAAATAATA--TTATTATTATAATATATCA
2801891 ATAAATAATATTATTAT
1 ATAAATAATATTATTAT
2801908 ATTAATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 9 0.22
29 6 0.15
30 2 0.05
31 23 0.57
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
ATAAATAATATTATTATTATAATATATCA
Found at i:2801867 original size:15 final size:15
Alignment explanation
Indices: 2801832--2801906 Score: 64
Period size: 15 Copynumber: 5.0 Consensus size: 15
2801822 AATTTTACTT
*
2801832 ATAAATAATAT-TTT
1 ATAAATAATATATTA
*
2801846 AT-TATAATATATTA
1 ATAAATAATATATTA
* *
2801860 GTAAATAATATGTTA
1 ATAAATAATATATTA
* *
2801875 TTAATATAATATATCA
1 ATAA-ATAATATATTA
2801891 ATAAATAATATTATTA
1 ATAAATAATA-TATTA
2801907 TATTAATAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
13 7 0.15
14 5 0.11
15 19 0.40
16 16 0.34
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAAATAATATATTA
Found at i:2801914 original size:21 final size:21
Alignment explanation
Indices: 2801876--2801939 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
2801866 AATATGTTAT
2801876 TAATA-TAATATATCAATAAA
1 TAATATTAATATATCAATAAA
* *
2801896 TAATATTATTATATTAATAAA
1 TAATATTAATATATCAATAAA
* *
2801917 TAATATAAAGA-AT-AATAAA
1 TAATATTAATATATCAATAAA
2801936 TAAT
1 TAAT
2801940 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 21 0.55
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATTAATATATCAATAAA
Found at i:2801921 original size:28 final size:29
Alignment explanation
Indices: 2801832--2801921 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 29
2801822 AATTTTACTT
*
2801832 ATAAATAATATT-TTAT-TATAATATATTA
1 ATAAATAATATTATTATATATAATA-AATA
* *
2801860 GTAAATAATATGTTATTA-ATATAATATATCA
1 ATAAATAATA--TTATTATATATAATAAAT-A
2801891 ATAAATAATATTATTATAT-TAATAAATA
1 ATAAATAATATTATTATATATAATAAATA
2801919 ATA
1 ATA
2801922 TAAAGAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
28 13 0.25
29 13 0.25
30 5 0.10
31 20 0.39
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (29 bp):
ATAAATAATATTATTATATATAATAAATA
Found at i:2801992 original size:18 final size:17
Alignment explanation
Indices: 2801938--2801992 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
2801928 ATAATAAATA
*
2801938 ATTTTATTTTAAGTATT
1 ATTTTATTTTAAATATT
* *
2801955 -TTTTATATTAACATAAT
1 ATTTTATTTTAA-ATATT
2801972 ATTTTAATTTTAAATATT
1 ATTTT-ATTTTAAATATT
2801990 ATT
1 ATT
2801993 ATAAAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 11 0.37
19 6 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTATTTTAAATATT
Found at i:2802082 original size:25 final size:24
Alignment explanation
Indices: 2802017--2802082 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 24
2802007 TTTTTTAATA
2802017 TTAATAATTTTAATAATAAATATTT
1 TTAAT-ATTTTAATAATAAATATTT
*
2802042 TCAATCTATTTTAATAATAAATAATTT
1 TTAA--TATTTTAATAATAAAT-ATTT
2802069 TTAATATTTTAATA
1 TTAATATTTTAATA
2802083 GTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 13 0.36
26 15 0.42
27 8 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATATTTTAATAATAAATATTT
Found at i:2805039 original size:73 final size:73
Alignment explanation
Indices: 2804910--2805048 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
2804900 AAAATACGAT
* * *
2804910 TTTTGTTGAAAATATGAAAATTTTATTTTTTATAATTCAACAAAGAGGATGATTTTAAAATAAAA
1 TTTTGTTGAAAATATGAAAATTTTATTTTTTAAAATTCAACAAAAACGAT-ATTTTAAAATAAAA
2804975 AAAACATGG
65 AAAACATGG
* * * *
2804984 TTTTGTT-TAAATATGAAAATTTTATTTTTTAAAAATTTAATAAAAACGACT-TTTTAAAGTAAA
1 TTTTGTTGAAAATATGAAAATTTTATTTTTT-AAAATTCAACAAAAACGA-TATTTTAAAATAAA
2805047 AA
64 AA
2805049 CGTAGTCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
73 35 0.62
74 20 0.36
75 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (73 bp):
TTTTGTTGAAAATATGAAAATTTTATTTTTTAAAATTCAACAAAAACGATATTTTAAAATAAAAA
AAACATGG
Found at i:2805295 original size:114 final size:113
Alignment explanation
Indices: 2805073--2805302 Score: 282
Period size: 115 Copynumber: 2.0 Consensus size: 113
2805063 AAAAGACAAC
* * * *
2805073 ATTTCCAAAATAAAAATACAGTTTTTGTTATAAACATGAAAAAAATATTTTTCAAAATTTAATAA
1 ATTTCCAAAATAAAAATACAGTCTTTGTTAAAAACATGAAAAAAATATTTATCAAAATTTAACAA
* * *
2805138 AAACAATGTTTCTAAGATAGAAAATATGATTTTTATTGAAAAAAATGAT
66 AAACAACGTTTCTAAGATAGAAAACATGATATTTATTGAAAAAAAT-AT
* * * *
2805187 ATTTCTAAAATAAAAATATAGTCTTTGTTAAAAACATGAAAAAATATATTTATCAAGATTTTACA
1 ATTTCCAAAATAAAAATACAGTCTTTGTTAAAAACATGAAAAAA-ATATTTATCAAAATTTAACA
* * * *
2805252 AAGACAACGTTTTTAATATAGAAAACAT-AGTATTTGTTGAAAAAATATAT
65 AAAACAACGTTTCTAAGATAGAAAACATGA-TATTTATTGAAAAAA-ATAT
2805302 A
1 A
2805303 ATTTTTAGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
114 41 0.42
115 55 0.56
116 2 0.02
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (113 bp):
ATTTCCAAAATAAAAATACAGTCTTTGTTAAAAACATGAAAAAAATATTTATCAAAATTTAACAA
AAACAACGTTTCTAAGATAGAAAACATGATATTTATTGAAAAAAATAT
Found at i:2805399 original size:40 final size:40
Alignment explanation
Indices: 2805323--2805401 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
2805313 TTCAATAAAG
* * * *
2805323 ACAATATTTCTAAAATAAAAACGTAATCTTTGTTGAAAAT
1 ACAATATTTCTAAAATAAAAACGAAATATCTATTGAAAAT
* * *
2805363 ACAATATTTTTAAGATAAAAATGAAATATCTATTGAAAA
1 ACAATATTTCTAAAATAAAAACGAAATATCTATTGAAAA
2805402 CATGAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (40 bp):
ACAATATTTCTAAAATAAAAACGAAATATCTATTGAAAAT
Found at i:2806801 original size:31 final size:32
Alignment explanation
Indices: 2806710--2806802 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
2806700 AATTGTTGTG
* * *
2806710 TAATATTTTAAAATGATATGGACTTTTTTATT
1 TAATATTTTAAAATGATATGAAATTTTTTACT
* * *
2806742 TAATATTTTAAATTAATAT-AAAGATTTTTACT
1 TAATATTTTAAAATGATATGAAA-TTTTTTACT
2806774 TAAT-TTTTAAAATGATATGAAATTTTTTA
1 TAATATTTTAAAATGATATGAAATTTTTTA
2806803 AAATGATTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 19 0.38
32 31 0.62
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (32 bp):
TAATATTTTAAAATGATATGAAATTTTTTACT
Found at i:2806820 original size:21 final size:20
Alignment explanation
Indices: 2806777--2806823 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2806767 TTTTACTTAA
2806777 TTTTTAAAATGATATGAAAT
1 TTTTTAAAATGATATGAAAT
* **
2806797 TTTTTAAAATGATTTTTAAT
1 TTTTTAAAATGATATGAAAT
2806817 TTTTTAA
1 TTTTTAA
2806824 CTTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTTTAAAATGATATGAAAT
Found at i:2806831 original size:20 final size:19
Alignment explanation
Indices: 2806794--2806856 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
2806784 AATGATATGA
* *
2806794 AATTTTTTAAAATGATTTTT
1 AATTTTTT-AATTAATTTTT
2806814 AATTTTTTAACTTAA-TTTT
1 AATTTTTTAA-TTAATTTTT
*
2806833 -ATTTTTTGAATTTATTTTT
1 AATTTTTT-AATTAATTTTT
2806852 AATTT
1 AATTT
2806857 AAAAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.28
19 12 0.33
20 14 0.39
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (19 bp):
AATTTTTTAATTAATTTTT
Found at i:2806832 original size:19 final size:20
Alignment explanation
Indices: 2806810--2806856 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2806800 TTAAAATGAT
2806810 TTTTAATTTTTT-AACTTAA
1 TTTTAATTTTTTGAACTTAA
* *
2806829 TTTT-ATTTTTTGAATTTAT
1 TTTTAATTTTTTGAACTTAA
2806848 TTTTAATTT
1 TTTTAATTT
2806857 AAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTAATTTTTTGAACTTAA
Found at i:2812615 original size:2 final size:2
Alignment explanation
Indices: 2812608--2812640 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2812598 CTTCACTTGA
2812608 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
2812641 GAGAGAGAGA
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:2812806 original size:2 final size:2
Alignment explanation
Indices: 2812799--2812833 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2812789 CTTCACTTGA
2812799 AT 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 AT A
2812834 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.