Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold402
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: 314471
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.31
Warning! 21029 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:184491 original size:3 final size:3
Alignment explanation
Indices: 184483--184536 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
184473 ACTTCGTTAC
184483 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
184531 TAT TAT
1 TAT TAT
184537 ATAGTTTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:185832 original size:24 final size:26
Alignment explanation
Indices: 185798--185849 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
185788 TTTATTCATG
185798 TTGTTTGAAGC-TTTTTATTTTAATT
1 TTGTTTGAAGCTTTTTTATTTTAATT
185823 TTGTTT-AAGCTTTTTTATTTTAATT
1 TTGTTTGAAGCTTTTTTATTTTAATT
185848 TT
1 TT
185850 TAATTAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (26 bp):
TTGTTTGAAGCTTTTTTATTTTAATT
Found at i:187325 original size:124 final size:124
Alignment explanation
Indices: 187083--187524 Score: 618
Period size: 124 Copynumber: 3.5 Consensus size: 124
187073 GATAAAATCA
* * * * * * * *
187083 AAGCAGGATGATTTATTAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
* *
187148 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAAGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTTAAAAAAGCTTC
* * * *
187207 AACCAGGATGCTTTATGAGAAGAATTTGTGAAATCGTGCCCTCATGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
*
187272 TGGTCCTGGAAGAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTT-AAAAAA-GCTTC
* *
187334 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
** * * *
187399 AGGTCCTGGAAAAATAATTTCGACATGATGTTTCTAAGCAAATAGTATAAAATCA-CTT-
66 AGGTCCTGGAAAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTTAAAA-AAGCTTC
*
187457 ATAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACCCGCTTTTGCTACAG
1 A-AGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACGCGCTTTTGCTACAG
187522 TAG
65 TAG
187525 CATGTTTGGG
Statistics
Matches: 285, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
123 1 0.00
124 129 0.45
125 39 0.14
126 40 0.14
127 76 0.27
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACATGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTTTAAAAAAGCTTC
Found at i:189579 original size:22 final size:22
Alignment explanation
Indices: 189493--190669 Score: 1419
Period size: 22 Copynumber: 54.0 Consensus size: 22
189483 TCAAATTATA
189493 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189514 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * **
189535 TTTTATTTAAGAG-TTACAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
189556 TTAAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
189578 TTTAATTTAAGGG-TTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189599 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189621 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
189642 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189663 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189685 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
189707 TTTAATTTAAAGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189729 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189751 TTTAAGTTTCAGGGTTT-GGGTT
1 TTTAAG-TTAAGGGTTTAGGGTT
* * *
189773 TTAAAGTTAAAGG-TTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
** *
189794 TTTAAGTTAAAAGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
189816 TTTAATTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189838 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
189860 TTTAAGTTAAGGG-TTAGGGGTT
1 TTTAAGTTAAGGGTTTA-GGGTT
189882 TTTAA-TTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
189903 TTAAATTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
189925 TTTAAGTTAAAGGG-TTAGGGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
*
189947 TTTAAGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
189968 TTCAAGTTAAAGGG-TTAGGGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
* *
189990 TTTAATTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190012 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190034 TTTAAGCTAAAGGG-TTAGGGTT
1 TTTAAG-TTAAGGGTTTAGGGTT
* *
190056 TTAAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190077 TTTAAGTTAAAGGTTTAGGGTA
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190099 TTTAATTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
190121 TTTAAGTTAAGGGGTTAGGGGC
1 TTTAAGTTAAGGGTTTAGGGTT
*
190143 TTTAAGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190164 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190186 TTTAAGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
190208 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
190229 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
190251 TTTAATTTAAGGGGTTAGGTTT
1 TTTAAGTTAAGGGTTTAGGGTT
190273 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190294 TTTAAGTTAAGGGGTTGGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190316 TTTAAGTTAAGGGGTTGGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
190338 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190360 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190381 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190403 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
190425 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190446 TTTAGGTTAAGGGTTTTTGGTTTTTGGTT
1 TTTAAGTTAAGGG--TTTAG-----GGTT
*
190475 TTTAAGTTAAGGGTTTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
190497 TTTATGTTAAAGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190519 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190541 TTTAAGTTAAGGGTTTGGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
190563 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
190584 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
***
190606 TTTAAGTTAATATTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
190628 TTTAATTTAAGGG-TTAGGGGT
1 TTTAAGTTAAGGGTTTAGGGTT
190649 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
190670 AGCGTTTTTA
Statistics
Matches: 1001, Mismatches: 128, Indels: 54
0.85 0.11 0.05
Matches are distributed among these distances:
20 2 0.00
21 329 0.33
22 628 0.63
23 19 0.02
24 3 0.00
27 4 0.00
29 16 0.02
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:189635 original size:65 final size:65
Alignment explanation
Indices: 189493--190669 Score: 1358
Period size: 65 Copynumber: 18.0 Consensus size: 65
189483 TCAAATTATA
* * * **
189493 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTA-TTTAAGAG-TTACAGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAG-GTTTAGGGT
189555 T
65 T
* * * * *
189556 TTAAAGTTAAGGGTTTAGTGTTTTTAATTTAAGGGTTACGATTTTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
*
189621 TTAAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
* * * * * *
189685 TTTAATTTAAGGGTTTAGGGTTTTTAATTTAAAGGTTTAGTGTTTTTAATTTAAGGGTTTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
189750 T
65 T
* * * * * *
189751 TTTAAGTTTCAGGGTTT-GGGTTTTAAAGTTAAAGGTTAGGGGTTTTAAGTTAAAAGTTTAAGGT
1 TTTAAG-TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
189815 T
65 T
* * * *
189816 TTTAATTTAAGGGTTTAGGATTTTTAATTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGG
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGGTTTA-GGG
189880 TT
64 TT
* * * *
189882 TTTAA-TTAAGGGTTTAGGGTTTTAAATTTAAAGGTTTAGGGTTTTTAAGTTAAAGGGTTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
189946 T
65 T
* * *
189947 TTTAAGTTAAGGG-TTAGAGTTTTCAAGTTAAAGGGTTAGGGTTTTTAA-TTTAAGAGTTTAGGG
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAG-GTTTAGGG
190010 TT
64 TT
* * *
190012 TTTAATTTAAGGGTTTAGGGTTTTTAAGCTAAAGGGTTAGGGTTTTAAAGTT-AA-GTGTTAGGG
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAG-TTAAGGGTTAGGGTTTTTAAGTTAAAGGT-TTAGGG
190075 TT
64 TT
* * * * * * *
190077 TTTAAGTTAAAGGTTTAGGGTATTTAATTTAAGAGTTTAGGGTTTTTAAGTTAAGGGGTTAGGGG
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
*
190142 C
65 T
* * * *
190143 TTTAAGTTAAGTG-TTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGAT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGGTTTAGGGT
190207 T
65 T
* * * *
190208 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGGTTAGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGGTTTAGGGT
190272 T
65 T
* * * *
190273 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGGTTGGGGTTTTTAAGTTAAGGGGTTGGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
190337 T
65 T
*
190338 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGTGTTTTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
* * * *
190403 TTTAATTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTTTGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGG--TTTAG--
190468 TTTGGTT
62 ---GGTT
* * * * * *
190475 TTTAAGTTAAGGGTTTAGGGGTTTTATGTTAAAGGTTTATGGTTTTTAAGTTAAGGGGTTAGGGT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
190540 T
65 T
* * *
190541 TTTAAGTTAAGGGTTTGGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
*** * * *
190606 TTTAAGTTAATATTTTAGGGTTTTTAATTTAAGGGTTAGGGGTTTTAAGTT-AAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
190670 AGCGTTTTTA
Statistics
Matches: 962, Mismatches: 121, Indels: 61
0.84 0.11 0.05
Matches are distributed among these distances:
63 12 0.01
64 118 0.12
65 567 0.59
66 191 0.20
67 17 0.02
71 3 0.00
72 31 0.03
73 23 0.02
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.46
Consensus pattern (65 bp):
TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGTT
Found at i:189775 original size:87 final size:88
Alignment explanation
Indices: 189493--190669 Score: 1368
Period size: 87 Copynumber: 13.5 Consensus size: 88
189483 TCAAATTATA
* * * **
189493 TTTAAG-TTAAGGG-TTAGGGTTTTTAAGTTAAGTGTTAGGGTTTTTTA-TTTAAGAG-TTACAG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAG-GTTTAGGG
* *
189554 TTTTAAAGTTAAGGGTTTAGTGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
189578 TTTAA-TTTAAGGG-TTACGATTTTTAAGTTAAAGGTTTAGGGTTTTAAAGTT-AAGGGTTAGGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGG
189640 TTTTTAAGTTAAGGG-TTAGGGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * *
189663 TTTAAG-TTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGGGTTTTTAATTTAAAGGTTTAGTG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGGTTTAGGG
*
189727 TTTTTAATTTAAGGGTTTAGGGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * * * *
189751 TTTAAGTTTCAGGGTTT-GGGTTTTAAAGTTAAAGGTTAGGGGTTTTAAGTTAAAAGTTTAAGGT
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
* *
189815 TTTTAATTTAAGGGTTTAGGATT
66 TTTTAAGTTAAGGGTTTAGGGTT
*
189838 TTTAA-TTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGGTTTTTAA-TTAAGGGTTTAGGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTA-GGGTTTTTAAGTTAAAGGTTTAGGG
* * *
189901 TTTTAAATTTAAAGGTTTAGGGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * *
189925 TTTAAGTTAAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTCAAGTTAAAGGGTTAGGGT
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
* *
189989 TTTTAATTTAAGAGTTTAGGGTT
66 TTTTAAGTTAAGGGTTTAGGGTT
* *
190012 TTTAA-TTTAAGGGTTTAGGGTTTTTAAGCTAAAGGGTTAGGGTTTTAAAGTT-AA-GTGTTAGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAG-TTAAGGGTTAGGGTTTTTAAGTTAAAGGT-TTAGG
* *
190074 GTTTTTAAGTTAAAGGTTTAGGGTA
64 GTTTTTAAGTTAAGGGTTTAGGGTT
* **
190099 TTTAA-TTTAAGAGTTTAGGGTTTTTAAGTTAAGGGGTTAGGGGCTTTAAGTT-AA-GTGTTAGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAAGGT-TTAGG
*
190161 GTTTTTAAGTTAAGGGTTTATGGTT
64 GTTTTTAAGTTAAGGGTTTAGGGTT
* *
190186 TTTAAG-TTAAGGGTTTAGGATTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
* * *
190250 TTTTAATTTAAGGGGTTAGGTTT
66 TTTTAAGTTAAGGGTTTAGGGTT
* * * *
190273 TTTAAG-TTAAGGG-TTAGGGTTTTTAAGTTAAGGGGTTGGGGTTTTTAAGTTAAGGGGTTGGGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAAGGTTTAGGG
190336 TTTTTAAGTTAAGGGTTTAGGGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * *
190360 TTTAAG-TTAAGGG-TTAGTGTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGGG
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGG
190423 TTTTTAAGTTAAGGG-TTAGGGTT
65 TTTTTAAGTTAAGGGTTTAGGGTT
* * * *
190446 TTT-AGGTTAAGGGTTTTTGGTTTTTGGTTTTTAAGTTAAGGGTTTAGGGGTTTTATGTTAAAGG
1 TTTAAGTTTAAGGG--TTTAG-----GGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGG
* *
190510 TTTATGGTTTTTAAGTTAAGGGGTTAGGGTT
58 TTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
190541 TTTAAG-TTAAGGGTTTGGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTATGGT
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
***
190605 TTTTAAGTTAATATTTTAGGGTT
66 TTTTAAGTTAAGGGTTTAGGGTT
*
190628 TTTAA-TTTAAGGG-TTAGGGGTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
190670 AGCGTTTTTA
Statistics
Matches: 951, Mismatches: 105, Indels: 71
0.84 0.09 0.06
Matches are distributed among these distances:
85 51 0.05
86 170 0.18
87 555 0.58
88 86 0.09
89 11 0.01
93 9 0.01
94 49 0.05
95 18 0.02
96 2 0.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.46
Consensus pattern (88 bp):
TTTAAGTTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGGGT
TTTTAAGTTAAGGGTTTAGGGTT
Found at i:190499 original size:29 final size:29
Alignment explanation
Indices: 190442--190499 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
190432 TAAGGGTTAG
* ** *
190442 GGTTTTTAGGTTAAGGGTTTTTGGTTTTT
1 GGTTTTTAAGTTAAGGGTTTAGGGGTTTT
190471 GGTTTTTAAGTTAAGGGTTTAGGGGTTTT
1 GGTTTTTAAGTTAAGGGTTTAGGGGTTTT
190500 ATGTTAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (29 bp):
GGTTTTTAAGTTAAGGGTTTAGGGGTTTT
Found at i:190668 original size:27 final size:27
Alignment explanation
Indices: 190637--190690 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
190627 TTTTAATTTA
*
190637 AGGGTTAGGGGTTTTAAGTTAAGGGTT
1 AGGGTTAGCGGTTTTAAGTTAAGGGTT
* *
190664 AGGGTTAGCGTTTTTAGGTTAAGGGTT
1 AGGGTTAGCGGTTTTAAGTTAAGGGTT
190691 TAAGGTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (27 bp):
AGGGTTAGCGGTTTTAAGTTAAGGGTT
Found at i:191265 original size:18 final size:18
Alignment explanation
Indices: 191239--191281 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
191229 GACTCGGAAA
* *
191239 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
191257 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
191275 AGGAAAC
1 AGGAAAC
191282 GCACCTAGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:192161 original size:20 final size:20
Alignment explanation
Indices: 192124--192161 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
192114 TTTATTTTTA
*
192124 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
192144 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
192162 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:193549 original size:29 final size:29
Alignment explanation
Indices: 193494--193548 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
193484 TAGGGGAAAA
193494 GGGCCCATTCCGGTAAATAATAAAAAACC
1 GGGCCCATTCCGGTAAATAATAAAAAACC
* *
193523 GGGCCCATTTCGGTAAAT-TTAAAAAA
1 GGGCCCATTCCGGTAAATAATAAAAAA
193549 AATTAGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (29 bp):
GGGCCCATTCCGGTAAATAATAAAAAACC
Found at i:194136 original size:11 final size:11
Alignment explanation
Indices: 194117--194173 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
194107 GGCCCGATAT
*
194117 AATAATTTTAA
1 AATATTTTTAA
194128 AATATTTTT-A
1 AATATTTTTAA
194138 AAT-TTTTT--
1 AATATTTTTAA
194146 -A-A-TTTTAA
1 AATATTTTTAA
194154 AATATTTTTAA
1 AATATTTTTAA
194165 AATATTTTT
1 AATATTTTT
194174 TTAATTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 4 0.10
7 1 0.03
9 6 0.15
10 5 0.13
11 23 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:194150 original size:16 final size:17
Alignment explanation
Indices: 194131--194164 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
194121 ATTTTAAAAT
*
194131 ATTTTTAAAT-TTTTTA
1 ATTTTAAAATATTTTTA
194147 ATTTTAAAATATTTTTA
1 ATTTTAAAATATTTTTA
194164 A
1 A
194165 AATATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTAAAATATTTTTA
Found at i:198025 original size:6 final size:6
Alignment explanation
Indices: 198014--198039 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
198004 AGAGGAAAAC
198014 AAAGGA AAAGGA AAAGGA AAAGGA AA
1 AAAGGA AAAGGA AAAGGA AAAGGA AA
198040 GAGCGAAGCG
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:201714 original size:20 final size:20
Alignment explanation
Indices: 201674--201714 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
201664 GCAGATGAAG
* *
201674 AAAGCTTGGCATGTGATAAT
1 AAAGCTTGGCATGCGACAAT
201694 AAAGCTTGGCATGCGACAAT
1 AAAGCTTGGCATGCGACAAT
201714 A
1 A
201715 GAGTTGTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
AAAGCTTGGCATGCGACAAT
Found at i:204662 original size:45 final size:44
Alignment explanation
Indices: 204593--204699 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 44
204583 GCTATACACC
* * * *
204593 TAAATTGAGTATGACCATAGCTGAATGATGCTATAACATCATCAT
1 TAAAATGAGTATGACCATAGCTGAAAGATGATATAACATCAT-AA
**
204638 TAAAATGAGTATGACCATAGCTGAAAGATGATATAGTATCATAA
1 TAAAATGAGTATGACCATAGCTGAAAGATGATATAACATCATAA
*
204682 TAGAAATGAGTAAGACCA
1 TA-AAATGAGTATGACCA
204700 CGGCTAAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 3 0.06
45 51 0.94
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (44 bp):
TAAAATGAGTATGACCATAGCTGAAAGATGATATAACATCATAA
Found at i:210630 original size:70 final size:70
Alignment explanation
Indices: 210450--210611 Score: 315
Period size: 70 Copynumber: 2.3 Consensus size: 70
210440 CTTTTAACTT
210450 AAAGAGTAAACATTTATCAAAATGACATATTTTTTTCTTTTAATGTAATGGTTTTGACTTTTAAC
1 AAAG-GTAAACATTTATCAAAATGACATATTTTTTTCTTTTAATGTAATGGTTTTGACTTTTAAC
210515 TTTAGA
65 TTTAGA
210521 AAAGGTAAACATTTATCAAAATGACATATTTTTTTCTTTTAATGTAATGGTTTTGACTTTTAACT
1 AAAGGTAAACATTTATCAAAATGACATATTTTTTTCTTTTAATGTAATGGTTTTGACTTTTAACT
210586 TTAGA
66 TTAGA
210591 AAAGGTAAACATTTATCAAAA
1 AAAGGTAAACATTTATCAAAA
210612 CGACGTAGTT
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 87 0.96
71 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (70 bp):
AAAGGTAAACATTTATCAAAATGACATATTTTTTTCTTTTAATGTAATGGTTTTGACTTTTAACT
TTAGA
Found at i:214968 original size:17 final size:18
Alignment explanation
Indices: 214946--214987 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
214936 TGGGAGATGG
214946 CAATTTTTCTAT-CACTT
1 CAATTTTTCTATCCACTT
214963 CAATTTTTTTCTATCCACTT
1 CAA--TTTTTCTATCCACTT
214983 CAATT
1 CAATT
214988 CCTTTCTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 2 0.09
19 9 0.41
20 8 0.36
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (18 bp):
CAATTTTTCTATCCACTT
Found at i:214973 original size:19 final size:20
Alignment explanation
Indices: 214949--214987 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
214939 GAGATGGCAA
214949 TTTTTCTAT-CACTTCAATT
1 TTTTTCTATCCACTTCAATT
214968 TTTTTCTATCCACTTCAATT
1 TTTTTCTATCCACTTCAATT
214988 CCTTTCTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTCTATCCACTTCAATT
Found at i:214993 original size:20 final size:19
Alignment explanation
Indices: 214951--214994 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
214941 GATGGCAATT
**
214951 TTTCTATCACTTCAATTTT
1 TTTCTATCACTTCAATTCC
214970 TTTCTATCCACTTCAATTCC
1 TTTCTAT-CACTTCAATTCC
214990 TTTCT
1 TTTCT
214995 GTGATATCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTCTATCACTTCAATTCC
Found at i:218482 original size:14 final size:15
Alignment explanation
Indices: 218457--218493 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
218447 CCTGTAGAAA
218457 TTAAATTAAACTAAG
1 TTAAATTAAACTAAG
218472 TTAAA-TAAACTAA-
1 TTAAATTAAACTAAG
*
218485 TGAAATTAA
1 TTAAATTAA
218494 GTAAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 11 0.55
15 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (15 bp):
TTAAATTAAACTAAG
Found at i:224898 original size:50 final size:50
Alignment explanation
Indices: 224839--224937 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
224829 TAGAGCTGGT
224839 AGTAACACAATACATAACAATTCCAATCAAGCAGCTAAGAAGCACATCTA
1 AGTAACACAATACATAACAATTCCAATCAAGCAGCTAAGAAGCACATCTA
*
224889 AGTAACACAATACATAACAATTCCAATCAAGCGGCTAAGAAGCACATCT
1 AGTAACACAATACATAACAATTCCAATCAAGCAGCTAAGAAGCACATCT
224938 TCCATAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.18
Consensus pattern (50 bp):
AGTAACACAATACATAACAATTCCAATCAAGCAGCTAAGAAGCACATCTA
Found at i:228122 original size:3 final size:3
Alignment explanation
Indices: 228114--228143 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
228104 CTTTGATCAC
228114 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
228144 ATTTTGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:229486 original size:44 final size:44
Alignment explanation
Indices: 229420--229550 Score: 144
Period size: 43 Copynumber: 3.0 Consensus size: 44
229410 ATAGGATTTC
*
229420 GATA-TGAGATTTGGTGTAAGACCAAGTCTGGGACGTTGGCATT
1 GATATTGAGATTTCGTGTAAGACCAAGTCTGGGACGTTGGCATT
** *
229463 GAT-TTGAGACTTTCGTGTAAGACCCTGTCTGGGACAG-TGGCATC
1 GATATTGAGA-TTTCGTGTAAGACCAAGTCTGGGAC-GTTGGCATT
* * * *
229507 GATATT-TGATTACATGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATTGAGATTTCGTGTAAGACCAAGTCTGGGACGTTGGCATT
229550 G
1 G
229551 TACGAGCTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 36 0.49
44 33 0.45
45 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (44 bp):
GATATTGAGATTTCGTGTAAGACCAAGTCTGGGACGTTGGCATT
Found at i:229537 original size:43 final size:44
Alignment explanation
Indices: 229434--229548 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 44
229424 TGAGATTTGG
* * * *
229434 TGTAAGACCAAGTCTGGGACGTTGGCATTGATTTGAGACTTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGACTTACA
*
229478 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT-TTGAGACTTACA
229521 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
229549 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 27 0.44
44 30 0.49
45 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGACTTACA
Found at i:231905 original size:155 final size:151
Alignment explanation
Indices: 231746--232045 Score: 342
Period size: 155 Copynumber: 1.9 Consensus size: 151
231736 CGTTTAACAA
*
231746 ATTTTATT-C-GATTTTG-TTTCCAAAATTA-GAAGT-AAATAAAATCCA-TTTCGGGATTTATT
1 ATTTTATTCCAGATTTTGTTTTCCAAAA--ACG-AGTAAAATAAAAT-CAGTTTCGGGATTGATT
* * * *
231805 CCCGCTGTTCAATGAATTTTATTCCATTATTTTGATTTTATTTCCAAAAACGAGTAAAATAAAAT
62 CCAGCCGTTCAACG-ATTTTATT-CA--AATTT--TTTTATTTCCAAAAACGAGTAAAATAAAAT
231870 CCGTTTCGGGATTGATTCCCGCCATTTAACG
121 CCGTTTCGGGATTGATTCCCGCCATTTAACG
* *
231901 ATTTTTTTCCATATTTTGTTTTATTTCCAAAAACGAGTAAAATAAAATCAGTTTCGGGATTGATT
1 ATTTTATTCCAGATTTTG---T-TTTCCAAAAACGAGTAAAATAAAATCAGTTTCGGGATTGATT
* **
231966 CCAGCCGTTTAACGATTTTATTCAAATTTTTTTATTTCCAAAAACGAGTAAAATAAAATCTTTTT
62 CCAGCCGTTCAACGATTTTATTCAAATTTTTTTATTTCCAAAAACGAGTAAAATAAAATCCGTTT
232031 CGGGATTGATTCCCG
127 CGGGATTGATTCCCG
232046 TCGTTCAACG
Statistics
Matches: 125, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
155 56 0.45
156 1 0.01
157 10 0.08
159 2 0.02
160 14 0.11
161 33 0.26
162 9 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (151 bp):
ATTTTATTCCAGATTTTGTTTTCCAAAAACGAGTAAAATAAAATCAGTTTCGGGATTGATTCCAG
CCGTTCAACGATTTTATTCAAATTTTTTTATTTCCAAAAACGAGTAAAATAAAATCCGTTTCGGG
ATTGATTCCCGCCATTTAACG
Found at i:231947 original size:79 final size:79
Alignment explanation
Indices: 231779--232061 Score: 383
Period size: 79 Copynumber: 3.6 Consensus size: 79
231769 AATTAGAAGT
* * * * *
231779 AAATAAAATCCATTTCGGGATTTATTCCCGCTGTTCAATGAATTTTATTCCATTATTTTGATTTT
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCGTTTAACG-ATTTTATTCCA-TATTTTG-TTTT
231844 ATTTCCAAAAACGAGTA
63 ATTTCCAAAAACGAGTA
* *
231861 AAATAAAATCCGTTTCGGGATTGATTCCCGCCATTTAACGATTTTTTTCCATATTTTGTTTTATT
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCGTTTAACGATTTTATTCCATATTTTGTTTTATT
231926 TCCAAAAACGAGTA
66 TCCAAAAACGAGTA
* * *
231940 AAATAAAATCAGTTTCGGGATTGATTCCAGCCGTTTAACGATTTTATT-CA-AATTT-TTTTATT
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCGTTTAACGATTTTATTCCATATTTTGTTTTATT
232002 TCCAAAAACGAGTA
66 TCCAAAAACGAGTA
** * * *
232016 AAATAAAATCTTTTTCGGGATTGATTCCCGTCGTTCAACGAATTTA
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCGTTTAACGATTTTA
232062 ATAAATTTTG
Statistics
Matches: 183, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
76 61 0.33
77 4 0.02
78 2 0.01
79 65 0.36
80 7 0.04
81 10 0.05
82 34 0.19
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (79 bp):
AAATAAAATCCGTTTCGGGATTGATTCCCGCCGTTTAACGATTTTATTCCATATTTTGTTTTATT
TCCAAAAACGAGTA
Found at i:232249 original size:84 final size:81
Alignment explanation
Indices: 231940--232403 Score: 307
Period size: 84 Copynumber: 5.7 Consensus size: 81
231930 AAAACGAGTA
* * * * * *
231940 AAATAAAATCAGTTTCGGGATTGATTCCAGCCGTTTAAC--GATTTTATTCAAATTT-TTTTATT
1 AAATAAAATCTGTTTCGGGATTTATTCC-GTCGTTTAACAAGATTTTATT-GATTTTATTTTGTT
* * *
232002 TCC-AA--AAA-CGAGTA
64 TCCAAATTAAATAGAATT
* * * * * **
232016 AAATAAAATCTTTTTCGGGATTGATTCCCGTCGTTCAACGA-ATTTAATAAATTTTGATTTTGTT
1 AAATAAAATCTGTTTCGGGATTTATT-CCGTCGTTTAACAAGATTTTATTGATTTT-ATTTTGTT
* * *
232080 GTCAAAAATGAGAAATTA-AATA
64 -TC-CAAAT--TAAA-TAGAATT
* *
232102 AAATAAAATCTGTTTCGGGATTTATTCATGGCGTTTAACAAGA--TT-TT-ATTTTATTTTGTTT
1 AAATAAAATCTGTTTCGGGATTTATTC-CGTCGTTTAACAAGATTTTATTGATTTTATTTTGTTT
232163 CCAAATTAGAATAGAATT
65 CCAAATTA-AATAGAATT
* * *
232181 AAATAAAATATGTTTCGCGATTTATTCCAGTCATTTAACAAGATTTTAATTGATTTTATTTTGTT
1 AAATAAAATCTGTTTCGGGATTTATTCC-GTCGTTTAACAAGATTTT-ATTGATTTTATTTTGTT
232246 TCCAAATTTAAATTA-AATT
64 TCCAAA-TTAAA-TAGAATT
* * * *
232265 AAATAAAATCTGTTTCGGGATTAATTTTCG-CTGTTTAACAAGATTTTATTCGATATTGTTTTGT
1 AAATAAAATCTGTTTCGGGATTTA-TTCCGTC-GTTTAACAAGATTTTATT-GATTTTATTTTGT
* * *
232329 TTCCAAA-AAAAGATGTAATC
63 TTCCAAATTAAATA-G-AATT
*
232349 AAAT-AATTCTGTTTCGGGATTTATTCTCGTCGTTTAAC-AGATTTTAATTTGATTT
1 AAATAAAATCTGTTTCGGGATTTATTC-CGTCGTTTAACAAGATTTT-A-TTGATTT
232404 AATGATATAA
Statistics
Matches: 311, Mismatches: 41, Indels: 65
0.75 0.10 0.16
Matches are distributed among these distances:
76 37 0.12
77 8 0.03
78 9 0.03
79 44 0.14
80 4 0.01
81 7 0.02
82 20 0.06
83 42 0.14
84 90 0.29
85 13 0.04
86 36 0.12
87 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (81 bp):
AAATAAAATCTGTTTCGGGATTTATTCCGTCGTTTAACAAGATTTTATTGATTTTATTTTGTTTC
CAAATTAAATAGAATT
Found at i:237987 original size:19 final size:18
Alignment explanation
Indices: 237963--238025 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
237953 TATTCTTTAA
237963 AAAAAAAAGCAAAAGGCGC
1 AAAAAAAAGCAAAA-GCGC
* ***
237982 AAAAAAAGGCAAAA-AAA
1 AAAAAAAAGCAAAAGCGC
237999 AAAGAAAAAGCAAAAAGCGC
1 AAA-AAAAAGC-AAAAGCGC
238019 AAAAAAA
1 AAAAAAA
238026 CCGCAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 21 0.64
20 3 0.09
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCAAAAGCGC
Found at i:238010 original size:37 final size:37
Alignment explanation
Indices: 237961--238040 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
237951 CTTATTCTTT
* *
237961 AAAAAAAAAAGCAAAAGGCGCAAAAAAA-GGCAAAAA
1 AAAAAAAAAAGCAAAAAGCGCAAAAAAACCGCAAAAA
237997 AAAAAGAAAAAGCAAAAAGCGCAAAAAAACCGCAAAAA
1 AAAAA-AAAAAGCAAAAAGCGCAAAAAAACCGCAAAAA
238035 AAAAAA
1 AAAAAA
238041 GTTGCCTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 5 0.12
37 23 0.57
38 12 0.30
ACGTcount: A:0.74, C:0.12, G:0.14, T:0.00
Consensus pattern (37 bp):
AAAAAAAAAAGCAAAAAGCGCAAAAAAACCGCAAAAA
Found at i:238024 original size:18 final size:18
Alignment explanation
Indices: 237964--238025 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
237954 ATTCTTTAAA
*
237964 AAAAAAAGCAAAAGGCGC
1 AAAAAAAGCAAAAAGCGC
***
237982 AAAAAAAGGCAAAAA-AAA
1 AAAAAAA-GCAAAAAGCGC
238000 AAGAAAAAGCAAAAAGCGC
1 AA-AAAAAGCAAAAAGCGC
238019 AAAAAAA
1 AAAAAAA
238026 CCGCAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAGCAAAAAGCGC
Found at i:248107 original size:37 final size:37
Alignment explanation
Indices: 248058--248137 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
248048 AGACATTTTT
*
248058 AAAAACTTGCAAAACTAACAC-TCAA-CACTCAAAAAG
1 AAAAATTTGCAAAACTAAC-CGTCAATCACTCAAAAAG
* * *
248094 AAAAATTTAGCAAACCTCACCGTTAATCACTCAAAAAG
1 AAAAATTT-GCAAAACTAACCGTCAATCACTCAAAAAG
248132 AAAAAT
1 AAAAAT
248138 CAAATTCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 8 0.22
37 12 0.32
38 17 0.46
ACGTcount: A:0.54, C:0.23, G:0.06, T:0.17
Consensus pattern (37 bp):
AAAAATTTGCAAAACTAACCGTCAATCACTCAAAAAG
Found at i:254888 original size:203 final size:203
Alignment explanation
Indices: 254539--254934 Score: 792
Period size: 203 Copynumber: 2.0 Consensus size: 203
254529 ATTATTTAAA
254539 TACATATTTGTTACTTGATAATACTATGTCTAAAACAGACATTTTATTTCTCAAAAGTATTTTTT
1 TACATATTTGTTACTTGATAATACTATGTCTAAAACAGACATTTTATTTCTCAAAAGTATTTTTT
254604 GACAGCAATTCTAAACACTAACATCAAACTTTCCAAAAGTACTTCTCTGAATCAGTTTTCCAAAG
66 GACAGCAATTCTAAACACTAACATCAAACTTTCCAAAAGTACTTCTCTGAATCAGTTTTCCAAAG
254669 CAATTTTTAAAAGCACTTCTCAAAAAACAATGCTAAACTATCCTTTAGTGTCTTGAGTCTTAATG
131 CAATTTTTAAAAGCACTTCTCAAAAAACAATGCTAAACTATCCTTTAGTGTCTTGAGTCTTAATG
254734 AAAATTAT
196 AAAATTAT
254742 TACATATTTGTTACTTGATAATACTATGTCTAAAACAGACATTTTATTTCTCAAAAGTATTTTTT
1 TACATATTTGTTACTTGATAATACTATGTCTAAAACAGACATTTTATTTCTCAAAAGTATTTTTT
254807 GACAGCAATTCTAAACACTAACATCAAACTTTCCAAAAGTACTTCTCTGAATCAGTTTTCCAAAG
66 GACAGCAATTCTAAACACTAACATCAAACTTTCCAAAAGTACTTCTCTGAATCAGTTTTCCAAAG
254872 CAATTTTTAAAAGCACTTCTCAAAAAACAATGCTAAACTATCCTTTAGTGTCTTGAGTCTTAA
131 CAATTTTTAAAAGCACTTCTCAAAAAACAATGCTAAACTATCCTTTAGTGTCTTGAGTCTTAA
254935 AAGAATGAAA
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 193 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (203 bp):
TACATATTTGTTACTTGATAATACTATGTCTAAAACAGACATTTTATTTCTCAAAAGTATTTTTT
GACAGCAATTCTAAACACTAACATCAAACTTTCCAAAAGTACTTCTCTGAATCAGTTTTCCAAAG
CAATTTTTAAAAGCACTTCTCAAAAAACAATGCTAAACTATCCTTTAGTGTCTTGAGTCTTAATG
AAAATTAT
Found at i:256418 original size:12 final size:12
Alignment explanation
Indices: 256401--256427 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
256391 TAAAATGCTT
256401 ATTAATTAAAAA
1 ATTAATTAAAAA
256413 ATTAATTAAAAA
1 ATTAATTAAAAA
256425 ATT
1 ATT
256428 TATAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTAATTAAAAA
Found at i:256426 original size:30 final size:31
Alignment explanation
Indices: 256357--256426 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
256347 AATACAAAAC
* * *
256357 TTAAAAACATGTTTGTTAATTAAAAACTTGAA
1 TTAAAAA-ATGCTTATTAATTAAAAAATTGAA
256389 --AATAAAATGCTTATTAATTAAAAAATT-AA
1 TTAA-AAAATGCTTATTAATTAAAAAATTGAA
256418 TTAAAAAAT
1 TTAAAAAAT
256427 TTATAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
29 2 0.06
30 25 0.78
31 5 0.16
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (31 bp):
TTAAAAAATGCTTATTAATTAAAAAATTGAA
Found at i:258482 original size:23 final size:23
Alignment explanation
Indices: 258455--258513 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
258445 TATTTATTAT
*
258455 ATGCATTGTGCGAAACTTCTTCC
1 ATGCATTGTGCGAAACCTCTTCC
* * *
258478 ATGCAATGTG-GGAACCTCTTCT
1 ATGCATTGTGCGAAACCTCTTCC
**
258500 ATGTGTTGTGCGAA
1 ATGCATTGTGCGAA
258514 CCTTTTAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (23 bp):
ATGCATTGTGCGAAACCTCTTCC
Found at i:258805 original size:74 final size:72
Alignment explanation
Indices: 258691--258832 Score: 162
Period size: 74 Copynumber: 1.9 Consensus size: 72
258681 ACAATACATG
* * * * *
258691 TATCTTTGCATTAAAAGGGGTTTTGAATTAAATGAGTGCATGTGCAGGTTTATATTATAAATAAT
1 TATCTTTGCATCAAAAAGGGTTTTGAATTAAATGAGTGCATGCG-AGGGTT-TACTATAAATAAT
258756 ATATGAACA
64 ATATGAACA
* * *
258765 TATCTTTGCATCAAAAATGGTTTT-ATATTATATGTA-TGCATGCGTGGGTTTACTATAAATAAT
1 TATCTTTGCATCAAAAAGGGTTTTGA-ATTAAATG-AGTGCATGCGAGGGTTTACTATAAATAAT
258828 ATATG
64 ATATG
258833 CACTTTTGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
72 17 0.29
73 5 0.09
74 35 0.60
75 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.40
Consensus pattern (72 bp):
TATCTTTGCATCAAAAAGGGTTTTGAATTAAATGAGTGCATGCGAGGGTTTACTATAAATAATAT
ATGAACA
Found at i:260736 original size:10 final size:9
Alignment explanation
Indices: 260715--260796 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 9
260705 CTTAAATAAA
260715 TTTTATATT
1 TTTTATATT
260724 TTTTATGATT
1 TTTTAT-ATT
*
260734 TTTTAATAAT
1 TTTT-ATATT
*
260744 TTTAATAATT
1 TTTTAT-ATT
260754 TTTT-TAACTT
1 TTTTAT-A-TT
**
260764 TTCGA-ATT
1 TTTTATATT
260772 TTTTATATT
1 TTTTATATT
260781 TTTTGA-ATT
1 TTTT-ATATT
260790 TTTTATA
1 TTTTATA
260797 AAAAAATCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
8 6 0.11
9 27 0.47
10 22 0.39
11 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTATATT
Found at i:260737 original size:19 final size:19
Alignment explanation
Indices: 260715--260797 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 19
260705 CTTAAATAAA
*
260715 TTTTATATTTTTTATG-ATT
1 TTTTATAATTTTT-TGAATT
*
260734 TTTTAATAATTTTAAT-AATT
1 TTTT-ATAATTTT-TTGAATT
* *
260754 TTTT-TAACTTTTCGAATT
1 TTTTATAATTTTTTGAATT
260772 TTTTAT-ATTTTTTGAATT
1 TTTTATAATTTTTTGAATT
260790 TTTTATAA
1 TTTTATAA
260798 AAAAATCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
18 30 0.59
19 6 0.12
20 15 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTGAATT
Found at i:263335 original size:25 final size:25
Alignment explanation
Indices: 263290--263387 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 25
263280 GTCATTAGGG
* **
263290 TTACCGATTC-CAGCTTTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
263314 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
* * * *
263339 TTACCGTTATTCAGCTCGGAGGAGC
1 TTACCGATACTCAGCTCGTATGAGC
* *
263364 TTATCGTATA-TC-GCTTGTATGAGC
1 TTACCG-ATACTCAGCTCGTATGAGC
263388 ATACATGTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 18 0.30
25 40 0.67
26 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:273375 original size:21 final size:21
Alignment explanation
Indices: 273349--273422 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
273339 GTTACAGGGG
*
273349 TACACGA-CTATGTGGCTGAGA
1 TACACGACCT-TGTGGCTAAGA
*
273370 TACACGACCTTGTGGCTAAGG
1 TACACGACCTTGTGGCTAAGA
* * * * *
273391 TACACAACCGTGTGACTGAGG
1 TACACGACCTTGTGGCTAAGA
*
273412 TATACGACCTT
1 TACACGACCTT
273423 ATGGGCAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
21 41 0.95
22 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (21 bp):
TACACGACCTTGTGGCTAAGA
Found at i:278474 original size:29 final size:29
Alignment explanation
Indices: 278432--278497 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
278422 ATAATCAAGG
278432 TCATAAGTTCATTTAATTGCCTATACACA
1 TCATAAGTTCATTTAATTGCCTATACACA
278461 TCATAAGTTCATTTAATTGCCTATACACA
1 TCATAAGTTCATTTAATTGCCTATACACA
278490 TCATAAGT
1 TCATAAGT
278498 CTCACAAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.38
Consensus pattern (29 bp):
TCATAAGTTCATTTAATTGCCTATACACA
Found at i:282607 original size:15 final size:16
Alignment explanation
Indices: 282587--282619 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
282577 TCCCAGTAAC
*
282587 TATTCTT-GTTTTAGT
1 TATTCTTAGTGTTAGT
282602 TATTCTTAGTGTTAGT
1 TATTCTTAGTGTTAGT
282618 TA
1 TA
282620 AGTTAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61
Consensus pattern (16 bp):
TATTCTTAGTGTTAGT
Found at i:288448 original size:45 final size:45
Alignment explanation
Indices: 288354--288575 Score: 295
Period size: 45 Copynumber: 5.0 Consensus size: 45
288344 AACCATTACA
* * **
288354 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* ** **
288397 CGGTGGAATCAGCATATAGCAACCACCTTTATTTTCAATGATTTC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* * * *
288442 CAGTGGAGTCAACACATAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* *
288487 CGGTGGAATCAGCACATGGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
288532 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
288576 TCAGTACACG
Statistics
Matches: 155, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
43 6 0.04
44 12 0.08
45 137 0.88
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
Found at i:291799 original size:29 final size:30
Alignment explanation
Indices: 291768--291825 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
291758 TAATTGAATC
291768 AAATAAAAATTCCATGTAT-AAAATTACACA
1 AAATAAAAATT-CATGTATAAAAATTACACA
* *
291798 AAATTAAAGTTCATGTATAAAAATTACA
1 AAATAAAAATTCATGTATAAAAATTACA
291826 TAATAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATAAAAATTCATGTATAAAAATTACACA
Found at i:304917 original size:123 final size:123
Alignment explanation
Indices: 304692--305222 Score: 929
Period size: 123 Copynumber: 4.3 Consensus size: 123
304682 TATTACATGA
* * * * **
304692 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT-CAGCGCGCTTTTGCTACATTAGGTCATATA
1 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGA-CGCGCTTTTGCTACAGTAGGTCATGGA
* * * * * * *
304756 AGAAATAATTTTTTTTACGTTTCTGAGTAAAAAATATAAAATCGCTTTTAGCAGGATGC
65 AGAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
304815 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
1 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
304880 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
66 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
304938 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
1 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
305003 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
66 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
305061 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
1 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
305126 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
66 GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
305184 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACG
1 TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACG
305223 GAGGCAATGG
Statistics
Matches: 394, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
123 393 1.00
124 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (123 bp):
TATTTGAGAAGAATTTGTGAAATCGCACCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
GAAATCATTTTTTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
Found at i:308323 original size:51 final size:52
Alignment explanation
Indices: 308244--308487 Score: 255
Period size: 51 Copynumber: 4.6 Consensus size: 52
308234 NNNNNNNNNN
*
308244 GGTTTTTAATTAAATTAGGTTAATGTTAGGGTT-TTTAAGTTAAGGGTTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAAGTTAAGGGTTTAG
308295 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT-TTTAAGTTAAGGGTTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAAGTTAAGGGTTTAG
* * * * *
308346 GGCTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGCTAGGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGG--T-TATTTAAGTTA----AGGGTTTAG
* * ** *
308405 GGTTTTTAATTAAATTAGGTTAGGGTTTGTAATTAATTTAGGTT-AGGG-TTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG-GGTT-ATTTAAGTTAAGGGTTTAG
**
308457 GGTTTTTAATTAAATTAAATT-AGGTTAGGGT
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGT
308488 GAGGGTTTTT
Statistics
Matches: 164, Mismatches: 19, Indels: 21
0.80 0.09 0.10
Matches are distributed among these distances:
50 1 0.01
51 84 0.51
52 23 0.14
53 5 0.03
54 1 0.01
55 7 0.04
57 1 0.01
58 7 0.04
59 35 0.21
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (52 bp):
GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAAGTTAAGGGTTTAG
Found at i:308352 original size:22 final size:20
Alignment explanation
Indices: 308313--308358 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
308303 ATTAAATTAG
*
308313 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGCTTTTAA
308333 GTTAAGGGTTTAGGGCTTTTAA
1 GTTAA-GG-TTAGGGCTTTTAA
308355 -TTAA
1 GTTAA
308359 ATTAGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.26, C:0.02, G:0.28, T:0.43
Consensus pattern (20 bp):
GTTAAGGTTAGGGCTTTTAA
Found at i:308376 original size:29 final size:29
Alignment explanation
Indices: 308337--308553 Score: 239
Period size: 29 Copynumber: 7.4 Consensus size: 29
308327 TTTTAAGTTA
*
308337 AGGGTTTAGGGCTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* * *
308367 AGGGTTAGGGTTTGTAATTAATTTAGGCT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
308396 AGGGGTTAGGGTTTTTAATT-AA--A--TT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
* *
308421 A-GGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
308449 AGGGTTAGGGTTTTTAATTAAATTAAATTAGGTT
1 AGGGTTAGGG--TTT--TT-AATTAAATTAGGTT
*
308483 AGGGTGAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
308512 AGGGTTAGGGTTTTTAATTAATTTAAGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
308541 AGGGTTTAGGGTT
1 AGGG-TTAGGGTT
308554 AAATTAGGTT
Statistics
Matches: 159, Mismatches: 15, Indels: 26
0.80 0.08 0.13
Matches are distributed among these distances:
23 16 0.10
24 1 0.01
25 2 0.01
26 1 0.01
27 1 0.01
28 3 0.02
29 75 0.47
30 31 0.19
31 3 0.02
32 3 0.02
33 1 0.01
34 22 0.14
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.44
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:308427 original size:23 final size:23
Alignment explanation
Indices: 308399--308454 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
308389 TTAGGCTAGG
*
308399 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTGTAATTAAATTA
*
308422 GGTTAGGGTTTGTAATTAATTTA
1 GGTTAGGGTTTGTAATTAAATTA
308445 GGTTAGGGTT
1 GGTTAGGGTT
308455 AGGGTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTGTAATTAAATTA
Found at i:308480 original size:52 final size:52
Alignment explanation
Indices: 308370--308569 Score: 204
Period size: 52 Copynumber: 3.6 Consensus size: 52
308360 TTAGGTTAGG
* * *
308370 GTTAGGGTTTGTAATTAATTTAGGCTAGGGGTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTTGTAATTAAATTAGGTTA-GGGTTAGGGTTTTTAATTAAATTAA
*
308423 GTTAGGGTTTGTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTA
1 GTTAGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATT--A--A
* *
308479 GGTTAGGGTGAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAA
1 -G-T----T-AGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAA
**
308538 GTTAGGGTTTAG-GGTTAAATTAGGTTAGGGTT
1 GTTAGGGTTT-GTAATTAAATTAGGTTAGGGTT
308570 TTTATTACAT
Statistics
Matches: 127, Mismatches: 8, Indels: 25
0.79 0.05 0.16
Matches are distributed among these distances:
52 48 0.38
53 27 0.21
54 1 0.01
57 2 0.02
58 2 0.02
59 1 0.01
61 1 0.01
62 1 0.01
63 44 0.35
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (52 bp):
GTTAGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAA
Found at i:308501 original size:63 final size:65
Alignment explanation
Indices: 308426--308552 Score: 204
Period size: 63 Copynumber: 2.0 Consensus size: 65
308416 AAATTAGGTT
*
308426 AGGGTTTGTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTA-GG-TTAGGGTG
1 AGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGGGTG
* * *
308489 AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAATTTAAGTTAGGGTTTAGGGT
1 AGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGGGT
308553 TAAATTAGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 49 0.84
64 2 0.03
65 7 0.12
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (65 bp):
AGGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTTAGGGTG
Found at i:308653 original size:43 final size:45
Alignment explanation
Indices: 308579--308664 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
308569 TTTTATTACA
*
308579 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
308624 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
308665 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:309110 original size:18 final size:18
Alignment explanation
Indices: 309087--309121 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
309077 TGGAAAAGGA
* *
309087 TACATATAAGGGTTAGGG
1 TACATAAAAGGGCTAGGG
309105 TACATAAAAGGGCTAGG
1 TACATAAAAGGGCTAGG
309122 AAACGCACCT
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:0.09, G:0.31, T:0.23
Consensus pattern (18 bp):
TACATAAAAGGGCTAGGG
Found at i:309780 original size:7 final size:7
Alignment explanation
Indices: 309770--309794 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
309760 TTATATACAT
309770 AATACTA
1 AATACTA
309777 AATACTA
1 AATACTA
309784 AATACTA
1 AATACTA
309791 AATA
1 AATA
309795 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:310916 original size:50 final size:51
Alignment explanation
Indices: 310816--310930 Score: 196
Period size: 50 Copynumber: 2.3 Consensus size: 51
310806 TTTTAATAAG
310816 GGAAATTGAGAGAAAATTGAAATTAAATATGGATTTCAGAGAATTTTGGAA
1 GGAAATTGAGAGAAAATTGAAATTAAATATGGATTTCAGAGAATTTTGGAA
* **
310867 GGAAATTGAGAGGAAATTGAAATT-AATATGGATTTGGGAGAATTTTGGAA
1 GGAAATTGAGAGAAAATTGAAATTAAATATGGATTTCAGAGAATTTTGGAA
310917 GGAAATTGAGAGAA
1 GGAAATTGAGAGAA
310931 TTTTGGAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 37 0.62
51 23 0.38
ACGTcount: A:0.43, C:0.01, G:0.28, T:0.28
Consensus pattern (51 bp):
GGAAATTGAGAGAAAATTGAAATTAAATATGGATTTCAGAGAATTTTGGAA
Found at i:310930 original size:22 final size:22
Alignment explanation
Indices: 310904--310955 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
310894 ATGGATTTGG
*
310904 GAGAATTTTGGAAGGAAATTGA
1 GAGAATTTTGGAAGAAAATTGA
310926 GAGAATTTTGGAAGAAAATTGA
1 GAGAATTTTGGAAGAAAATTGA
310948 GAGGAATT
1 GA-GAATT
310956 GAGAGGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
GAGAATTTTGGAAGAAAATTGA
Found at i:312063 original size:7 final size:8
Alignment explanation
Indices: 312046--312070 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
312036 ATAATAAATA
312046 TTTATTTT
1 TTTATTTT
312054 TTTATTTT
1 TTTATTTT
312062 TTTATTTT
1 TTTATTTT
312070 T
1 T
312071 AAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:312092 original size:12 final size:11
Alignment explanation
Indices: 312064--312113 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
312054 TTTATTTTTT
312064 TATTTTTAAAA
1 TATTTTTAAAA
312075 TATTTTTAAAA
1 TATTTTTAAAA
*
312086 TACTTTTT---T
1 TA-TTTTTAAAA
312095 TATTTTTAAAA
1 TATTTTTAAAA
312106 TAATTTTT
1 T-ATTTTT
312114 TGGTGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
11 14 0.44
12 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:312098 original size:20 final size:20
Alignment explanation
Indices: 312075--312114 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
312065 ATTTTTAAAA
*
312075 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTT
312095 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTT
312115 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTT
Found at i:312122 original size:20 final size:20
Alignment explanation
Indices: 312079--312122 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
312069 TTAAAATATT
* * *
312079 TTTAAAATACTTTTTTTATT
1 TTTAAAATAATTTTTTGATG
*
312099 TTTAAAATAATTTTTTGGTG
1 TTTAAAATAATTTTTTGATG
312119 TTTA
1 TTTA
312123 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTAAAATAATTTTTTGATG
Found at i:312326 original size:84 final size:88
Alignment explanation
Indices: 312219--312391 Score: 246
Period size: 95 Copynumber: 1.9 Consensus size: 88
312209 GGGTCCTGGC
312219 CTAGGACGCGGGCTGGAAA-TTTTT-T-CTAGGCCCGG-CCATGAGCACCTCTACTTGGGAGAAA
1 CTAGGACGCGGGCTGGAAATTTTTTCTGCTAGGCCCGGCCCATGAGCACCTCTACTTGGGAGAAA
312280 CAAATAGTTTAGGTATTCACAAG
66 CAAATAGTTTAGGTATTCACAAG
*
312303 CTAGGACGCGGGCTGGAAATTTTTTCTGGGCCCGGCTCGGCCCGGCCCATGAGCACCTCTACTTG
1 CTAGGACGCGGGCTGGAAATTTTTTCT-------GCTAGGCCCGGCCCATGAGCACCTCTACTTG
312368 GGAGAAACAAATAGTTTAGGTATT
59 GGAGAAACAAATAGTTTAGGTATT
312392 ACTTGTGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
84 19 0.25
85 5 0.06
86 1 0.01
94 9 0.12
95 43 0.56
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (88 bp):
CTAGGACGCGGGCTGGAAATTTTTTCTGCTAGGCCCGGCCCATGAGCACCTCTACTTGGGAGAAA
CAAATAGTTTAGGTATTCACAAG
Found at i:313072 original size:22 final size:22
Alignment explanation
Indices: 312990--313069 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
312980 AATCTTCAAG
312990 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
313009 GATATGCAATCTTAGAAGATGT
1 GATATGCAATCTTAGAAGATAT
313031 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
313053 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
313070 GATTTAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.25
22 28 0.53
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:313363 original size:15 final size:16
Alignment explanation
Indices: 313337--313368 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
313327 TTTTCCCTTA
313337 TCATTCATTTTCAAAT
1 TCATTCATTTTCAAAT
313353 TCATT-ATTTTCAAAT
1 TCATTCATTTTCAAAT
313368 T
1 T
313369 TGTTTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTCATTTTCAAAT
Done.