Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold301
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: 1013018
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32220 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:675003 original size:123 final size:123
Alignment explanation
Indices: 674858--675207 Score: 388
Period size: 123 Copynumber: 2.9 Consensus size: 123
674848 CTTTCGGGGC
* * *
674858 TTTAGCGGCTTTTTTGATAAAGCGCCGCTAATGCTCAGAGC-TTTAGCGGTGTTTTTTAAAAAGC
1 TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAG-GCTTTTAGCGG-GTTTTTTAAAAAGC
* * *
674922 GCCGCTAATACTCGA-G-CTTTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCT
64 GCCGCTAATGCTCGAGGAC-TTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
* * * *
674981 TTTAGCAGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAATAAGCG
1 TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGG-GTTTTTTAAAAAGCG
** *
675046 CCGCTAATGCTC-AGGACTTTAGTGGTGTTTTTAAAAAAGCGCCGCTAATGATCAGGCT
65 CCGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
* * * * * *
675104 TTTAG-TGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCTTTTAGCGGCTTTTTTAAAAAGCA
1 TTTAGCAG-CATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGGTTTTTTAAAAAGCG
* * ** * *
675168 TCGCTAATGCTCG-GGGCTTTAGCAGCGTTTTTGAAAAAGC
65 CCGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGC
675208 GCTGCAAAAA
Statistics
Matches: 193, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
122 48 0.25
123 144 0.75
124 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (123 bp):
TTTAGCAGCATTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTTAGCGGGTTTTTTAAAAAGCGC
CGCTAATGCTCGAGGACTTTAGTGGCATTTTTAAAAAAGCACCGCTAATGATCAGGCT
Found at i:675636 original size:14 final size:15
Alignment explanation
Indices: 675608--675640 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
675598 AAGGTTTATA
675608 GATTATGGAATTAGG
1 GATTATGGAATTAGG
675623 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
675637 GATT
1 GATT
675641 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:675842 original size:136 final size:137
Alignment explanation
Indices: 675662--675936 Score: 288
Period size: 136 Copynumber: 2.0 Consensus size: 137
675652 GTTGTGACTT
* * * * *
675662 AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGGTTTAGAGATTCGG-GGTCGAGTTA-
1 AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTAG
* * *
675725 GGGTTTAATGTTTAGATTAATTAGTATTTTTTAAAATTTATATATTAATTAAGTTC-TTATATAA
66 GGGTTTAAGGCTTAGATTAATTAGTATTTTTT--AATTTATATATTAAATAAGTTCTTTATATAA
675789 TTATAAAAG
129 TTATAAAAG
* * * * * * * * *
675798 AGGGGTTAGGGGTTAGGGGTTTAATATTTA-TGTTTTATGATTTAGGGTTTAGGAGATAGGGGTA
1 AGGGGTTAGAGGTTAGAGG-TTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTA
* * * * *
675862 GGGGTTTAGGGCTTAGATTATTTGGTATTTTTTAATTTATATATTAAATAATTTCTTTTTATAAT
65 GGGGTTTAAGGCTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGTTCTTTATATAAT
*
675927 TGTAAAAG
130 TATAAAAG
675935 AG
1 AG
675937 ATCATTTTAA
Statistics
Matches: 112, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
136 54 0.48
137 31 0.28
138 27 0.24
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (137 bp):
AGGGGTTAGAGGTTAGAGGTTAAGAGTTAGTGATTTAAGATTTAGAGATTAGGAGATAGAGGTAG
GGGTTTAAGGCTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAAGTTCTTTATATAATT
ATAAAAG
Found at i:680016 original size:5 final size:5
Alignment explanation
Indices: 680006--680070 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
679996 AAATTTAAAA
680006 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
680056 AATAT AATAT AATAT
1 AATAT AATAT AATAT
680071 TTATCATAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:680225 original size:45 final size:44
Alignment explanation
Indices: 680119--680266 Score: 169
Period size: 43 Copynumber: 3.4 Consensus size: 44
680109 TTTAAACGTT
* *
680119 ATGTT-TTTAGCGGCGTTTTTG-CAAGAAGCGCCGCTAAAGGT-
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
* * * *
680160 TTGATCTATAGCGGCGTTTGTGACAAAAAAACGCCGCTAAAGGTC
1 ATGTTCTTTAGCGGCGTTTGTGAC-AAAAAGCGCCGCTAAAGGTC
* * *
680205 ATGTTCTTTAGCGGCGTTTGT-ACCAAAAGCACCGCTAAATGTC
1 ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
*
680248 ATGGTCTTTAGCGGCGTTT
1 ATGTTCTTTAGCGGCGTTT
680267 TTTCACATAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
41 3 0.03
42 14 0.16
43 35 0.39
44 19 0.21
45 18 0.20
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (44 bp):
ATGTTCTTTAGCGGCGTTTGTGACAAAAAGCGCCGCTAAAGGTC
Found at i:680453 original size:20 final size:20
Alignment explanation
Indices: 680416--680454 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
680406 GACTTATAAA
*
680416 TAAATATTAATATTTTTATT
1 TAAATATTAATATCTTTATT
680436 TAAATA-TAATTATCTTTAT
1 TAAATATTAA-TATCTTTAT
680455 ATTATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATATTAATATCTTTATT
Found at i:681540 original size:30 final size:31
Alignment explanation
Indices: 681495--681554 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
681485 AGAGGTGGGA
*
681495 TGGGAAGGGAATAAAAGTTTTAGAGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
* * *
681526 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAA
681555 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
Found at i:682464 original size:20 final size:20
Alignment explanation
Indices: 682439--682498 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
682429 AATTAGATTT
682439 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATATTAA
* *
682459 ATTTAAATTTAAAAATA-GAA
1 ATTTAAA-ATAAAAATATTAA
* *
682479 AATTAAAATATCAAATATTA
1 ATTTAAAATA-AAAATATTA
682499 TTGAAAACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.06
20 20 0.65
21 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAAATAAAAATATTAA
Found at i:682481 original size:21 final size:21
Alignment explanation
Indices: 682439--682489 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
682429 AATTAGATTT
**
682439 ATTTAAA-ATAAAAATATTAA
1 ATTTAAATATAAAAATAGAAA
*
682459 ATTTAAATTTAAAAATAGAAA
1 ATTTAAATATAAAAATAGAAA
*
682480 ATTAAAATAT
1 ATTTAAATAT
682490 CAAATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATTTAAATATAAAAATAGAAA
Found at i:686279 original size:25 final size:25
Alignment explanation
Indices: 686242--686348 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
686232 GACACACCAC
* * * *
686242 AGCTCGCAAGAGCGTCCCGTTATTT
1 AGCTCTCATGAGCATCCCGTTATAT
*
686267 AGCTCTTATGAGCATCCCGTTATAT
1 AGCTCTCATGAGCATCCCGTTATAT
* * * *
686292 GGCTCTCATGAGCTTCCTGATATAT
1 AGCTCTCATGAGCATCCCGTTATAT
* *
686317 TGCTCTC-TGGAGCTTCCCGATTA-AT
1 AGCTCTCAT-GAGCATCCCG-TTATAT
*
686342 GGCTCTC
1 AGCTCTC
686349 TTAAGCTTCT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
24 1 0.02
25 63 0.95
26 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTCTCATGAGCATCCCGTTATAT
Found at i:686344 original size:50 final size:50
Alignment explanation
Indices: 686265--686394 Score: 142
Period size: 50 Copynumber: 2.6 Consensus size: 50
686255 GTCCCGTTAT
* * *
686265 TTAGCTCTTATGAGCATCCCG-TTATATGGCTCTCATGAGCTTC-CTGATATA
1 TTAGCTCTAATGAGCTTCCCGATTA-ATGGCTCTCATAAGCTTCTC-GATA-A
* *
686316 TT-GCTCT-CTGGAGCTTCCCGATTAATGGCTCTCTTAAGCTTCTCGATAA
1 TTAGCTCTAAT-GAGCTTCCCGATTAATGGCTCTCATAAGCTTCTCGATAA
*
686365 TTAGCTCTAATGAGCTTCTCGATTAATGGC
1 TTAGCTCTAATGAGCTTCCCGATTAATGGC
686395 CTTCGGAGCT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
49 4 0.06
50 57 0.84
51 7 0.10
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (50 bp):
TTAGCTCTAATGAGCTTCCCGATTAATGGCTCTCATAAGCTTCTCGATAA
Found at i:686349 original size:25 final size:23
Alignment explanation
Indices: 686275--686444 Score: 108
Period size: 25 Copynumber: 6.9 Consensus size: 23
686265 TTAGCTCTTA
* *
686275 TGAGCATCCCGTTATATGGCTCTC
1 TGAGCTTCCCGATA-ATGGCTCTC
* *
686299 ATGAGCTTCCTGATATATTGCTCTC
1 -TGAGCTTCCCGATA-ATGGCTCTC
686324 TGGAGCTTCCCGATTAATGGCTCTC
1 T-GAGCTTCCCGA-TAATGGCTCTC
* * * *
686349 TTAAGCTTCTCGATAATTAGCTCTAA
1 -TGAGCTTCCCGATAA-TGGCTCT-C
*
686375 TGAGCTTCTCGATTAATGGC-CTTC
1 TGAGCTTCCCGA-TAATGGCTC-TC
* * * *
686399 GGAGCTTCCCAATATTGGCTCATA
1 TGAGCTTCCCGATAATGGCTC-TC
686423 TGAGCTTCCCGATAATTGGCTC
1 TGAGCTTCCCGATAA-TGGCTC
686445 GCAAGTGTTT
Statistics
Matches: 114, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.05
24 28 0.25
25 74 0.65
26 6 0.05
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (23 bp):
TGAGCTTCCCGATAATGGCTCTC
Found at i:688538 original size:56 final size:50
Alignment explanation
Indices: 688442--688687 Score: 201
Period size: 49 Copynumber: 4.8 Consensus size: 50
688432 ATTTGGGTAA
* * * *
688442 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
*
688498 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
688548 AGAGGTCCCATGTAAGACCATGTCTGGGGCATGGCGTTGGCAGCTATAT-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * * *
688597 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** * * *
688646 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
688688 TGTTACATTC
Statistics
Matches: 159, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
48 2 0.01
49 68 0.43
50 47 0.30
53 3 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:688549 original size:50 final size:50
Alignment explanation
Indices: 688450--688638 Score: 200
Period size: 50 Copynumber: 3.7 Consensus size: 50
688440 AAAGAGATCC
* *
688450 CATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCT
* *
688506 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
* * * * * **
688556 CATGTAAGACCATGTCTGGGGCATGGCGTTGGCAGCTATAT-AGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
* *
688605 CATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
688639 GTACAAGAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 35 0.30
50 47 0.40
53 3 0.03
55 1 0.01
56 32 0.27
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCT
Found at i:693148 original size:27 final size:27
Alignment explanation
Indices: 693118--693186 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
693108 GTCTTGAAAG
**
693118 ACTATCTTGTGTTTACCATCCCATTAA
1 ACTATCTTGTGTTTACCATCCCAGCAA
* *
693145 ACTATCTCGTGTTTACCGTCCCAGCAA
1 ACTATCTTGTGTTTACCATCCCAGCAA
693172 ACTATCTTGTGTTTA
1 ACTATCTTGTGTTTA
693187 GTGTCTCGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (27 bp):
ACTATCTTGTGTTTACCATCCCAGCAA
Found at i:696255 original size:30 final size:28
Alignment explanation
Indices: 696189--696255 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
696179 CTTCAAAATG
* * *
696189 TTAGAATTTAGTCACTGTATTTTTATTT
1 TTAGAATTTAATCACTCTATTTTTAATT
*
696217 TTAGGAATTTAATCCCTCTACTTTTTAGATT
1 TTA-GAATTTAATCACTCTA-TTTTTA-ATT
696248 TTAGAATT
1 TTAGAATT
696256 CAAGTCCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 11 0.34
31 5 0.16
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TTAGAATTTAATCACTCTATTTTTAATT
Found at i:700684 original size:2 final size:2
Alignment explanation
Indices: 700677--700703 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
700667 GCTTGAAAGC
700677 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 A
700704 GGGACGAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:703392 original size:14 final size:14
Alignment explanation
Indices: 703355--703400 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
703345 TTATAAATGA
703355 AATTAGAATTGATTT
1 AATTAGAATT-ATTT
703370 -ATGTA-AATTATTT
1 AAT-TAGAATTATTT
*
703383 AATTAGAATTAATT
1 AATTAGAATTATTT
703397 AATT
1 AATT
703401 TTTGGAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.22
14 19 0.70
15 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (14 bp):
AATTAGAATTATTT
Found at i:717279 original size:92 final size:92
Alignment explanation
Indices: 717122--717308 Score: 322
Period size: 92 Copynumber: 2.0 Consensus size: 92
717112 TCCTGGTATG
*
717122 GAAAAAGCTATAACAATGTATTGTGATAACGGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
1 GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
717187 TCACAAGAGGACCAAACATATTGACCA
66 TCACAAGAGGACCAAACATATTGACCA
* * *
717214 GAAAAAGTTATAACAATGTATTGTGATAACAGTGCTGTAATAACTAATACCAAGGAAAA-AAGAA
1 GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAA-GAAAATAAGAA
717278 GTCACAAGAGGACCAAACATATTGACCA
65 GTCACAAGAGGACCAAACATATTGACCA
717306 GAA
1 GAA
717309 GTATCACTTG
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 85 0.94
93 5 0.06
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (92 bp):
GAAAAAGCTATAACAATGTATTGTGATAACAGTGCAGCAATAACTAATACCAAGAAAATAAGAAG
TCACAAGAGGACCAAACATATTGACCA
Found at i:717607 original size:15 final size:15
Alignment explanation
Indices: 717587--717616 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
717577 TTCACTATTA
*
717587 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
717602 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
717617 GCATGCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:719219 original size:24 final size:25
Alignment explanation
Indices: 719183--719232 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
719173 TAACTATACC
*
719183 AAAAATAATATT-ATTTTAATAGTTT
1 AAAAATAATATTAAATTTAATA-TTT
*
719208 AAAATTAA-ATTAAATTTAATATTT
1 AAAAATAATATTAAATTTAATATTT
719232 A
1 A
719233 TCTTAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAAATAATATTAAATTTAATATTT
Found at i:719341 original size:17 final size:17
Alignment explanation
Indices: 719316--719348 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
719306 TATTATTTTA
*
719316 ATTAGATTTAATATTAG
1 ATTAAATTTAATATTAG
719333 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
719349 AAGTGATTAA
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:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:719503 original size:23 final size:25
Alignment explanation
Indices: 719455--719504 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
719445 AGTTGTAGAG
719455 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATTCTCT-AAGAGATTATTTT
*
719481 AGAAAATT-TCT-AGAGATTTTTTT
1 AGAAAATTCTCTAAGAGATTATTTT
719504 A
1 A
719505 ATTTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (25 bp):
AGAAAATTCTCTAAGAGATTATTTT
Found at i:720987 original size:21 final size:21
Alignment explanation
Indices: 720942--720993 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
720932 GTATCGATCC
*
720942 AGTATCGATAGT--TTTCTTAA
1 AGTATCGATA-TAATTTCCTAA
*
720962 AGTATTGATATAATTTCCTAA
1 AGTATCGATATAATTTCCTAA
*
720983 GGTATCGATAT
1 AGTATCGATAT
720994 TCCTACTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 16 0.62
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (21 bp):
AGTATCGATATAATTTCCTAA
Found at i:722007 original size:14 final size:13
Alignment explanation
Indices: 721981--722014 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
721971 TCAACTAGAG
721981 AATTTAATTAAAA
1 AATTTAATTAAAA
*
721994 AATTTTATTAAAA
1 AATTTAATTAAAA
722007 AA-TTAATT
1 AATTTAATT
722015 TGGAAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAATTAAAA
Found at i:722218 original size:16 final size:16
Alignment explanation
Indices: 722194--722247 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
722184 TTTGGTTCGC
* *
722194 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
722210 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
722226 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
722242 TGTAAT
1 TGTAAT
722248 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:722292 original size:45 final size:44
Alignment explanation
Indices: 722226--722316 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
722216 GGAATAGAGG
*
722226 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
722271 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
722315 TG
1 TG
722317 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:722331 original size:39 final size:42
Alignment explanation
Indices: 722226--722335 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 42
722216 GGAATAGAGG
*
722226 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAG-TAATCAACTGTTTGGTT--A
* ***
722271 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGTAATCAACTGTTTGGTTA
722311 TG-AATGGAATAGAGGTGTAATAGTA
1 TGTAATGGAATAGAGGTGTAATAGTA
722336 TAATGGAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 22 0.37
40 2 0.03
43 1 0.02
44 11 0.19
45 23 0.39
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (42 bp):
TGTAATGGAATAGAGGTGTAATAGTAATCAACTGTTTGGTTA
Found at i:722502 original size:18 final size:17
Alignment explanation
Indices: 722481--722515 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
722471 TTATTATTAA
*
722481 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
722499 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
722516 TCTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:728539 original size:13 final size:13
Alignment explanation
Indices: 728523--728573 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
728513 TTTAAACCAA
728523 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
728536 ACTTTTCAATAGC
1 ACTTTTCAAAAGC
* *
728549 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
728562 ACTTTTCCAAAG
1 ACTTTTCAAAAG
728574 TATTGTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:735301 original size:20 final size:21
Alignment explanation
Indices: 735278--735317 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
735268 TAAATAATTT
*
735278 TTAAAAA-TTGGAAAAAAAAA
1 TTAAAAAGTTAGAAAAAAAAA
735298 TTAAAAAGTTAGAAAAAAAA
1 TTAAAAAGTTAGAAAAAAAA
735318 CTAGTAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (21 bp):
TTAAAAAGTTAGAAAAAAAAA
Found at i:735573 original size:32 final size:32
Alignment explanation
Indices: 735510--735583 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
735500 ATAAATTTGG
**
735510 ATAATTTTTTTCAGTTTATTTAAATAATAAAA
1 ATAATTTTTTTCAGTTTAAATAAATAATAAAA
735542 ATAATTTTATTTCAG-TTAAAT-AATAATTAAAA
1 ATAATTTT-TTTCAGTTTAAATAAATAA-TAAAA
*
735574 A-AATATTTTT
1 ATAATTTTTTT
735584 AATTATTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.08
31 10 0.27
32 18 0.49
33 6 0.16
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATTTTTTTCAGTTTAAATAAATAATAAAA
Found at i:736249 original size:10 final size:9
Alignment explanation
Indices: 736234--736291 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
736224 TTAAAAAAAA
736234 TTACAATCTT
1 TTACAAT-TT
736244 TTACAATTT
1 TTACAATTT
* *
736253 CTAATAATTT
1 -TTACAATTT
*
736263 TTATAATTT
1 TTACAATTT
736272 CTTACAATATT
1 -TTACAAT-TT
736283 TTACAATTT
1 TTACAATTT
736292 CTATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 12 0.29
10 27 0.66
11 2 0.05
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (9 bp):
TTACAATTT
Found at i:736279 original size:39 final size:38
Alignment explanation
Indices: 736234--736340 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
736224 TTAAAAAAAA
736234 TTACAATCTTTTACAATTTCTAATAATTTTTATAATTTC
1 TTACAAT-TTTTACAATTTCTAATAATTTTTATAATTTC
*
736273 TTACAATATTTTACAATTTCT-AT--TTTTTATAATTTT
1 TTACAAT-TTTTACAATTTCTAATAATTTTTATAATTTC
* * * *
736309 TTATAATTTTTAAAAATTCTAACATATTTTTA
1 TTACAATTTTTACAATTTCTAATA-ATTTTTA
736341 ATTTTTGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 11 0.19
36 19 0.33
38 2 0.03
39 26 0.45
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (38 bp):
TTACAATTTTTACAATTTCTAATAATTTTTATAATTTC
Found at i:736290 original size:20 final size:19
Alignment explanation
Indices: 736234--736340 Score: 76
Period size: 19 Copynumber: 5.6 Consensus size: 19
736224 TTAAAAAAAA
736234 TTACAATCTTTTACAATTTC
1 TTACAAT-TTTTACAATTTC
* * *
736254 TAATAATTTTTATAATTTC
1 TTACAATTTTTACAATTTC
736273 TTACAATATTTTACAATTTC
1 TTACAAT-TTTTACAATTTC
* * *
736293 -T--ATTTTTTATAATTTT
1 TTACAATTTTTACAATTTC
* * *
736309 TTATAATTTTTAAAAATTC
1 TTACAATTTTTACAATTTC
*
736328 TAACATATTTTTA
1 TTACA-ATTTTTA
736341 ATTTTTGAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
16 10 0.15
17 3 0.04
19 31 0.46
20 23 0.34
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
TTACAATTTTTACAATTTC
Found at i:736308 original size:8 final size:9
Alignment explanation
Indices: 736242--736454 Score: 72
Period size: 10 Copynumber: 23.6 Consensus size: 9
736232 AATTACAATC
*
736242 TTTTACAAT
1 TTTTATAAT
*
736251 TTCTAATAAT
1 TT-TTATAAT
736261 TTTTATAAT
1 TTTTATAAT
*
736270 TTCTTACAAT
1 TT-TTATAAT
*
736280 ATTTTACAAT
1 -TTTTATAAT
*
736290 TTCTAT--T
1 TTTTATAAT
736297 TTTTATAATT
1 TTTTATAA-T
736307 TTTTATAAT
1 TTTTATAAT
* *
736316 TTTTAAAAA
1 TTTTATAAT
*
736325 TTCTA-ACAT
1 TTTTATA-AT
736334 ATTTT-TAAT
1 -TTTTATAAT
*
736343 TTTT-GAAT
1 TTTTATAAT
*
736351 ATTT-T--T
1 TTTTATAAT
*
736357 TTTTGTAATT
1 TTTTATAA-T
736367 TTTATATAAT
1 TTT-TATAAT
736377 TTTTA-AAT
1 TTTTATAAT
* *
736385 TTTTAAAAAA
1 TTTT-ATAAT
*
736395 TTCTA-ACAT
1 TTTTATA-AT
736404 GTTTT-TAAT
1 -TTTTATAAT
*
736413 TTTTAAATAT
1 TTTTATA-AT
*
736423 TTTTGTAAT
1 TTTTATAAT
736432 TTTTAT-AT
1 TTTTATAAT
*
736440 TTTTAAAGAT
1 TTTTATA-AT
736450 TTTTA
1 TTTTA
736455 GGGTTTTTTT
Statistics
Matches: 155, Mismatches: 26, Indels: 45
0.69 0.12 0.20
Matches are distributed among these distances:
6 4 0.03
7 7 0.05
8 30 0.19
9 44 0.28
10 64 0.41
11 6 0.04
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:736356 original size:46 final size:47
Alignment explanation
Indices: 736259--736356 Score: 105
Period size: 46 Copynumber: 2.1 Consensus size: 47
736249 ATTTCTAATA
* * * *
736259 ATTTTTATAATTTCTTACAATATTTTACAATTTCTATTTTTTATAAT
1 ATTTTTATAATTTCTTACAAAATTTAACAATTTCTAATTTTTAGAAT
*
736306 -TTTTTATAATTT-TTA-AAAATTCTAACATATTTTTAATTTTT-GAAT
1 ATTTTTATAATTTCTTACAAAATT-TAACA-ATTTCTAATTTTTAGAAT
736351 ATTTTT
1 ATTTTT
736357 TTTTGTAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
44 5 0.12
45 10 0.23
46 28 0.65
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (47 bp):
ATTTTTATAATTTCTTACAAAATTTAACAATTTCTAATTTTTAGAAT
Found at i:736379 original size:23 final size:22
Alignment explanation
Indices: 736335--736380 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
736325 TTCTAACATA
*
736335 TTTTTAATTTTTGAATATTTTT
1 TTTTTAATTTTTGAATAATTTT
736357 TTTTGTAATTTTT-ATATAATTTT
1 TTTT-TAATTTTTGA-ATAATTTT
736380 T
1 T
736381 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTTAATTTTTGAATAATTTT
Found at i:736385 original size:19 final size:19
Alignment explanation
Indices: 736363--736444 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
736353 TTTTTTTTGT
736363 AATTTTTATATAATTTTTA
1 AATTTTTATATAATTTTTA
* * *
736382 AATTTTTA-AAAAATTCTA
1 AATTTTTATATAATTTTTA
*
736400 ACATGTTT-T-TAATTTTTA
1 A-ATTTTTATATAATTTTTA
*
736418 AATATTTT-TGTAATTTTTA
1 AAT-TTTTATATAATTTTTA
*
736437 TATTTTTA
1 AATTTTTA
736445 AAGATTTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.04
18 23 0.47
19 24 0.49
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTATATAATTTTTA
Found at i:736397 original size:70 final size:70
Alignment explanation
Indices: 736294--736426 Score: 216
Period size: 70 Copynumber: 1.9 Consensus size: 70
736284 TACAATTTCT
*
736294 ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTGAATATTTTTTT
1 ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTAAATATTTTTTT
736359 TTGTA
66 TTGTA
*
736364 ATTTTTATATAA-TTTTTA-AATTTTTAAAAAATTCTAACATGTTTTTAATTTTTAAATATTTTT
1 ATTTTT-TATAATTTTTTATAATTTTT-AAAAATTCTAACATATTTTTAATTTTTAAATATTTTT
736427 GTAATTTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
69 7 0.12
70 47 0.80
71 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (70 bp):
ATTTTTTATAATTTTTTATAATTTTTAAAAATTCTAACATATTTTTAATTTTTAAATATTTTTTT
TTGTA
Found at i:744234 original size:19 final size:19
Alignment explanation
Indices: 744199--744249 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
744189 TTTATAACGT
*
744199 ATACCAAAATCTTTAA-CAG
1 ATACCAAAAT-TTTAACCAA
744218 ATACCAAAATTTGTAACCAA
1 ATACCAAAATTT-TAACCAA
744238 ATACCAAAATTT
1 ATACCAAAATTT
744250 CTAATGATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (19 bp):
ATACCAAAATTTTAACCAA
Found at i:747476 original size:16 final size:16
Alignment explanation
Indices: 747455--747524 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 16
747445 ATAATATTAT
747455 TTTAATGAATTTAATA
1 TTTAATGAATTTAATA
*
747471 TTTAATTTAATTTAATA
1 TTTAA-TGAATTTAATA
** *
747488 TTT-ATCTATATAATA
1 TTTAATGAATTTAATA
* *
747503 TTTTATTAATTTAATA
1 TTTAATGAATTTAATA
747519 -TTAATG
1 TTTAATG
747525 TGATTAATTC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
15 15 0.35
16 15 0.35
17 13 0.30
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTAATGAATTTAATA
Found at i:754240 original size:20 final size:20
Alignment explanation
Indices: 754215--754256 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
754205 CAAGTTAAAC
*
754215 AATATACAAAATAAATATAT
1 AATATACAAAATAAAAATAT
* *
754235 AATATATAATATAAAAATAT
1 AATATACAAAATAAAAATAT
754255 AA
1 AA
754257 AATAAATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATACAAAATAAAAATAT
Found at i:754256 original size:13 final size:14
Alignment explanation
Indices: 754215--754256 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
754205 CAAGTTAAAC
754215 AATATACAAAATA-
1 AATATACAAAATAT
* *
754228 AATATATAATATAT
1 AATATACAAAATAT
754242 AATATA-AAAATAT
1 AATATACAAAATAT
754255 AA
1 AA
754257 AATAAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AATATACAAAATAT
Found at i:760324 original size:22 final size:19
Alignment explanation
Indices: 760298--760346 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
760288 ATATTTTGAT
760298 TTTTTAAAATTTATATTTATA
1 TTTTTAAAATTT-TATTT-TA
*
760319 TATTTTAGAATTTTATTTTA
1 T-TTTTAAAATTTTATTTTA
760339 TTTTTAAA
1 TTTTTAAA
760347 CTTTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 6 0.24
22 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTAAAATTTTATTTTA
Found at i:761614 original size:16 final size:16
Alignment explanation
Indices: 761581--761617 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
761571 AATCATAATC
*
761581 TAATATAATTATTATT
1 TAATATAATAATTATT
*
761597 TAATATAATAATTTTT
1 TAATATAATAATTATT
761613 TAATA
1 TAATA
761618 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATATAATAATTATT
Found at i:767527 original size:27 final size:26
Alignment explanation
Indices: 767445--767530 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
767435 ATTTAAAGAT
* *
767445 ATATGATAAAAATTTTAAAAATTCAAAA
1 ATAT-ATAAAAATTATAAAAA-TAAAAA
* * * *
767473 ATATATAGAAATTATAAAAGTTATAA
1 ATATATAAAAATTATAAAAATAAAAA
* *
767499 ATTTATCAAAAATTGTAAAAATAAAAA
1 ATATAT-AAAAATTATAAAAATAAAAA
767526 ATATA
1 ATATA
767531 ATCAATTACC
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
26 9 0.20
27 32 0.71
28 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATATAAAAATTATAAAAATAAAAA
Found at i:769473 original size:2 final size:2
Alignment explanation
Indices: 769466--769491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
769456 TAACAAGTAA
769466 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
769492 TTGTTGTTAT
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:770869 original size:117 final size:113
Alignment explanation
Indices: 770620--770937 Score: 381
Period size: 117 Copynumber: 2.8 Consensus size: 113
770610 TGTGTGTGTA
* * * * * * *
770620 TTTTATTAAGTTTAAGTTTGTATTAAAAGTATGATTTGTTTGTTTTATTATTGTTTTTATGATAC
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
* *
770685 CTTATATCA-GTTTTATGTATTTAA-GACAAATAATTTTTTTATTGTG
66 CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
* * * *
770731 TTTTATTAGCTTTAAGTTTGTATTAACGGCATGATTAGTTTGTTTTGTTAATGTTTTTGTGGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
** * *
770796 CTTATATCAGGTTTTTTTGTATTTAAGGGGAAGGACATTTTTTTTTGCTGTG
66 CTTATATCAGG-TTTTTTGTATTTAAGGACAAAGA-ATTTTTTTAT--TGTG
* * * **
770848 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGCTTAATCTGTTTTATTAATGTTTTTGAAGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
770913 CTTATATC-GGTTTTTTGTATTTAAG
66 CTTATATCAGGTTTTTTGTATTTAAG
770938 ATATGAACAT
Statistics
Matches: 175, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
111 63 0.36
112 1 0.01
113 13 0.07
114 4 0.02
115 24 0.14
116 2 0.01
117 68 0.39
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (113 bp):
TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
Found at i:771826 original size:143 final size:144
Alignment explanation
Indices: 771567--771854 Score: 544
Period size: 143 Copynumber: 2.0 Consensus size: 144
771557 ATATTGTTAC
771567 TTTTAAATACCAAAATGCATGGCTTTTGTCAAATATTGGTACCACATTAAGAAAAAAATATGTAC
1 TTTTAAATACCAAAATGCATGGCTTTTGTCAAATATTGGTACCACATTAAGAAAAAAATATGTAC
*
771632 ACATTAGAGAAAAAAAAAGGGCCTAAATTCATGTATTAAAAAATGTAGAAGATTATATATTATGT
66 ACATTAGAGAAAAAAAAAGGGCCTAAAATCATGTATTAAAAAATGTAGAAGATTATATATTATGT
771697 TATTATATAATGGT
131 TATTATATAATGGT
771711 TTTTAAATACC-AAATGCATGGCTTTTGTCAAATATTGGTACCACATTAAGAAAAAAATATGTAC
1 TTTTAAATACCAAAATGCATGGCTTTTGTCAAATATTGGTACCACATTAAGAAAAAAATATGTAC
771775 ACATTAGAGAAAAAAAAAGGGCCTAAAATCAAT-TATTAAAAAATGTAGAAGATTATATATTATG
66 ACATTAGAGAAAAAAAAAGGGCCTAAAATC-ATGTATTAAAAAATGTAGAAGATTATATATTATG
771839 TTATTATATAATGGT
130 TTATTATATAATGGT
771854 T
1 T
771855 ATATAAATTT
Statistics
Matches: 142, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
143 129 0.91
144 13 0.09
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.33
Consensus pattern (144 bp):
TTTTAAATACCAAAATGCATGGCTTTTGTCAAATATTGGTACCACATTAAGAAAAAAATATGTAC
ACATTAGAGAAAAAAAAAGGGCCTAAAATCATGTATTAAAAAATGTAGAAGATTATATATTATGT
TATTATATAATGGT
Found at i:771963 original size:15 final size:16
Alignment explanation
Indices: 771935--771984 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
771925 TATAATTTAA
771935 AAATAAATA--ATTTT
1 AAATAAATATTATTTT
771949 AAAT-AAT-TTATTTTT
1 AAATAAATATTA-TTTT
771964 AATATAAATATTATTTT
1 AA-ATAAATATTATTTT
771981 AAAT
1 AAAT
771985 TTTTTTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 6 0.20
16 4 0.13
17 9 0.30
18 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAAATATTATTTT
Found at i:773191 original size:117 final size:113
Alignment explanation
Indices: 772942--773259 Score: 381
Period size: 117 Copynumber: 2.8 Consensus size: 113
772932 TGTGTGTGTA
* * * * * * *
772942 TTTTATTAAGTTTAAGTTTGTATTAAAAGTATGATTTGTTTGTTTTATTATTGTTTTTATGATAC
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
* *
773007 CTTATATCA-GTTTTATGTATTTAA-GACAAATAATTTTTTTATTGTG
66 CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
* * * *
773053 TTTTATTAGCTTTAAGTTTGTATTAACGGCATGATTAGTTTGTTTTGTTAATGTTTTTGTGGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
** * *
773118 CTTATATCAGGTTTTTTTGTATTTAAGGGGAAGGACATTTTTTTTTGCTGTG
66 CTTATATCAGG-TTTTTTGTATTTAAGGACAAAGA-ATTTTTTTAT--TGTG
* * * **
773170 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGCTTAATCTGTTTTATTAATGTTTTTGAAGTAT
1 TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
773235 CTTATATC-GGTTTTTTGTATTTAAG
66 CTTATATCAGGTTTTTTGTATTTAAG
773260 ATATGAACAT
Statistics
Matches: 175, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
111 63 0.36
112 1 0.01
113 13 0.07
114 4 0.02
115 24 0.14
116 2 0.01
117 68 0.39
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (113 bp):
TTTTATTAGGTTTAAGTTTGTATTAAAGGTATGATTAGTTTGTTTTATTAATGTTTTTGTGGTAT
CTTATATCAGGTTTTTTGTATTTAAGGACAAAGAATTTTTTTATTGTG
Found at i:774142 original size:15 final size:16
Alignment explanation
Indices: 774114--774163 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
774104 TATAATTTAA
774114 AAATAAATA--ATTTT
1 AAATAAATATTATTTT
774128 AAAT-AAT-TTATTTTT
1 AAATAAATATTA-TTTT
774143 AATATAAATATTATTTT
1 AA-ATAAATATTATTTT
774160 AAAT
1 AAAT
774164 TTTTTTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 6 0.20
16 4 0.13
17 9 0.30
18 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAAATATTATTTT
Found at i:776874 original size:14 final size:14
Alignment explanation
Indices: 776855--776882 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
776845 CCAATTTATT
776855 AATGAATTATTAAA
1 AATGAATTATTAAA
776869 AATGAATTATTAAA
1 AATGAATTATTAAA
776883 TATAACTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:781250 original size:18 final size:18
Alignment explanation
Indices: 781229--781271 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
781219 CATTCGTTTC
781229 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
781246 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
781265 CAAAACA
1 CAAAACA
781272 CTTTTTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:787499 original size:25 final size:25
Alignment explanation
Indices: 787444--787505 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
787434 TTTTAAGTGT
* *
787444 TTTCAGTATAGT-CTATCTATAATAG
1 TTTCAGTATA-TACTACCTATAACAG
* *
787469 TCTCAGTATATACTACCTATAGCAG
1 TTTCAGTATATACTACCTATAACAG
*
787494 TTTCAGGATATA
1 TTTCAGTATATA
787506 ATATCAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (25 bp):
TTTCAGTATATACTACCTATAACAG
Found at i:787871 original size:18 final size:18
Alignment explanation
Indices: 787840--787888 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
787830 GTATCGTTCG
*
787840 TTTCTAAATTATTATTC-A
1 TTTC-AAATCATTATTCAA
787858 TTTACAAATCATTATTCAA
1 TTT-CAAATCATTATTCAA
*
787877 TTTCAAAACATT
1 TTTCAAATCATT
787889 TTTTTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCAAATCATTATTCAA
Found at i:799260 original size:25 final size:25
Alignment explanation
Indices: 799226--799285 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
799216 CAGTGGTGCA
*
799226 GTGGCAAGGTGGT-G-A-CACAGGT
1 GTGGCAAGGAGGTGGCATCACAGGT
799248 GTGGCAAGGAGGTGGCATCACAGGT
1 GTGGCAAGGAGGTGGCATCACAGGT
*
799273 GTGGTAAGGAGGT
1 GTGGCAAGGAGGT
799286 CAAAGGTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.36
23 1 0.03
24 1 0.03
25 19 0.58
ACGTcount: A:0.23, C:0.12, G:0.47, T:0.18
Consensus pattern (25 bp):
GTGGCAAGGAGGTGGCATCACAGGT
Found at i:801408 original size:121 final size:122
Alignment explanation
Indices: 801183--801425 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 122
801173 AAAAAGATGA
801183 ATATGTTCATCTTTGTTAGCCGAATATTGAAAAGGAAGAAACCATCCATGGCTTCCTAAGTTTCG
1 ATATGTTCATCTTTGTTAGCCGAATATTGAAAAGGAAGAAACCATCCATGGCTTCCTAAGTTTCG
801248 GCACTTCCTTAGCTTGATTAAGGTATGTTTTGGTTTCGGTTTTTTATGATTTTTTAT
66 GCACTTCCTTAGCTTGATTAAGGTATGTTTTGGTTTCGGTTTTTTATGATTTTTTAT
801305 ATATGTTCAT-TTTGTTAGCCGAATATTGAAAAGGAAGAAACCATCCATGGCTTCCTAAGTTTCG
1 ATATGTTCATCTTTGTTAGCCGAATATTGAAAAGGAAGAAACCATCCATGGCTTCCTAAGTTTCG
801369 GCACTTCCTTAGCTTGATTAAGGTATGTTTTGGTTTCGGTTTTTTATGATTTTTTAT
66 GCACTTCCTTAGCTTGATTAAGGTATGTTTTGGTTTCGGTTTTTTATGATTTTTTAT
801426 GTTTTTGTGA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 111 0.92
122 10 0.08
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (122 bp):
ATATGTTCATCTTTGTTAGCCGAATATTGAAAAGGAAGAAACCATCCATGGCTTCCTAAGTTTCG
GCACTTCCTTAGCTTGATTAAGGTATGTTTTGGTTTCGGTTTTTTATGATTTTTTAT
Found at i:802769 original size:40 final size:40
Alignment explanation
Indices: 802653--802787 Score: 216
Period size: 41 Copynumber: 3.3 Consensus size: 40
802643 GCTCTGTACT
802653 TAGCAGGCTTAATGCTAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGC-AGTGAAATAATTCAGACTTTACGTC
*
802694 TAGCAGGCTTAATGCCAGTGAAATAATTCAAACTTTACGTC
1 TAGCAGGCTTAATG-CAGTGAAATAATTCAGACTTTACGTC
* *
802735 TAGCAGGCTTAATGCAGTGAAATATTTCAGACTTTACATC
1 TAGCAGGCTTAATGCAGTGAAATAATTCAGACTTTACGTC
*
802775 TAGTAGGCTTAAT
1 TAGCAGGCTTAAT
802788 ACCGGTGTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
40 35 0.40
41 52 0.59
42 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (40 bp):
TAGCAGGCTTAATGCAGTGAAATAATTCAGACTTTACGTC
Found at i:805716 original size:11 final size:11
Alignment explanation
Indices: 805702--805726 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
805692 TATATATAAG
805702 TAATTTAATGA
1 TAATTTAATGA
805713 TAATTTAATGA
1 TAATTTAATGA
805724 TAA
1 TAA
805727 AAGTGGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
TAATTTAATGA
Found at i:809392 original size:64 final size:64
Alignment explanation
Indices: 809291--809421 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 64
809281 TAAAATTGTC
*
809291 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATGAAGTTTTAATCATTTAAT
1 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
* * *
809355 TTAACAATAAAATTTAGGAGAAATATAGAAATATTAATATAAAATAAATTTTTAGTCATTTAAT
1 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
809419 TTA
1 TTA
809422 GAATAGGAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (64 bp):
TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
Found at i:809397 original size:32 final size:32
Alignment explanation
Indices: 809297--809399 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
809287 TGTCTTAACA
*
809297 ATAAAATTTAGGAGAAACATAGAAATATTAAT
1 ATAAAATTTAGGAGAAATATAGAAATATTAAT
** **** ** *
809329 ATAAAATGAAGTTTTAATCAT-TTAAT-TTAACA
1 ATAAAATTTAGGAGAAAT-ATAGAAATATTAA-T
809361 ATAAAATTTAGGAGAAATATAGAAATATTAAT
1 ATAAAATTTAGGAGAAATATAGAAATATTAAT
809393 ATAAAAT
1 ATAAAAT
809400 AAATTTTTAG
Statistics
Matches: 48, Mismatches: 19, Indels: 8
0.64 0.25 0.11
Matches are distributed among these distances:
31 6 0.12
32 36 0.75
33 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (32 bp):
ATAAAATTTAGGAGAAATATAGAAATATTAAT
Found at i:809572 original size:46 final size:46
Alignment explanation
Indices: 809505--809611 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
809495 ACTTTATTTC
* * *
809505 AAAATTTCAAAAGTTTCTTAATATATAAATAATTTACCCTGATAGT
1 AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
* *
809551 AAAATTTTATAATTTTCTTAATATATAAATAATTTATCCTAATAGT
1 AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
*
809597 AAACTTTTAAAATTT
1 AAAATTTTAAAATTT
809612 ATACAAATGA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (46 bp):
AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
Found at i:811830 original size:9 final size:9
Alignment explanation
Indices: 811813--811849 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
811803 TGAGTTTTCG
811813 AATTCGAAT
1 AATTCGAAT
*
811822 AACTCGAAT
1 AATTCGAAT
*
811831 AATTAGAAT
1 AATTCGAAT
811840 AATTCGAAT
1 AATTCGAAT
811849 A
1 A
811850 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:811955 original size:28 final size:28
Alignment explanation
Indices: 811902--811955 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
811892 CTTTTTATTT
*
811902 TTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTCCCTCAAAACTTTTACTCCCTCCCAC
811930 TTCCC-CAAAACTTTTACTCTCCTCCC
1 TTCCCTCAAAACTTTTACTC-CCTCCC
811956 CTCCCAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.35
Consensus pattern (28 bp):
TTCCCTCAAAACTTTTACTCCCTCCCAC
Found at i:812851 original size:5 final size:5
Alignment explanation
Indices: 812841--812866 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
812831 CTCGAAAATT
812841 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
812867 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:821136 original size:247 final size:248
Alignment explanation
Indices: 820687--821184 Score: 908
Period size: 247 Copynumber: 2.0 Consensus size: 248
820677 GAGTGCAATA
820687 TTTTAAATCCTCAAAATTAAATTTATCTCTCGTCTTTTAAAACCTATGCATCTTGAGGGGGATGT
1 TTTTAAATCCTCAAAATTAAATTTATCTCTCGTCTTTTAAAACCTATGCATCTTGAGGGGGATGT
820752 CTGATTATCTGAGTCAAATGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTCAAAAAATTC
66 CTGATTATCTGAGTCAAATGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTCAAAAAATTC
* *
820817 CTAAATATCGAACATTGCCTTAAAATCCTCATCTCGAGAAAATAATACGTCATATTCAATGCGTT
131 CTAAATATCGAACATTACCTTAAAATCCTCATCTCAAGAAAATAATACGTCATATTCAATGCGTT
820882 AGGACACAACGCGTAAAATTCCCGAGAATGAGCTTTTATTTGAAATTTGTATG
196 AGGACACAACGCGTAAAATTCCCGAGAATGAGCTTTTATTTGAAATTTGTATG
820935 TTTTAAATCCTC-AAATTAAATTTATCTCTCGTCTTTTAAAACCTATGCATCTTGAGGGGGATGT
1 TTTTAAATCCTCAAAATTAAATTTATCTCTCGTCTTTTAAAACCTATGCATCTTGAGGGGGATGT
***
820999 CTGATTATCTGAGTCAAATGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTTGCAAAATTC
66 CTGATTATCTGAGTCAAATGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTCAAAAAATTC
* *
821064 CTAGATATCGAACATTACCTTAAAATCCTCGTCTCAAGAAAATAATACGTCATATTCAATGCGTT
131 CTAAATATCGAACATTACCTTAAAATCCTCATCTCAAGAAAATAATACGTCATATTCAATGCGTT
* *
821129 AGGACACAACGCGTCAAATTTCCGAGAATGAGCTTTTATTTGAAATTTGTATG
196 AGGACACAACGCGTAAAATTCCCGAGAATGAGCTTTTATTTGAAATTTGTATG
821182 TTT
1 TTT
821185 AAAAAAATTT
Statistics
Matches: 241, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
247 229 0.95
248 12 0.05
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (248 bp):
TTTTAAATCCTCAAAATTAAATTTATCTCTCGTCTTTTAAAACCTATGCATCTTGAGGGGGATGT
CTGATTATCTGAGTCAAATGAGAAAATCAAAACCCAGTAAGTTAGGGTTCGATTTCAAAAAATTC
CTAAATATCGAACATTACCTTAAAATCCTCATCTCAAGAAAATAATACGTCATATTCAATGCGTT
AGGACACAACGCGTAAAATTCCCGAGAATGAGCTTTTATTTGAAATTTGTATG
Found at i:823434 original size:7 final size:7
Alignment explanation
Indices: 823423--823490 Score: 84
Period size: 7 Copynumber: 9.7 Consensus size: 7
823413 CTTCAATCTC
*
823423 CAATTTC
1 CAATTTT
823430 CAATTTT
1 CAATTTT
*
823437 CTATTTT
1 CAATTTT
*
823444 CAATATT
1 CAATTTT
823451 CAATTTT
1 CAATTTT
823458 CAA-TTT
1 CAATTTT
823464 CGAATTTT
1 C-AATTTT
823472 CAATTTT
1 CAATTTT
*
823479 CTATTTT
1 CAATTTT
823486 CAATT
1 CAATT
823491 CTAAATCCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 4 0.08
7 44 0.85
8 4 0.08
ACGTcount: A:0.28, C:0.16, G:0.01, T:0.54
Consensus pattern (7 bp):
CAATTTT
Found at i:843403 original size:3 final size:3
Alignment explanation
Indices: 843395--843435 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
843385 TGATAAGGTT
843395 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
843436 TACACAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:849058 original size:21 final size:22
Alignment explanation
Indices: 849034--849079 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
849024 CTGTTGAAAA
849034 TAATA-AAAAATAATCAAAATT
1 TAATATAAAAATAATCAAAATT
* * *
849055 TAATATAAAATTAATTAAGATT
1 TAATATAAAAATAATCAAAATT
849077 TAA
1 TAA
849080 CATGTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATATAAAAATAATCAAAATT
Found at i:851161 original size:7 final size:7
Alignment explanation
Indices: 851148--851178 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
851138 TTTGGTTGTA
851148 ATTGGAC
1 ATTGGAC
*
851155 TTTGGAC
1 ATTGGAC
851162 ATTGGAC
1 ATTGGAC
851169 ATTGGAC
1 ATTGGAC
851176 ATT
1 ATT
851179 TTATTTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (7 bp):
ATTGGAC
Found at i:853876 original size:45 final size:46
Alignment explanation
Indices: 853811--853937 Score: 150
Period size: 45 Copynumber: 2.8 Consensus size: 46
853801 TTGATTCAAA
** * *
853811 TGAGTAAGACCATAATTGAAAGACATTATGGCATCATGACAGA-AG
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
* * * **
853856 TGAGTAAGACCATGGCTGAAAGATGCTATGGCATCATGGTAAATAG
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
*
853902 -GACTAAGACCATAGCTGAAAGACGTTATGGCATCAT
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCAT
853938 TTCATAGTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 66 0.97
46 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
Found at i:856731 original size:5 final size:5
Alignment explanation
Indices: 856721--856748 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
856711 AAAAGAAGGA
856721 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
856749 TAGGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:862588 original size:23 final size:23
Alignment explanation
Indices: 862515--862588 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
862505 CTGGGTCTCA
* *
862515 CACACGACCATACCTTTGACAGT
1 CACACGACCACACCCTTGACAGT
*
862538 CACACGACCACACCCTCGACAGT
1 CACACGACCACACCCTTGACAGT
* *
862561 CACACGACTACACCCTTGATAGT
1 CACACGACCACACCCTTGACAGT
*
862584 TACAC
1 CACAC
862589 AGTCAGCCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.31, C:0.39, G:0.12, T:0.18
Consensus pattern (23 bp):
CACACGACCACACCCTTGACAGT
Found at i:863759 original size:17 final size:17
Alignment explanation
Indices: 863728--863760 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
863718 GTATTGATTT
863728 TGACATTCTTATGTCAA
1 TGACATTCTTATGTCAA
863745 TGACAATTCTT-TGTCA
1 TGAC-ATTCTTATGTCA
863761 TCAATCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACATTCTTATGTCAA
Found at i:863977 original size:17 final size:17
Alignment explanation
Indices: 863955--864010 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
863945 AACAAGTATG
863955 TGATTACAATAATCTCA
1 TGATTACAATAATCTCA
* * * *
863972 TGATTAAAACAAGTAT-G
1 TGATTACAATAA-TCTCA
863989 TGATTACAATAATCTCA
1 TGATTACAATAATCTCA
864006 TGATT
1 TGATT
864011 GGCCTTTGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (17 bp):
TGATTACAATAATCTCA
Found at i:863980 original size:34 final size:34
Alignment explanation
Indices: 863942--864010 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
863932 ATAAACAAGG
863942 TAAAACAAGTATGTGATTACAATAATCTCATGAT
1 TAAAACAAGTATGTGATTACAATAATCTCATGAT
863976 TAAAACAAGTATGTGATTACAATAATCTCATGAT
1 TAAAACAAGTATGTGATTACAATAATCTCATGAT
864010 T
1 T
864011 GGCCTTTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (34 bp):
TAAAACAAGTATGTGATTACAATAATCTCATGAT
Found at i:864474 original size:20 final size:20
Alignment explanation
Indices: 864449--864490 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
864439 CATCATAGTT
864449 AATACCATGAACTTAGCGAA
1 AATACCATGAACTTAGCGAA
864469 AATACCATGAACTTAGCGAA
1 AATACCATGAACTTAGCGAA
864489 AA
1 AA
864491 CCTTTAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (20 bp):
AATACCATGAACTTAGCGAA
Found at i:866434 original size:29 final size:30
Alignment explanation
Indices: 866387--866444 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
866377 TTGGCTTTGA
866387 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
1 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
866417 CATT-TCCTTAGGCTTTGCCTTAGACTTA
1 CATTGTCCTTAGGCTTTGCCTTAGACTTA
866445 ACAATTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (30 bp):
CATTGTCCTTAGGCTTTGCCTTAGACTTAG
Found at i:868006 original size:16 final size:17
Alignment explanation
Indices: 867973--868006 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
867963 TCGGGCTATA
*
867973 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
867990 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
868006 A
1 A
868007 TAGTATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:869454 original size:11 final size:11
Alignment explanation
Indices: 869438--869462 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
869428 TCCATTTGAG
869438 TTTTTCTTTGC
1 TTTTTCTTTGC
869449 TTTTTCTTTGC
1 TTTTTCTTTGC
869460 TTT
1 TTT
869463 ATTAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTGC
Found at i:872348 original size:18 final size:17
Alignment explanation
Indices: 872326--872365 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
872316 AAAAATTAGA
*
872326 TAAATGATATACTTTAT
1 TAAATGATACACTTTAT
*
872343 TCAAATTATACACTTTAT
1 T-AAATGATACACTTTAT
872361 TAAAT
1 TAAAT
872366 ATAATACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATGATACACTTTAT
Found at i:872485 original size:22 final size:24
Alignment explanation
Indices: 872430--872485 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
872420 ACGATGAGAG
*
872430 AAATTTTAATATGAAAAAAAATGT
1 AAATTTAAATATGAAAAAAAATGT
*
872454 AAATTAAAATA-GAAAAAAAA-G-
1 AAATTTAAATATGAAAAAAAATGT
872475 ATAATTTAAAT
1 A-AATTTAAAT
872486 GACAAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
23 9 0.32
24 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATTTAAATATGAAAAAAAATGT
Found at i:872497 original size:26 final size:27
Alignment explanation
Indices: 872460--872532 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
872450 ATGTAAATTA
**
872460 AAAT-AGAAAAAAAAGATAATTTAAATG
1 AAATGAGAAAAAAATTA-AATTTAAATG
*
872487 ACAA-GAGAAAAAAATTAAATTTAAGTG
1 A-AATGAGAAAAAAATTAAATTTAAATG
872514 AAATGAGAAAAAAATTAAA
1 AAATGAGAAAAAAATTAAA
872533 ATGGAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 26 0.65
28 12 0.30
ACGTcount: A:0.66, C:0.01, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATGAGAAAAAAATTAAATTTAAATG
Found at i:872497 original size:27 final size:27
Alignment explanation
Indices: 872443--872532 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
872433 TTTTAATATG
* *
872443 AAAAA-AAATGTAAATTAAAAT-AGAAA
1 AAAAATAAATTTAAA-TGAAATGAGAAA
*
872469 AAAAAGATAATTTAAATGACAA-GAGAAA
1 AAAAATA-AATTTAAATGA-AATGAGAAA
* *
872497 AAAATTAAATTTAAGTGAAATGAGAAA
1 AAAAATAAATTTAAATGAAATGAGAAA
*
872524 AAAATTAAA
1 AAAAATAAA
872533 ATGGAAAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 7 0.13
27 28 0.52
28 19 0.35
ACGTcount: A:0.67, C:0.01, G:0.11, T:0.21
Consensus pattern (27 bp):
AAAAATAAATTTAAATGAAATGAGAAA
Found at i:872543 original size:27 final size:27
Alignment explanation
Indices: 872491--872544 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
872481 TAAATGACAA
** *
872491 GAGAAAAAAATTAAATTTAAGTGAAAT
1 GAGAAAAAAATTAAATGGAAGAGAAAT
872518 GAGAAAAAAATTAAAATGGAA-AGAAAT
1 GAGAAAAAAATT-AAATGGAAGAGAAAT
872545 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (27 bp):
GAGAAAAAAATTAAATGGAAGAGAAAT
Found at i:872559 original size:43 final size:45
Alignment explanation
Indices: 872495--872622 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 45
872485 TGACAAGAGA
*
872495 AAAAAATTAAATTTAAGTGAAATGAGAAAAAAATTAAAATGGAAA-G
1 AAAAAA-T-AATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
* * **
872541 -AAATATAATTTAAATGAAATGAGGAAGAAATTAAATTTAAATTTAAATG
1 AAAAAATAATTTAAATGAAATGA-G-A-AAA--AAATTAAAATGGAAATG
872590 AAAAAAATAATTTAAATGAAATGAGAAAAAAAT
1 -AAAAAATAATTTAAATGAAATGAGAAAAAAAT
872623 AAATTTAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
43 15 0.22
44 2 0.03
45 5 0.07
46 7 0.10
48 15 0.22
49 2 0.03
50 1 0.01
51 21 0.31
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (45 bp):
AAAAAATAATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
Found at i:872572 original size:70 final size:71
Alignment explanation
Indices: 872454--872610 Score: 192
Period size: 70 Copynumber: 2.2 Consensus size: 71
872444 AAAAAAATGT
872454 AAATTAAAATAGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTT-AAGTGAAAT
1 AAATTAAAAT-GAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAAT
*
872518 GAGAAAA
65 GAAAAAA
* * * * * * *
872525 AAATTAAAATGGAAAGAAATATAATTTAAATGA-AATGAGGAAGAAATTAAATTTAAATTTAAAT
1 AAATTAAAATGAAAAAAAAGATAATTTAAATGACAA-GAGAAAAAAATTAAATTTAAAGTGAAAT
872589 GAAAAAA
65 GAAAAAA
*
872596 ATAATTTAAATGAAA
1 A-AATTAAAATGAAA
872611 TGAGAAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
69 2 0.03
70 36 0.49
71 24 0.33
72 11 0.15
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (71 bp):
AAATTAAAATGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAATG
AAAAAA
Found at i:872610 original size:51 final size:53
Alignment explanation
Indices: 872525--872632 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 53
872515 AATGAGAAAA
* *
872525 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGGAAGAAATTAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGA-GAAAAAAATAAATTT
*
872579 AAATTTAAAT-GAAA-AAA-ATAATTTAAATGAAATGAGAAAAAAATAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
872629 AAAT
1 AAAT
872633 AGAAAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 17 0.33
51 18 0.35
52 3 0.06
53 4 0.08
54 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (53 bp):
AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
Found at i:873065 original size:19 final size:18
Alignment explanation
Indices: 873043--873081 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
873033 GTATATTAGG
*
873043 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
873062 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
873080 AA
1 AA
873082 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:873080 original size:5 final size:5
Alignment explanation
Indices: 873070--873170 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
873060 GAAAAAAATT
* *
873070 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
873122 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
873171 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:873088 original size:30 final size:30
Alignment explanation
Indices: 873046--873170 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
873036 TATTAGGAAA
873046 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
873074 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
873104 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
873137 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
873165 AAATGA
1 AAATGA
873171 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:873091 original size:12 final size:12
Alignment explanation
Indices: 873072--873141 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
873062 AAAAAATTAA
873072 TGAAATGAAATG
1 TGAAATGAAATG
* *
873084 TTAAATGAAATA
1 TGAAATGAAATG
873096 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
873107 TGAAATGTAATT
1 TGAAATGAAATG
* *
873119 TGTAATG-AATA
1 TGAAATGAAATG
873130 TGAAATGAAATG
1 TGAAATGAAATG
873142 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:873109 original size:35 final size:33
Alignment explanation
Indices: 873072--873142 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
873062 AAAAAATTAA
*
873072 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
873107 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
873140 TGA
1 TGA
873143 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:873153 original size:28 final size:27
Alignment explanation
Indices: 873095--873170 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
873085 TAAATGAAAT
*
873095 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
873123 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
873151 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
873171 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:873259 original size:20 final size:20
Alignment explanation
Indices: 873205--873304 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
873195 AAATGAAAAT
*
873205 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
873223 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
873242 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
873262 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
873284 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
873303 AA
1 AA
873305 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:873280 original size:21 final size:21
Alignment explanation
Indices: 873236--873302 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
873226 TCAAAAACTG
873236 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
873255 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
873277 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
873297 AAATGA
1 AAATGA
873303 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:873319 original size:19 final size:17
Alignment explanation
Indices: 873270--873332 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
873260 GAGAAATAAT
873270 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
873287 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
873300 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
873319 TTAATTTAAATGGA
1 TAAATTTAAATGGA
873333 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:873328 original size:29 final size:30
Alignment explanation
Indices: 873271--873330 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
873261 AGAAATAATT
873271 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
873302 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
873331 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:873368 original size:5 final size:5
Alignment explanation
Indices: 873358--873419 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
873348 ATGTAGATGT
* * *
873358 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
873407 AAATG AAATG AAA
1 AAATG AAATG AAA
873420 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:873371 original size:22 final size:22
Alignment explanation
Indices: 873357--873420 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
873347 AATGTAGATG
873357 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
873379 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
873400 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
873421 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:873388 original size:27 final size:27
Alignment explanation
Indices: 873358--873419 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
873348 ATGTAGATGT
*
873358 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
873385 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
873412 AAATGAAA
1 AAATGAAA
873420 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:873403 original size:11 final size:11
Alignment explanation
Indices: 873358--873416 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
873348 ATGTAGATGT
873358 AAATG-AAATG
1 AAATGCAAATG
* *
873368 AAATGAAAATAT
1 AAATGCAAAT-G
873380 AAATG-AAATG
1 AAATGCAAATG
*
873390 AAATGCAAAGG
1 AAATGCAAATG
*
873401 AAATACAAATG
1 AAATGCAAATG
873412 AAATG
1 AAATG
873417 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:873729 original size:753 final size:753
Alignment explanation
Indices: 872783--876294 Score: 6850
Period size: 753 Copynumber: 4.7 Consensus size: 753
872773 ATTTCAAGCG
* *
872783 TAAAAAAAAATCCTCAAAAAGAA-TGAAATGAGAAATATTTTTTATTTTAAATGAAATTTAAAAT
1 TAAAAAAAAA-CC-CAAAAA-AATTGAAATGAGAAAT-TTTTTTAATTTAAGTGAAATTT-AAAT
* * * *
872847 TTTT-TAATGGAATAATATTTAAATTGACAAAAAATTTAAATTAAAA-ATAAAAAAATTTTAAAT
61 TTTTGTAATGGAATTATATTTAATTTGA-AAAAAATTTAAA-TAAAATAT-GATAAATTTTAAAT
* * *
872910 GACCTTGATATTGAGACTACTACTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATT
123 AATCTTGATATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATT
872975 TGAACTGAGAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATT
188 TGAACTGAGAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATT
873040 AGGAAAAAATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGA
253 AGGAAAAAATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGA
873105 AATGAAATGTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATG
318 AATGAAATGTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATG
873170 ATGATTATGAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACT
383 ATGATTATGAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACT
873235 GAAATGAAAATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAA
448 GAAATGAAAATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAA
873300 TGAAATTATAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAA
513 TGAAATTATAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAA
873365 ATGAAATGAAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGT
578 ATGAAATGAAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGT
873430 GAAATGACATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAAC
643 GAAATGACATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAAC
873495 AGGCCTACTCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
708 AGGCCTACTCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
873541 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
1 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
873606 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
66 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
873671 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
131 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
873736 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
196 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
873801 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
261 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
873866 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
326 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
873931 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
391 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
873996 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
456 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
874061 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
521 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
874126 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
586 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
874191 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
651 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
874256 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
716 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
874294 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
1 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
874359 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
66 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
874424 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
131 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
874489 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
196 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
874554 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
261 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
874619 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
326 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
874684 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
391 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
874749 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
456 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
874814 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
521 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
874879 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
586 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
874944 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
651 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
875009 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
716 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
875047 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
1 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
875112 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
66 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
875177 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
131 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
875242 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
196 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
875307 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
261 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
875372 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
326 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
875437 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
391 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
875502 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
456 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
875567 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
521 TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
875632 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
586 AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
875697 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
651 ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
875762 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
716 TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
875800 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
1 TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
875865 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
66 TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
875930 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
131 TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
875995 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
196 GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
876060 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
261 ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
876125 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
326 GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
876190 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
391 GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
876255 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGG
456 AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGG
876295 TTGAAATAAT
Statistics
Matches: 2742, Mismatches: 9, Indels: 11
0.99 0.00 0.00
Matches are distributed among these distances:
753 2646 0.96
754 22 0.01
755 43 0.02
756 19 0.01
757 2 0.00
758 10 0.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (753 bp):
TAAAAAAAAACCCAAAAAAATTGAAATGAGAAATTTTTTTAATTTAAGTGAAATTTAAATTTTTG
TAATGGAATTATATTTAATTTGAAAAAAATTTAAATAAAATATGATAAATTTTAAATAATCTTGA
TATTGAGACTACTTCTAATTAATATGAAAAAATATGAAATGAATTGAAAAAAAAATTTGAACTGA
GAAAAGATAAATTGAAATGAGAGTACTTGTGAATAATATGAAAAAAAATTGTATATTAGGAAAAA
ATAAATTTAAATGAAAAAAATTAATGAAATGAAATGTTAAATGAAATATGAATATGAAATGAAAT
GTAATTTGTAATGAATATGAAATGAAATGAGGTGTTAAATGAATATAAAATGAAATGATGATTAT
GAAATGGAGTGATGTTTAAATGAAAATAAATTATAAATTTAAATGAAATCAAAAACTGAAATGAA
AATAAAAATTTTGAAATGAGAAATAATTAAATTTAAATGGAAAATAATTAATTTAAATGAAATTA
TAAATGGAAAATTAATTTAAATGGAGAAAAATTCATTTAAATGTAGATGTAAATGAAATGAAATG
AAAATATAAATGAAATGAAATGCAAAGGAAATACAAATGAAATGAAAAAAAAAAGGTGAAATGAC
ATGTTAGGCAGGCCTGCGCTAGGCCTGGAAAATGGGGTGTCATTGGTCGGCACCAACAGGCCTAC
TCCTTAGTATTTGATTTAATATTTCAAGCCTTAAAAAC
Found at i:873818 original size:19 final size:18
Alignment explanation
Indices: 873796--873834 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
873786 GTATATTAGG
*
873796 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
873815 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
873833 AA
1 AA
873835 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:873833 original size:5 final size:5
Alignment explanation
Indices: 873823--873923 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
873813 GAAAAAAATT
* *
873823 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
873875 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
873924 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:873841 original size:30 final size:30
Alignment explanation
Indices: 873799--873923 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
873789 TATTAGGAAA
873799 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
873827 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
873857 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
873890 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
873918 AAATGA
1 AAATGA
873924 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:873844 original size:12 final size:12
Alignment explanation
Indices: 873825--873894 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
873815 AAAAAATTAA
873825 TGAAATGAAATG
1 TGAAATGAAATG
* *
873837 TTAAATGAAATA
1 TGAAATGAAATG
873849 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
873860 TGAAATGTAATT
1 TGAAATGAAATG
* *
873872 TGTAATG-AATA
1 TGAAATGAAATG
873883 TGAAATGAAATG
1 TGAAATGAAATG
873895 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:873862 original size:35 final size:33
Alignment explanation
Indices: 873825--873895 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
873815 AAAAAATTAA
*
873825 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
873860 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
873893 TGA
1 TGA
873896 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:873906 original size:28 final size:27
Alignment explanation
Indices: 873848--873923 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
873838 TAAATGAAAT
*
873848 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
873876 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
873904 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
873924 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:874012 original size:20 final size:20
Alignment explanation
Indices: 873958--874057 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
873948 AAATGAAAAT
*
873958 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
873976 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
873995 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
874015 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
874037 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
874056 AA
1 AA
874058 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:874033 original size:21 final size:21
Alignment explanation
Indices: 873989--874055 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
873979 TCAAAAACTG
873989 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
874008 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
874030 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
874050 AAATGA
1 AAATGA
874056 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:874072 original size:19 final size:17
Alignment explanation
Indices: 874023--874085 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
874013 GAGAAATAAT
874023 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
874040 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
874053 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
874072 TTAATTTAAATGGA
1 TAAATTTAAATGGA
874086 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:874081 original size:29 final size:30
Alignment explanation
Indices: 874024--874083 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
874014 AGAAATAATT
874024 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
874055 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
874084 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:874121 original size:5 final size:5
Alignment explanation
Indices: 874111--874172 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
874101 ATGTAGATGT
* * *
874111 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
874160 AAATG AAATG AAA
1 AAATG AAATG AAA
874173 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:874124 original size:22 final size:22
Alignment explanation
Indices: 874110--874173 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
874100 AATGTAGATG
874110 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
874132 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
874153 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
874174 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:874141 original size:27 final size:27
Alignment explanation
Indices: 874111--874172 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
874101 ATGTAGATGT
*
874111 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
874138 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
874165 AAATGAAA
1 AAATGAAA
874173 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:874156 original size:11 final size:11
Alignment explanation
Indices: 874111--874169 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
874101 ATGTAGATGT
874111 AAATG-AAATG
1 AAATGCAAATG
* *
874121 AAATGAAAATAT
1 AAATGCAAAT-G
874133 AAATG-AAATG
1 AAATGCAAATG
*
874143 AAATGCAAAGG
1 AAATGCAAATG
*
874154 AAATACAAATG
1 AAATGCAAATG
874165 AAATG
1 AAATG
874170 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:874571 original size:19 final size:18
Alignment explanation
Indices: 874549--874587 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
874539 GTATATTAGG
*
874549 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
874568 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
874586 AA
1 AA
874588 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Done.