Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 3 of 100
Found at i:289583 original size:2 final size:2
Alignment explanation
Indices: 289576--289613 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
289566 CAAACCACAA
289576 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
289614 GGATAGTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:293284 original size:77 final size:77
Alignment explanation
Indices: 293157--293303 Score: 267
Period size: 77 Copynumber: 1.9 Consensus size: 77
293147 CTTCTTCACA
* **
293157 TAAAACTCCATCATTGCTATAGGATCTGCACCTGTTGGTGCACTGGATGGGCCTGCAACTTAGAA
1 TAAAACTCCATCATTGCTATAGGATCTGCACCTGGTGGCACACTGGATGGGCCTGCAACTTAGAA
293222 AAACAGTTATAG
66 AAACAGTTATAG
293234 TAAAACTCCATCATTGCTATAGGATCTGCACCTGGTGGCACACTGGATGGGCCTGCAACTTAGAA
1 TAAAACTCCATCATTGCTATAGGATCTGCACCTGGTGGCACACTGGATGGGCCTGCAACTTAGAA
293299 AAACA
66 AAACA
293304 TGTATATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (77 bp):
TAAAACTCCATCATTGCTATAGGATCTGCACCTGGTGGCACACTGGATGGGCCTGCAACTTAGAA
AAACAGTTATAG
Found at i:299226 original size:15 final size:16
Alignment explanation
Indices: 299196--299234 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
299186 ATTTTTAAAA
*
299196 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
299212 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
*
299227 ATTTTAAA
1 ATTATAAA
299235 ACTAATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:301644 original size:13 final size:14
Alignment explanation
Indices: 301619--301647 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
301609 ATATTAAGTT
301619 AAAATTTTCAAAAA
1 AAAATTTTCAAAAA
301633 AAAATTTT-AAAAA
1 AAAATTTTCAAAAA
301646 AA
1 AA
301648 TTTATATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTTTCAAAAA
Found at i:301677 original size:30 final size:30
Alignment explanation
Indices: 301643--301762 Score: 109
Period size: 30 Copynumber: 3.9 Consensus size: 30
301633 AAAATTTTAA
301643 AAAAATTTATATCATTTTAAAAAATTAAAT
1 AAAAATTTATATCATTTTAAAAAATTAAAT
* * *
301673 AAAAATTT-TAT-TTTGATTTAAAAATGAAAT
1 AAAAATTTATATCATT--TTAAAAAATTAAAT
* ** *
301703 AAAACTCCATATCATTTTAAAATATTAAAT
1 AAAAATTTATATCATTTTAAAAAATTAAAT
**
301733 AAAGTTTTTCATATCATTTTAAAAAATTAA
1 AAA-AATTT-ATATCATTTTAAAAAATTAA
301763 TTTATTAATC
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.03
29 3 0.04
30 39 0.57
31 4 0.06
32 21 0.30
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAAATTTATATCATTTTAAAAAATTAAAT
Found at i:301917 original size:19 final size:18
Alignment explanation
Indices: 301872--301918 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
301862 AAAAAATATT
301872 TAATATTTTTAATAAAAA
1 TAATATTTTTAATAAAAA
*
301890 CAGAT-TTTTTGAATAAAAA
1 TA-ATATTTTT-AATAAAAA
301909 TAATATTTTT
1 TAATATTTTT
301919 TATTATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (18 bp):
TAATATTTTTAATAAAAA
Found at i:303013 original size:8 final size:8
Alignment explanation
Indices: 303000--303024 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
302990 TAAGATATAA
303000 TAAAATTT
1 TAAAATTT
303008 TAAAATTT
1 TAAAATTT
303016 TAAAATTT
1 TAAAATTT
303024 T
1 T
303025 TTGAATATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAAAATTT
Found at i:306085 original size:14 final size:15
Alignment explanation
Indices: 306066--306095 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
306056 AAGGCAGTTA
306066 TATCC-AAAACACCT
1 TATCCAAAAACACCT
306080 TATCCAAAAACACCT
1 TATCCAAAAACACCT
306095 T
1 T
306096 TAATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
TATCCAAAAACACCT
Found at i:306781 original size:304 final size:302
Alignment explanation
Indices: 306080--306902 Score: 1030
Period size: 304 Copynumber: 2.7 Consensus size: 302
306070 CAAAACACCT
* * * * * * *
306080 TATCCAAAAACACCTTTAATAATATTTTGTTAGGGATTATTCAAGGCGTTACCTATAGGAAAACG
1 TATCCAAAAACGCCTTCAATAACATTTTGTTAGAGATTATTCAATGTGTTACCTATAGGAAAATG
* ** *
306145 CCTTTCATAATCCATTCGATTAATTTTTAGTTGATATTATTGAA-GAAATTTTAAAAAAACGCTT
66 CCTTTCATAATCCATTCGATTAATTTTTAGTTGGTATTATTGAAGGATTTTTTAAAAATAC-CTT
306209 TCAATAATCCATACAAAAAAGATGCGAC-GAATTCTTGAAGGCATTTTTTTTTTCAAAATGCCTT
130 T-AATAAT-CATACAAAAAAGATGCGACAG-ATTCTTGAAGGCATTTTTTTTTTCAAAATGCCTT
* ** * * * ** *
306273 TAATATTCCACACAA-CAA-CGTTGGTGGGAGTATTGAAGGCAGTTTTGGTAAAAAATGCCATTG
192 TAATATTCCACACAATAAATTTTTGGTGAGAGTATGGAAGACAGTTTTGGTAAAAAACACCATTA
* * *
306336 ATATACTAGATGATAAATTTAATGGTCGAATTATTAAAGACGGTTA
257 ATATACCAAATAATAAATTTAATGGTCGAATTATTAAAGACGGTTA
* * * * *
306382 TATCCAAAAATGCTTTCAATAACATTTTGTTA-AGGATTATTTAATGTGTTTCCTGTAGGAAAAT
1 TATCCAAAAACGCCTTCAATAACATTTTGTTAGA-GATTATTCAATGTGTTACCTATAGGAAAAT
*
306446 GGCCTTT-ATAATCCATTCGATTAATTTTTAGTTGGTATTATTGAAGGTATTTTTTTAAAATACC
65 -GCCTTTCATAATCCATTCGATTAATTTTTAGTTGGTATTATTGAAGG-ATTTTTTAAAAATACC
* * * * * *
306510 TTTAATAATCTATACAAACAAGAAGCAACAGATTCTTGAAGGTATTTTTTTTCTCAAAACGCCTT
128 TTTAATAATC-ATACAAAAAAGATGCGACAGATTCTTGAAGGCATTTTTTTTTTCAAAATGCCTT
*
306575 TAATATTCCACACAATAAATTTTTGGTGAGATTATGGAAGACAGTTTTGGTAAAAAACACCATTA
192 TAATATTCCACACAATAAATTTTTGGTGAGAGTATGGAAGACAGTTTTGGTAAAAAACACCATTA
* * * *
306640 ATATTCCAAATAATAAATTTTAATGGT-GGATTATTGAAGGCGGTTA
257 ATATACCAAATAATAAA-TTTAATGGTCGAATTATTAAAGACGGTTA
** * *
306686 TATTTAAAAACGCCTTCAATAACATTTTGTTAGAGATTATTCAATGTGTTACCCATAGAAAAATG
1 TATCCAAAAACGCCTTCAATAACATTTTGTTAGAGATTATTCAATGTGTTACCTATAGGAAAATG
* * *
306751 CCTTTCATAATCCATTCGATTAAGTTTTAGTTGGTATTATTGAAGGCATTTTTTAAAAATGCGTT
66 CCTTTCATAATCCATTCGATTAATTTTTAGTTGGTATTATTGAAGG-ATTTTTTAAAAATACCTT
* * *
306816 CAATAATCATACAAAAAAGATGCGACAAATTCTTGAAGGCATTTTTTTTTTTCAAAATGCTTTTA
130 TAATAATCATACAAAAAAGATGCGACAGATTCTTGAAGGCA-TTTTTTTTTTCAAAATGCCTTTA
* *
306881 ATATTCTATACAATAAATTTTT
194 ATATTCCACACAATAAATTTTT
306903 AAGATGATTA
Statistics
Matches: 444, Mismatches: 65, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
301 1 0.00
302 155 0.35
303 48 0.11
304 230 0.52
305 10 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (302 bp):
TATCCAAAAACGCCTTCAATAACATTTTGTTAGAGATTATTCAATGTGTTACCTATAGGAAAATG
CCTTTCATAATCCATTCGATTAATTTTTAGTTGGTATTATTGAAGGATTTTTTAAAAATACCTTT
AATAATCATACAAAAAAGATGCGACAGATTCTTGAAGGCATTTTTTTTTTCAAAATGCCTTTAAT
ATTCCACACAATAAATTTTTGGTGAGAGTATGGAAGACAGTTTTGGTAAAAAACACCATTAATAT
ACCAAATAATAAATTTAATGGTCGAATTATTAAAGACGGTTA
Found at i:310322 original size:12 final size:12
Alignment explanation
Indices: 310303--310361 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
310293 GCTTAAACAC
310303 ACCATTCAGCAA
1 ACCATTCAGCAA
* *
310315 ATCATTCAGAAA
1 ACCATTCAGCAA
310327 TACCATTCAGCAA
1 -ACCATTCAGCAA
*
310340 ACCATTCAACAA
1 ACCATTCAGCAA
310352 ACCATTCAGC
1 ACCATTCAGC
310362 CTCTCAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
12 30 0.75
13 10 0.25
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.20
Consensus pattern (12 bp):
ACCATTCAGCAA
Found at i:310337 original size:25 final size:24
Alignment explanation
Indices: 310298--310361 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
310288 AATGTGCTTA
* *
310298 AACACACCATTCAGCAAATCATTC
1 AACAAACCATTCAGCAAACCATTC
310322 AGA-AATACCATTCAGCAAACCATTC
1 A-ACAA-ACCATTCAGCAAACCATTC
310347 AACAAACCATTCAGC
1 AACAAACCATTCAGC
310362 CTCTCAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 13 0.37
25 22 0.63
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (24 bp):
AACAAACCATTCAGCAAACCATTC
Found at i:310449 original size:80 final size:80
Alignment explanation
Indices: 310332--310583 Score: 276
Period size: 80 Copynumber: 3.2 Consensus size: 80
310322 AGAAATACCA
* * ** * * * * *
310332 TTCAGCAAACCATTCAACAAACCATTCAGCCTCTCAATATTATACAAAACTATTCAGCAAAACAA
1 TTCAGCAAACCATTCAGCATATGATTAAGCCCCTCAATATCATACAATACCATTCAGCAAAACAA
*
310397 TATTAGATAACAAAG
66 TATTAGATAACAAGG
* * * *
310412 TTTAGCAAACCATTCAGCATATGATTTAGCCCCTCAATATCATACAATACCACTC-GACAATACA
1 TTCAGCAAACCATTCAGCATATGATTAAGCCCCTCAATATCATACAATACCATTCAG-CAAAACA
* *
310476 ATATCAAATAACAAGG
65 ATATTAGATAACAAGG
* * *
310492 TTCAGCAAACCATTCAGCATATGATTCAAG-ACTTCAATATCATACAATACCATTCAGTAAAA-A
1 TTCAGCAAACCATTCAGCATATGATT-AAGCCCCTCAATATCATACAATACCATTCAGCAAAACA
* *
310555 AAATTAGACAACAAGG
65 ATATTAGATAACAAGG
310571 TTCAGCAAACCAT
1 TTCAGCAAACCAT
310584 AATATTTACG
Statistics
Matches: 143, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
79 27 0.19
80 113 0.79
81 3 0.02
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.24
Consensus pattern (80 bp):
TTCAGCAAACCATTCAGCATATGATTAAGCCCCTCAATATCATACAATACCATTCAGCAAAACAA
TATTAGATAACAAGG
Found at i:320606 original size:133 final size:133
Alignment explanation
Indices: 320236--320608 Score: 401
Period size: 133 Copynumber: 2.8 Consensus size: 133
320226 GGTATTTTTA
* * * * *
320236 TACAAATGCCATTAAAGCAATGGTGTTTTTCTCATAAAAATATCACTAAATTAACGGCGTCTTAA
1 TACAAATGCCACTAAAGCAATGATGTTTTTCTCATAAAAAT-TCACTAAATTAGCGGCATCTCAA
* * * * * ** *
320301 AAATACAAATGTCACTAATATAGACGTATTTTCAGATATAAATACCTCCAAAGTAAGGGTATTTT
65 AGATACAAATGTCACTAATATAGAGGCATTTTCAGATATAAACACCTCCAAAATAACAGCATTTT
320366 CAGT
130 CAGT
** * * * * *
320370 TACAAACACCACAAAAGCAATGACGTTTTTTTCATAAAAACTCCACTAAATTAGTGGCATCTCAA
1 TACAAATGCCACTAAAGCAATGATGTTTTTCTCATAAAAA-TTCACTAAATTAGCGGCATCTCAA
* ** * * ** * *
320435 AGA-AAAAAAATCACTAATATAGAGGCATTTTTAAATATAAACGTCTCTAAAATAACAGCGTTTT
65 AGATACAAATGTCACTAATATAGAGGCATTTTCAGATATAAACACCTCCAAAATAACAGCATTTT
320499 CAGT
130 CAGT
* *
320503 TACAAATGCCACTAAAGCAATGATATTTTTCTCATAAAAATGTCACTAATTTAGCGGCATCTCAA
1 TACAAATGCCACTAAAGCAATGATGTTTTTCTCATAAAAAT-TCACTAAATTAGCGGCATCTCAA
*
320568 AGATACAAATGTCACTAAAAT-GAAGGCA-TTTCAGATATAAA
65 AGATACAAATGTCACTAATATAG-AGGCATTTTCAGATATAAA
320609 TGCCACTAAT
Statistics
Matches: 191, Mismatches: 44, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
132 1 0.01
133 118 0.62
134 71 0.37
135 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (133 bp):
TACAAATGCCACTAAAGCAATGATGTTTTTCTCATAAAAATTCACTAAATTAGCGGCATCTCAAA
GATACAAATGTCACTAATATAGAGGCATTTTCAGATATAAACACCTCCAAAATAACAGCATTTTC
AGT
Found at i:331863 original size:56 final size:56
Alignment explanation
Indices: 331777--331882 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 56
331767 AGGAAAGGTT
331777 ATGCCTCGACTCCATTTTCCTGCTTGATGGATTGATAAGCTATATATATGAAGATA
1 ATGCCTCGACTCCATTTTCCTGCTTGATGGATTGATAAGCTATATATATGAAGATA
*
331833 ATGCCTCGACTCCATTTTCCTGTTTGATGGATTGATAAGCTATATATATG
1 ATGCCTCGACTCCATTTTCCTGCTTGATGGATTGATAAGCTATATATATG
331883 CTTAAGTTGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (56 bp):
ATGCCTCGACTCCATTTTCCTGCTTGATGGATTGATAAGCTATATATATGAAGATA
Found at i:335314 original size:15 final size:15
Alignment explanation
Indices: 335294--335323 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
335284 TGTATTTCTC
335294 TCTCCATTTCTTTTT
1 TCTCCATTTCTTTTT
335309 TCTCCATTTCTTTTT
1 TCTCCATTTCTTTTT
335324 AGTTACTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTCCATTTCTTTTT
Found at i:340894 original size:11 final size:10
Alignment explanation
Indices: 340870--340902 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
340860 AATATTTTAT
340870 TAATTAAA-A
1 TAATTAAATA
340879 TAATTAAAATA
1 TAATT-AAATA
340890 TAATTAAATA
1 TAATTAAATA
340900 TAA
1 TAA
340903 AAGCTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 11 0.50
11 6 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATTAAATA
Found at i:347317 original size:58 final size:59
Alignment explanation
Indices: 347249--347416 Score: 252
Period size: 58 Copynumber: 2.9 Consensus size: 59
347239 AACTTTTTCG
*
347249 AAAA-TTATTTTAAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA-A
1 AAAACTTATTTTCAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGA
* *
347306 AAAACTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTCTCTCAAAAATAATTTTTAGA
1 AAAACTTATTTTCAAAAAAAATTGATACTTTCAACTTTTC-CTCAAAAATATTTTTTAGA
* * *
347365 AAAACTTATTTTCAAAGAAAATTGATACTTTCAACTTTTCTTTAAAAATATT
1 AAAACTTATTTTCAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATT
347417 ATTCTTGAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
57 8 0.08
58 44 0.44
59 43 0.43
60 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (59 bp):
AAAACTTATTTTCAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGA
Found at i:347371 original size:59 final size:57
Alignment explanation
Indices: 347202--347414 Score: 243
Period size: 58 Copynumber: 3.6 Consensus size: 57
347192 TTTGTACAAT
* * * *
347202 AAAAATTGATACTTTCAACTTTTTCTTAAAAAAAAAAAACTTTTTCG-AAAA-TTATTTTAAAA
1 AAAAATTGATACTTTCAAC-TTTTC-T---CAAAAATAA-TTTTTAGAAAAACTTATTTT-CAA
*
347264 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTA-AAAAACTTATTTTCAA
1 AAAAATTGATACTTTCAACTTTT-CTCAAAAATAATTTTTAGAAAAACTTATTTTCAA
347321 GAAAAATTGATACTTTCAACTTTCTCTCAAAAATAATTTTTAGAAAAACTTATTTTCAA
1 -AAAAATTGATACTTTCAACTTT-TCTCAAAAATAATTTTTAGAAAAACTTATTTTCAA
*
347380 AGAAAATTGATACTTTCAACTTTTCTTTAAAAATA
1 A-AAAATTGATACTTTCAACTTTTC-TCAAAAATA
347415 TTATTCTTGA
Statistics
Matches: 136, Mismatches: 7, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
57 11 0.08
58 54 0.40
59 46 0.34
61 5 0.04
62 20 0.15
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCTCAAAAATAATTTTTAGAAAAACTTATTTTCAA
Found at i:347485 original size:24 final size:23
Alignment explanation
Indices: 347470--347541 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 23
347460 AAAAATATTC
*
347470 TAAAAAAATAAACAAACACATAAA
1 TAAAAAAATAAACAAA-AAATAAA
347494 TAAAAAAATAAA-AAAAACTATAAAA
1 TAAAAAAATAAACAAAAA--AT-AAA
*
347519 TAAATAAAA-ATACAAAAAA-AAA
1 TAAA-AAAATAAACAAAAAATAAA
347541 T
1 T
347542 CGAAACGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
22 5 0.12
23 3 0.07
24 15 0.37
25 9 0.22
26 9 0.22
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (23 bp):
TAAAAAAATAAACAAAAAATAAA
Found at i:347520 original size:17 final size:16
Alignment explanation
Indices: 347498--347540 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
347488 CATAAATAAA
*
347498 AAAATAAAAAAAACTAT
1 AAAATAAAAAAAA-TAC
347515 AAAATAAATAAAAATAC
1 AAAATAAA-AAAAATAC
347532 AAAA-AAAAA
1 AAAATAAAAA
347541 TCGAAACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 3 0.12
17 14 0.58
18 5 0.21
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAAATAC
Found at i:347906 original size:126 final size:126
Alignment explanation
Indices: 347678--347921 Score: 445
Period size: 126 Copynumber: 1.9 Consensus size: 126
347668 CCCCACCTCT
* *
347678 AGCAACCATTGTCCAGATACGCCCTTTTGGATTCAAAATAGTGAATTTCAGGGATGCATTCGTCT
1 AGCAACCATTGTCCAGATACGCCCTTTTGGATTCAAAACAGTGAATTTCAGGGATGCACTCGTCT
*
347743 TTTCATCCAATGAATGAATGAAGCTTTTTGTTGGGCTCAAGGCTCTTCCAAAAGGCAGAGG
66 TTTCATCCAATGAATGAATGAAGCTTTTTGTTAGGCTCAAGGCTCTTCCAAAAGGCAGAGG
347804 AGCAACCATTGTCCAGATACGCCCTTTTGGATTCAAAACAGTGAATTTCAGGGATGCACTCGT-T
1 AGCAACCATTGTCCAGATACGCCCTTTTGGATTCAAAACAGTGAATTTCAGGGATGCACTCGTCT
347868 TTCTCATCCAATGAATGAATGAAGCTTTTTGTTAGGCTCAAGGCTCTTCCAAAA
66 TT-TCATCCAATGAATGAATGAAGCTTTTTGTTAGGCTCAAGGCTCTTCCAAAA
347922 AGTAGAGAAA
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
125 3 0.03
126 111 0.97
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (126 bp):
AGCAACCATTGTCCAGATACGCCCTTTTGGATTCAAAACAGTGAATTTCAGGGATGCACTCGTCT
TTTCATCCAATGAATGAATGAAGCTTTTTGTTAGGCTCAAGGCTCTTCCAAAAGGCAGAGG
Found at i:349491 original size:27 final size:28
Alignment explanation
Indices: 349442--349507 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
349432 GATAATGAAG
* *
349442 AAAAAAAAATTAAACAATAGATAGATCAT
1 AAAAAAAAAATAAACAATAGATAAAT-AT
349471 AAAAAAAAAATAAA-AAT-GATAAATAT
1 AAAAAAAAAATAAACAATAGATAAATAT
349497 AAAAATAAAAA
1 AAAAA-AAAAA
349508 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 11 0.32
28 3 0.09
29 13 0.38
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (28 bp):
AAAAAAAAAATAAACAATAGATAAATAT
Found at i:349519 original size:21 final size:23
Alignment explanation
Indices: 349472--349531 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 23
349462 ATAGATCATA
* *
349472 AAAAAAAAATAAAAATGATAAATAT
1 AAAAATAAAT-AAAAT-TTAAATAT
349497 AAAAATAAA-AAAATTTAAA-AT
1 AAAAATAAATAAAATTTAAATAT
349518 AAAAATAAATAAAA
1 AAAAATAAATAAAA
349532 ATCCTTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 11 0.34
22 8 0.25
23 5 0.16
25 8 0.25
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAATAAATAAAATTTAAATAT
Found at i:349530 original size:15 final size:14
Alignment explanation
Indices: 349474--349533 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 14
349464 AGATCATAAA
349474 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
* *
349488 GATAAATATAAAAAT
1 -AAAAAAATAAAAAT
*
349503 AAAAAAATTTAAAAT
1 AAAAAAA-TAAAAAT
349518 AAAAATAAATAAAAAT
1 -AAAA-AAATAAAAAT
349534 CCTTACCATC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
14 5 0.14
15 18 0.50
16 10 0.28
17 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:350391 original size:2 final size:2
Alignment explanation
Indices: 350384--350414 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
350374 TTAAAGTAAC
350384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
350415 CACATCGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:351343 original size:21 final size:21
Alignment explanation
Indices: 351303--351343 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
351293 TATTAACTGA
*
351303 AAAAAAACCCATATAAAAAGC
1 AAAAAAACCCACATAAAAAGC
* *
351324 AAAAAAATCCACATAGAAAG
1 AAAAAAACCCACATAAAAAG
351344 GCCAAAGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.17, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAAAACCCACATAAAAAGC
Found at i:352770 original size:2 final size:2
Alignment explanation
Indices: 352763--352803 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
352753 GATCATTTCT
352763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
352804 TAAAAGAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:364685 original size:2 final size:2
Alignment explanation
Indices: 364678--364711 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
364668 CAACAATTTG
* *
364678 AT AT AT AT AT AT AT AG AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
364712 GCACTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:365222 original size:2 final size:2
Alignment explanation
Indices: 365210--365243 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
365200 TCTCTTTAGG
* *
365210 CT CT TT CT CT CT CT GT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
365244 TCTAGGGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:365617 original size:2 final size:2
Alignment explanation
Indices: 365610--365643 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
365600 CATGAAGCCT
365610 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
365644 CCTGATGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:366113 original size:2 final size:2
Alignment explanation
Indices: 366094--366134 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
366084 AACTACATAC
* *
366094 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
366135 GTTCTGGTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:368649 original size:2 final size:2
Alignment explanation
Indices: 368633--368668 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
368623 CGTGTGTGTG
* *
368633 TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
368669 CACGATCTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:393542 original size:12 final size:11
Alignment explanation
Indices: 393525--393561 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
393515 GATAGGCACA
393525 TTTTTCTTTTT
1 TTTTTCTTTTT
393536 CTTTTTCTTTTT
1 -TTTTTCTTTTT
393548 TTTTT-TTTTT
1 TTTTTCTTTTT
393558 TTTT
1 TTTT
393562 GCCACTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:398218 original size:69 final size:69
Alignment explanation
Indices: 398113--398250 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
398103 AAATACTTAG
* *
398113 TGTTAATAAACAACTCCTAAAAACAACAAAACATCTCACAAATGTAATATATTTATGGAAAATCT
1 TGTTAATAAACAACTCCTAAAAACAACAAAAAATCTCACAAATGTAATATATCTATGGAAAATCT
398178 GAAA
66 GAAA
* * *
398182 TGTTAATAGACAACTCCTAAAAACAACAAAAAATCTCACAAATGTAATATATCTGTGGAACATCT
1 TGTTAATAAACAACTCCTAAAAACAACAAAAAATCTCACAAATGTAATATATCTATGGAAAATCT
398247 GAAA
66 GAAA
398251 ACCATGTGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (69 bp):
TGTTAATAAACAACTCCTAAAAACAACAAAAAATCTCACAAATGTAATATATCTATGGAAAATCT
GAAA
Found at i:399759 original size:2 final size:2
Alignment explanation
Indices: 399752--399789 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
399742 CACGTAACAG
399752 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
399790 GCAGATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:400932 original size:35 final size:35
Alignment explanation
Indices: 400893--400961 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
400883 CAACCGAACA
*
400893 TGGCGTTGGCACTGATTATTTTAGCTTGTCATTGT
1 TGGCGTTGGCACTGATTATTTTAGCTTATCATTGT
400928 TGGCGTTGGCACTGATTATTTTAGCTTATCATTG
1 TGGCGTTGGCACTGATTATTTTAGCTTATCATTG
400962 GTGGGATCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (35 bp):
TGGCGTTGGCACTGATTATTTTAGCTTATCATTGT
Found at i:408869 original size:20 final size:20
Alignment explanation
Indices: 408844--408894 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
408834 TTCGAAATTA
*
408844 ATAAAATATTTTTTTAAAAT
1 ATAAAATATTGTTTTAAAAT
408864 ATAAAATGATATGTTTTAAAAT
1 ATAAAAT-AT-TGTTTTAAAAT
*
408886 -TTAAATATT
1 ATAAAATATT
408895 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 7 0.26
22 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
ATAAAATATTGTTTTAAAAT
Found at i:410254 original size:23 final size:23
Alignment explanation
Indices: 410212--410255 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
410202 ACTACTTTAT
* *
410212 TAATAATATTATTAAAAAAATAA
1 TAATAATAATAATAAAAAAATAA
*
410235 TAATAATAATAATAACAAAAT
1 TAATAATAATAATAAAAAAAT
410256 GTAGATGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAATAATAATAAAAAAATAA
Found at i:410395 original size:2 final size:2
Alignment explanation
Indices: 410388--410414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
410378 AGGTTGCTGT
410388 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
410415 CGTCCAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:412551 original size:2 final size:2
Alignment explanation
Indices: 412544--412575 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
412534 ATTGTAAGGC
412544 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
412576 AACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:414692 original size:2 final size:2
Alignment explanation
Indices: 414681--414717 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
414671 GCTGCTGCTG
414681 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
414718 AAATGTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:416815 original size:2 final size:2
Alignment explanation
Indices: 416768--416801 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
416758 TTTTGGGTTC
*
416768 AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
416802 GCAGGGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:417674 original size:2 final size:2
Alignment explanation
Indices: 417635--417665 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
417625 AGTCTATTGG
417635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
417666 CACATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:421172 original size:3 final size:3
Alignment explanation
Indices: 421164--421199 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
421154 TTTCTCAAGG
421164 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
421200 GAGAATGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:422150 original size:19 final size:20
Alignment explanation
Indices: 422126--422170 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
422116 TTTTTTATAA
*
422126 TTTTTTTAAAG-TCATCTCT
1 TTTTTTTAAAGTTCATATCT
* *
422145 TTTTTTTTAAGTTCATATGT
1 TTTTTTTAAAGTTCATATCT
422165 TTTTTT
1 TTTTTT
422171 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTTTTAAAGTTCATATCT
Found at i:422643 original size:20 final size:20
Alignment explanation
Indices: 422614--422692 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 20
422604 ATAGATCTCA
*
422614 TTTTTTTTTCTTTAAAAAAC
1 TTTTTCTTTCTTTAAAAAAC
* **
422634 TTTTTCTTTCCTCTGTAAATATT
1 TTTTTCTTT-CT-T-TAAAAAAC
422657 TATTTTCTTTTTCTTTAAAAAAC
1 T-TTTTC--TTTCTTTAAAAAAC
422680 TTTCTT-TTTCTTT
1 TTT-TTCTTTCTTT
422693 CCTCTAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
20 15 0.33
21 2 0.04
22 3 0.07
23 14 0.31
24 6 0.13
25 2 0.04
26 3 0.07
ACGTcount: A:0.22, C:0.14, G:0.01, T:0.63
Consensus pattern (20 bp):
TTTTTCTTTCTTTAAAAAAC
Found at i:422662 original size:25 final size:24
Alignment explanation
Indices: 422634--422707 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
422624 TTTAAAAAAC
422634 TTTTTCTTTCCTCTGTAAATATTTA
1 TTTTTCTTTCCTCT-TAAATATTTA
* * *
422659 -TTTTCTTT-TTCTTTAAAAAACTTTC
1 TTTTTCTTTCCTC-TT-AAATA-TTTA
422684 TTTTTCTTTCCTC-TAAATATTTA
1 TTTTTCTTTCCTCTTAAATATTTA
422707 T
1 T
422708 CCAAATACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
23 7 0.18
24 17 0.45
25 4 0.11
26 8 0.21
27 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.01, T:0.61
Consensus pattern (24 bp):
TTTTTCTTTCCTCTTAAATATTTA
Found at i:422674 original size:46 final size:44
Alignment explanation
Indices: 422613--422707 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 44
422603 TATAGATCTC
422613 ATTTTTTTTTCTTTAAAAAA-CTTTTTCTTTCCTCTGTAAATATTT
1 ATTTTTTTTTCTTTAAAAAATCTTTTTCTTTCCTC--TAAATATTT
422658 ATTTTCTTTTTCTTTAAAAAACTTTCTTTTTCTTTCCTCTAAATATTT
1 ATTTT-TTTTTCTTTAAAAAA---TCTTTTTCTTTCCTCTAAATATTT
422706 AT
1 AT
422708 CCAAATACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
45 5 0.11
46 15 0.33
48 11 0.24
50 14 0.31
ACGTcount: A:0.24, C:0.15, G:0.01, T:0.60
Consensus pattern (44 bp):
ATTTTTTTTTCTTTAAAAAATCTTTTTCTTTCCTCTAAATATTT
Found at i:426806 original size:2 final size:2
Alignment explanation
Indices: 426799--426845 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
426789 TTAAAGGAAT
426799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
426841 AG AG A
1 AG AG A
426846 CAGGTTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:431090 original size:13 final size:13
Alignment explanation
Indices: 431060--431110 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
431050 GGTTTTATTA
*
431060 AATTTTGATATAT
1 AATTTTGATAAAT
431073 AATTTTAGATAAAT
1 AATTTT-GATAAAT
* *
431087 ATTTTTAATAAA-
1 AATTTTGATAAAT
*
431099 AATATTGATAAA
1 AATTTTGATAAA
431111 ATTTTTATCG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 9 0.29
13 11 0.35
14 11 0.35
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
AATTTTGATAAAT
Found at i:431218 original size:11 final size:11
Alignment explanation
Indices: 431202--431260 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
431192 TATAAATTAA
431202 AAAATTTTATT
1 AAAATTTTATT
431213 AAAATTTTTATT
1 AAAA-TTTTATT
431225 AAATTATTTT-TT
1 AAA--ATTTTATT
431237 -AAATTTTA-T
1 AAAATTTTATT
431246 -AAATTTTACTT
1 AAAATTTTA-TT
431257 AAAA
1 AAAA
431261 AATTTCATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
9 14 0.34
11 7 0.17
12 15 0.37
13 4 0.10
14 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
AAAATTTTATT
Found at i:441874 original size:22 final size:21
Alignment explanation
Indices: 441849--441916 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
441839 AATTTTTTTT
441849 ATTTTAATATATTTAATATCAA
1 ATTTTAATAT-TTTAATATCAA
* *
441871 ATTTTAA-ATTTTATTAAATTAA
1 ATTTTAATATTTTA--ATATCAA
*
441893 AGTTTAATAATTTTTAATATCAA
1 ATTTTAAT-A-TTTTAATATCAA
441916 A
1 A
441917 AAATAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.11
21 2 0.06
22 18 0.50
23 6 0.17
24 1 0.03
25 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (21 bp):
ATTTTAATATTTTAATATCAA
Found at i:444920 original size:2 final size:2
Alignment explanation
Indices: 444913--444937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
444903 GGATTATAAT
444913 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
444938 GTGTCACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:447208 original size:14 final size:14
Alignment explanation
Indices: 447189--447215 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
447179 TTCAGTTAAT
447189 TTTTTGAAAAATAA
1 TTTTTGAAAAATAA
447203 TTTTTGAAAAATA
1 TTTTTGAAAAATA
447216 TATATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTTTGAAAAATAA
Found at i:447456 original size:15 final size:15
Alignment explanation
Indices: 447430--447661 Score: 67
Period size: 15 Copynumber: 14.9 Consensus size: 15
447420 TATTAATAAA
447430 TAAATAATATTATAT
1 TAAATAATATTATAT
447445 TACAAT-ATATTA-A-
1 TA-AATAATATTATAT
447458 TAAATAATATTATAT
1 TAAATAATATTATAT
*
447473 GAATAAATAATA-GACTAT
1 ---TAAATAATATTA-TAT
* *
447491 TAATATTATACT-TA-
1 TAA-ATAATATTATAT
447505 TAAATAATATATTATAT
1 TAAAT-A-ATATTATAT
* *
447522 ATTAATAAATATGAT-T
1 -TAAAT-AATATTATAT
* *
447538 ATAAATAA-ATAAATAC
1 -TAAATAATAT-TATAT
447554 T-AAT-ATATTATAT
1 TAAATAATATTATAT
447567 TAATAAGTAATATTATATT
1 T-A-AA-TAATATTATA-T
* *
447586 AATAAATAATATAATAA
1 --TAAATAATATTATAT
*
447603 TAAATATTATTA-ATT
1 TAAATAATATTATA-T
* *
447618 TAATTAATA-AATAT
1 TAAATAATATTATAT
*
447632 TATAATAATA-TATGAA
1 TA-AATAATATTAT-AT
447648 TAAATAATATTATA
1 TAAATAATATTATA
447662 ATATATTATT
Statistics
Matches: 163, Mismatches: 23, Indels: 62
0.66 0.09 0.25
Matches are distributed among these distances:
12 3 0.02
13 15 0.09
14 17 0.10
15 56 0.34
16 24 0.15
17 8 0.05
18 35 0.21
19 3 0.02
20 1 0.01
21 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
TAAATAATATTATAT
Found at i:447477 original size:18 final size:18
Alignment explanation
Indices: 447408--447683 Score: 128
Period size: 18 Copynumber: 15.6 Consensus size: 18
447398 AATTTTACTT
447408 ATAAAT-ATATTATATTA
1 ATAAATAATATTATATTA
*
447425 ATAAATAA-ATAATATT-
1 ATAAATAATATTATATTA
*
447441 AT-ATTACA-A-TATATTA
1 ATAAATA-ATATTATATTA
*
447457 ATAAATAATATTATATGA
1 ATAAATAATATTATATTA
*
447475 ATAAATAATA-GACTATTA
1 ATAAATAATATTA-TATTA
*
447493 AT--ATTATACTTATA--A
1 ATAAATAATA-TTATATTA
*
447508 ATAATATATTA-TATATTA
1 ATAA-ATAATATTATATTA
*
447526 ATAAAT-ATGATTATAAATAA
1 ATAAATAAT-ATTAT--ATTA
447546 ATAAATACTAATATATTATATTA
1 AT-AA-A-T-A-ATATTATATTA
*
447569 ATAAGTAATATTATATTA
1 ATAAATAATATTATATTA
447587 ATAAATAATA-TA-A-TA
1 ATAAATAATATTATATTA
*
447602 ATAAATATTATTA-ATTTA
1 ATAAATAATATTATA-TTA
* *
447620 ATTAATAAATATTATAATA
1 ATAAAT-AATATTATATTA
*
447639 ATATATGAATA--A-A-TA
1 ATAAAT-AATATTATATTA
*
447654 ATATTATAATA-TATTATTA
1 ATA-AATAATATTA-TATTA
447673 ATAAATAATAT
1 ATAAATAATAT
447684 AAAGAATAAT
Statistics
Matches: 200, Mismatches: 24, Indels: 68
0.68 0.08 0.23
Matches are distributed among these distances:
15 31 0.16
16 26 0.13
17 26 0.13
18 70 0.35
19 22 0.11
20 7 0.04
21 2 0.01
22 3 0.01
23 6 0.03
25 5 0.03
26 2 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:447518 original size:20 final size:19
Alignment explanation
Indices: 447493--447598 Score: 81
Period size: 20 Copynumber: 5.2 Consensus size: 19
447483 TAGACTATTA
447493 ATATTATACTTATAAATAAT
1 ATATTATA-TTATAAATAAT
*
447513 ATATTATA-TATTAATAAAT
1 ATATTATATTATAAAT-AAT
*
447532 ATGATTATA-AATAAATAAAT
1 AT-ATTATATTATAAAT-AAT
*
447552 ACTAATATATTATATTAATAAGT
1 A-TATTATATTATA--AATAA-T
447575 AATATTATATTAATAAATAAT
1 -ATATTATATT-ATAAATAAT
447596 ATA
1 ATA
447599 ATAATAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
18 6 0.08
19 5 0.07
20 32 0.45
21 5 0.07
22 7 0.10
23 12 0.17
24 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATTATATTATAAATAAT
Found at i:447562 original size:45 final size:45
Alignment explanation
Indices: 447507--447686 Score: 154
Period size: 49 Copynumber: 3.8 Consensus size: 45
447497 TATACTTATA
447507 AATAATATATTATA-TATTAATAAATATGATTATAAATAAATAAAT
1 AATAATATATTATATTATTAATAAATAT-ATTATAAATAAATAAAT
* *
447552 ACTAATATATTATATTAATAAGTAATATTATATTAATAAAT-AATATAAT
1 AATAATATATTATATTATTAA-TAA-A-TATATT-ATAAATAAATA-AAT
*
447601 AATAA-ATATTATTAATTTAATTAATAAATATTATAATAATATATGAATAAAT
1 AATAATATATTA-T-A-TT-ATTAATAAATA-TATTATAA-ATA--AATAAAT
* *
447653 AATATTATAATATATTATTAATAAATA-A-TATAAA
1 AATAATATATTATATTATTAATAAATATATTATAAA
447687 GAATAATAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
45 14 0.13
46 9 0.08
47 4 0.04
48 14 0.13
49 34 0.31
50 9 0.08
51 6 0.05
52 12 0.11
53 9 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (45 bp):
AATAATATATTATATTATTAATAAATATATTATAAATAAATAAAT
Found at i:447588 original size:61 final size:67
Alignment explanation
Indices: 447449--447593 Score: 171
Period size: 69 Copynumber: 2.2 Consensus size: 67
447439 TTATATTACA
*
447449 ATATATTAATAAATAATATTATATGAATAAATAATAGACTATTAATATTATACTTATAAATAATA
1 ATATATTAATAAAT-ATATTATA-GAATAAATAATAGACTAATAATATTATACTTATAAATAATA
447514 TATT
64 TATT
* *
447518 ATATATTAATAAATATGATTATA-AATAAATAA-ATACTAAT-ATATTATA-TTAATAAGT-A-A
1 ATATATTAATAAATAT-ATTATAGAATAAATAATAGACTAATAATATTATACTT-ATAAATAATA
447577 TA-T
64 TATT
447580 -TATATTAATAAATA
1 ATATATTAATAAATA
447594 ATATAATAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
61 14 0.20
62 1 0.01
63 3 0.04
64 3 0.04
65 13 0.18
66 6 0.08
67 9 0.13
68 2 0.03
69 20 0.28
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (67 bp):
ATATATTAATAAATATATTATAGAATAAATAATAGACTAATAATATTATACTTATAAATAATATA
TT
Found at i:447603 original size:26 final size:28
Alignment explanation
Indices: 447569--447685 Score: 100
Period size: 26 Copynumber: 4.1 Consensus size: 28
447559 TATTATATTA
447569 ATAAGTAAT-ATTA-TATTAATAAATAAT
1 ATAA-TAATAATTATTATTAATAAATAAT
* *
447596 ATAATAATAAATATTATTAATTTAATTAAT
1 ATAATAATAATTATTATTAA--TAAATAAT
* *
447626 A-AATATTATAATAATATATGAATAAATAAT
1 ATAATA--ATAATTAT-TATTAATAAATAAT
*
447656 ATTATAAT-A-TATTATTAATAAATAAT
1 ATAATAATAATTATTATTAATAAATAAT
447682 ATAA
1 ATAA
447686 AGAATAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
26 20 0.28
27 9 0.12
28 7 0.10
29 6 0.08
30 16 0.22
31 9 0.12
32 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
ATAATAATAATTATTATTAATAAATAAT
Found at i:447628 original size:22 final size:21
Alignment explanation
Indices: 447592--447659 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
447582 TATTAATAAA
447592 TAATATAATAATAAATATTAT
1 TAATATAATAATAAATATTAT
*
447613 TAATTTAATTAATAAATATTA-
1 TAATATAA-TAATAAATATTAT
*
447634 TAATAATATATGAATAAATAATAT
1 TAAT-ATA-AT-AATAAATATTAT
447658 TA
1 TA
447660 TAATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 11 0.28
22 15 0.38
23 11 0.28
24 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (21 bp):
TAATATAATAATAAATATTAT
Found at i:447812 original size:26 final size:26
Alignment explanation
Indices: 447779--447844 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
447769 TTTGAATATT
*
447779 AATA-ATTTTAATAATAAATTATTTC
1 AATATATTTTAATAATAAATAATTTC
* *
447804 AATATATTTTAATATTAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
447830 AA-ATATTTTAATAAT
1 AATATATTTTAATAAT
447845 TACATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:447830 original size:16 final size:18
Alignment explanation
Indices: 447804--447836 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
447794 AAATTATTTC
447804 AATATATTTT-AATATTA
1 AATATATTTTAAATATTA
447821 AATA-ATTTTAAATATT
1 AATATATTTTAAATATT
447837 TTAATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATATTTTAAATATTA
Found at i:447981 original size:14 final size:14
Alignment explanation
Indices: 447962--447995 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
447952 AAAATATAAA
447962 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
447976 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
*
447990 CATTTT
1 TATTTT
447996 CTATAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:463372 original size:12 final size:12
Alignment explanation
Indices: 463355--463382 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
463345 TCCCTTTCTC
463355 TTTTATTTTAAT
1 TTTTATTTTAAT
463367 TTTTATTTTAAT
1 TTTTATTTTAAT
463379 TTTT
1 TTTT
463383 TCTCTTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:464284 original size:18 final size:18
Alignment explanation
Indices: 464257--464298 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
464247 TGAGTTTGAT
* *
464257 CCTGAACCTCAGGCTGAG
1 CCTGAACCTCAGCCTGAA
*
464275 CCTGAGCCTCAGCCTGAA
1 CCTGAACCTCAGCCTGAA
464293 CCTGAA
1 CCTGAA
464299 GCTGGAATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (18 bp):
CCTGAACCTCAGCCTGAA
Found at i:467146 original size:84 final size:84
Alignment explanation
Indices: 467020--467189 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
467010 AAGAAAATTA
* ** *
467020 CTATGAATAGCACCTTAGGGCAATTGTTAGCAGAATTTATCTATAAAACAGATATAAGTCGTTTC
1 CTATGAATAGCACCTTAGGGCAATTGTTAGCAAAATCCATCTATAAAACAGATATAAATCGTTTC
**
467085 ATTATAGTTGTAAATTATT
66 ATTATAGTCCTAAATTATT
* *
467104 CTATGAATAGCACCTTAGGGCAATTTTTAGCAAAATCCATCTATAAAACAGATATAAATTGTTTC
1 CTATGAATAGCACCTTAGGGCAATTGTTAGCAAAATCCATCTATAAAACAGATATAAATCGTTTC
467169 ATTATAGTCCTAAATTATT
66 ATTATAGTCCTAAATTATT
467188 CT
1 CT
467190 GATTAGTGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (84 bp):
CTATGAATAGCACCTTAGGGCAATTGTTAGCAAAATCCATCTATAAAACAGATATAAATCGTTTC
ATTATAGTCCTAAATTATT
Found at i:475593 original size:5 final size:5
Alignment explanation
Indices: 475583--475608 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
475573 TTTGAAACGC
475583 TCTCA TCTCA TCTCA TCTCA TCTCA T
1 TCTCA TCTCA TCTCA TCTCA TCTCA T
475609 TTACTGATTA
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:0.38, G:0.00, T:0.42
Consensus pattern (5 bp):
TCTCA
Found at i:476500 original size:21 final size:21
Alignment explanation
Indices: 476475--476563 Score: 56
Period size: 22 Copynumber: 4.0 Consensus size: 21
476465 ATTTAAAATT
476475 ATTTATAAAAATATTTTTTAA
1 ATTTATAAAAATATTTTTTAA
* *
476496 ATTTATTAAATTATTTAAAATTTAA
1 ATTTATAAAAATATTT----TTTAA
*
476521 ATTTAATAAAAA-ATTAATTTAA
1 ATTT-ATAAAAATATT-TTTTAA
*
476543 ATTT-TAATGAAATTTTTTTTA
1 ATTTATAA--AAATATTTTTTA
476564 TTCTGTACAT
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
20 3 0.06
21 14 0.27
22 16 0.31
23 2 0.04
25 12 0.23
26 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTTATAAAAATATTTTTTAA
Found at i:477664 original size:25 final size:25
Alignment explanation
Indices: 477636--477700 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 25
477626 ATTATATTTA
477636 TATAATCAATTAAATAATAAATTA-T
1 TATAATCAATTAAATAAT-AATTATT
*
477661 TAT-ATCATATTCAAATTATAATTATT
1 TATAATCA-ATT-AAATAATAATTATT
477687 TAATAATCAATTAA
1 T-ATAATCAATTAA
477701 TAAACTAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 4 0.12
25 11 0.32
26 10 0.29
27 5 0.15
28 4 0.12
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
TATAATCAATTAAATAATAATTATT
Found at i:477696 original size:22 final size:22
Alignment explanation
Indices: 477625--477696 Score: 54
Period size: 25 Copynumber: 3.0 Consensus size: 22
477615 AATTATTAAT
* * *
477625 AATTATATTTATATAATCAATTA
1 AATTATAATTATTTAAT-AATCA
* *
477648 AATAATAAATTATTATATCATATTCA
1 AATTAT-AATTATT-TA--ATAATCA
477674 AATTATAATTATTTAATAATCA
1 AATTATAATTATTTAATAATCA
477696 A
1 A
477697 TTAATAAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 7 0.18
23 5 0.13
24 7 0.18
25 9 0.24
26 8 0.21
27 2 0.05
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTATAATTATTTAATAATCA
Found at i:492636 original size:2 final size:2
Alignment explanation
Indices: 492629--492663 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
492619 CTGTCTGGCG
492629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492664 GATTTTGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:493988 original size:16 final size:17
Alignment explanation
Indices: 493967--494006 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
493957 AATCTGCCTC
* *
493967 TAAATATGTATAAAA-A
1 TAAATATATAAAAAATA
493983 TAAATATATAAAAAATA
1 TAAATATATAAAAAATA
494000 TAAATAT
1 TAAATAT
494007 TTTAGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAATATATAAAAAATA
Found at i:500166 original size:2 final size:2
Alignment explanation
Indices: 500159--500193 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
500149 AATTTAACAT
500159 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
500194 GAGATAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:501056 original size:13 final size:13
Alignment explanation
Indices: 501038--501063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501028 ATAGGAGAAT
501038 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
501051 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
501064 GAAGGAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:507236 original size:22 final size:22
Alignment explanation
Indices: 507210--507253 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
507200 TGTATATTTA
*
507210 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
507232 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
507254 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:517169 original size:20 final size:19
Alignment explanation
Indices: 517135--517178 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
517125 ATTTTTATTT
*
517135 TATAAAAATTTTAAAAATA
1 TATAAAAATTATAAAAATA
*
517154 TATAAAAATTAATAAATATA
1 TATAAAAATT-ATAAAAATA
517174 TATAA
1 TATAA
517179 TTCTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATAAAAATTATAAAAATA
Found at i:517170 original size:18 final size:18
Alignment explanation
Indices: 517135--517175 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
517125 ATTTTTATTT
517135 TATAAAAATTTTAAAAATA
1 TATAAAAA-TTTAAAAATA
517154 TATAAAAA-TTAATAAATA
1 TATAAAAATTTAA-AAATA
517172 TATA
1 TATA
517176 TAATTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TATAAAAATTTAAAAATA
Found at i:518152 original size:22 final size:20
Alignment explanation
Indices: 518114--518153 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
518104 TTAAATTTAA
*
518114 TATAAAAATTAATAATATGT
1 TATAAAAATTAAAAATATGT
518134 TATAAAATTATTAAAAATAT
1 TATAAAA--ATTAAAAATAT
518154 TATTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TATAAAAATTAAAAATATGT
Found at i:520220 original size:19 final size:19
Alignment explanation
Indices: 520181--520222 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
520171 GAGTAATATT
*
520181 TTAAATATTTAATCATAAA
1 TTAAATATTTAATAATAAA
520200 TTAAATATTTAACTAAT-AA
1 TTAAATATTTAA-TAATAAA
520219 TTAA
1 TTAA
520223 TTTAACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATATTTAATAATAAA
Found at i:525210 original size:24 final size:26
Alignment explanation
Indices: 525183--525251 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 26
525173 TATATAAAAA
525183 TTATTTTTA-ATTAAT-TATTTAATT
1 TTATTTTTATATTAATATATTTAATT
*
525207 TTATATTTATATATTTAAATATGTTTAATT
1 TTAT-TTT-TATA-TT-AATATATTTAATT
*
525237 TTATATTTATATTAA
1 TTATTTTTATATTAA
525252 AAAATAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
24 4 0.11
25 3 0.08
26 4 0.11
27 3 0.08
28 6 0.16
29 5 0.14
30 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (26 bp):
TTATTTTTATATTAATATATTTAATT
Found at i:531718 original size:2 final size:2
Alignment explanation
Indices: 531705--531737 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
531695 ACTGGTGGTG
*
531705 GT GT GC GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
531738 AGAGAGAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.52, T:0.45
Consensus pattern (2 bp):
GT
Found at i:531742 original size:2 final size:2
Alignment explanation
Indices: 531737--531767 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
531727 GTGTGTGTGT
531737 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
531768 GGGACAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:542703 original size:18 final size:18
Alignment explanation
Indices: 542680--542715 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
542670 AAACATATAA
542680 CATTCAAAATATTGGGAG
1 CATTCAAAATATTGGGAG
542698 CATTCAAAATATTGGGAG
1 CATTCAAAATATTGGGAG
542716 AGAATGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
CATTCAAAATATTGGGAG
Found at i:547185 original size:2 final size:2
Alignment explanation
Indices: 547178--547207 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
547168 AACAAAACAA
547178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547208 TGCTTCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:551973 original size:15 final size:16
Alignment explanation
Indices: 551953--551991 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
551943 ATAATTAATA
551953 TTTATTTAAATTA-TT
1 TTTATTTAAATTAGTT
*
551968 TTTATTTTAATTAGTT
1 TTTATTTAAATTAGTT
551984 TTTATTTA
1 TTTATTTA
551992 TTTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATTTAAATTAGTT
Found at i:552818 original size:18 final size:18
Alignment explanation
Indices: 552791--552825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
552781 ATTAAAGAAT
*
552791 ATATATTAAAAAATTTAC
1 ATATAATAAAAAATTTAC
*
552809 ATATAATAAAAATTTTA
1 ATATAATAAAAAATTTA
552826 AATTATTTAA
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:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATAAAAAATTTAC
Found at i:552856 original size:19 final size:18
Alignment explanation
Indices: 552812--552872 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
552802 AATTTACATA
*
552812 TAATAAAAATTT-TAAAT
1 TAATAAATATTTATAAAT
* *
552829 TATTTAATATTTATACAAT
1 TAATAAATATTTATA-AAT
* *
552848 TAATAAATAATTATAGAT
1 TAATAAATATTTATAAAT
552866 T-ATAAAT
1 TAATAAAT
552873 TATAAATTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 15 0.43
18 5 0.14
19 15 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATAAATATTTATAAAT
Found at i:553530 original size:24 final size:24
Alignment explanation
Indices: 553495--553551 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
553485 GCTGTGTTAT
553495 TTTTATTTAATATTTATA-TAAAA
1 TTTTATTTAATATTTATATTAAAA
*
553518 TTTTCTTTAAATATTTATATTAAAA
1 TTTTATTT-AATATTTATATTAAAA
553543 -TTTATTTAA
1 TTTTATTTAA
553552 GTATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.30
24 16 0.53
25 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATTTAATATTTATATTAAAA
Found at i:553540 original size:13 final size:13
Alignment explanation
Indices: 553492--553551 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
553482 AATGCTGTGT
* *
553492 TATTTTTATTTAA
1 TATTTATATTAAA
*
553505 TATTTATATAAAA
1 TATTTATATTAAA
*
553518 T-TTTCT-TTAAA
1 TATTTATATTAAA
553529 TATTTATATTAAA
1 TATTTATATTAAA
553542 -ATTTAT-TTAA
1 TATTTATATTAA
553552 GTATAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.23
12 14 0.36
13 16 0.41
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTTATATTAAA
Found at i:553634 original size:29 final size:28
Alignment explanation
Indices: 553536--553647 Score: 95
Period size: 30 Copynumber: 3.9 Consensus size: 28
553526 AAATATTTAT
*
553536 ATTAAAATTTATTTAAGTATAAATTACAA
1 ATTAAAATTTATTTAAATATAAATTA-AA
** *
553565 ATTAAAGATTTATTTGGATATGAATTAAAA
1 ATTAAA-ATTTATTTAAATATAAATT-AAA
553595 ATTAAAAATTTATTTAAATAT-AA-TAAA
1 ATT-AAAATTTATTTAAATATAAATTAAA
*
553622 AGTATAAATATTTATATAAATA-AAAT
1 A-T-TAAA-ATTTATTTAAATATAAAT
553648 AATAAAGTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
27 4 0.06
28 5 0.07
29 23 0.34
30 32 0.47
31 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (28 bp):
ATTAAAATTTATTTAAATATAAATTAAA
Found at i:558005 original size:52 final size:51
Alignment explanation
Indices: 557853--558009 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 51
557843 TATAACCATA
* * * * * *
557853 CAAACTTGTCCATTAAAAATCCTTCTCATCTTAGAATTCTTCTCCTGTAAAT
1 CAAACTTATCTATTAAAAATCCTTTTC-TCTTAGAATTCTTCTCTTGCAAGT
* * ** *
557905 CAAACTTACCTATTAAGAATTTTTTTTCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTATCTATTAA-AAATCCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
* *
557957 CAAACTTATCTATTAATAATCCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTATCTATTAAAAATCCT-TTTCTCTTAGAATTCTTCTCTTGCAAGT
558009 C
1 C
558010 TTCTTATCCA
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
51 3 0.04
52 75 0.88
53 7 0.08
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (51 bp):
CAAACTTATCTATTAAAAATCCTTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:560541 original size:14 final size:14
Alignment explanation
Indices: 560498--560533 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
560488 TATTTAACAT
*
560498 TAAAAAAATTCAAA
1 TAAAAAAATTAAAA
560512 -AAAAAAATTAAAA
1 TAAAAAAATTAAAA
560525 TAAAAAAAT
1 TAAAAAAAT
560534 AATAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAAAAATTAAAA
Found at i:560720 original size:58 final size:57
Alignment explanation
Indices: 560604--560723 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 57
560594 TTGTACAAGA
* *
560604 AAAATTGATGCTTTCAACTTTTTCCTAAAATATTTTTCTGAAAGTTTAATTTCGAAG
1 AAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTCTGAAAGTTTAATTTCAAAG
* *
560661 AAAATTGATACTTTCAAC-TTTTCCTCAACAATATTTTTTTTTGAAA-TTTTATTT-AAAG
1 AAAATTGATACTTTCAACTTTTTCCT-AA-AATA--TTTTTCTGAAAGTTTAATTTCAAAG
560719 AAAAT
1 AAAAT
560724 CAAAAAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
56 7 0.13
57 19 0.35
58 12 0.22
59 7 0.13
60 10 0.18
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTCTGAAAGTTTAATTTCAAAG
Found at i:560754 original size:22 final size:23
Alignment explanation
Indices: 560728--560771 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
560718 GAAAATCAAA
* *
560728 AAATAAAATAAGATAA-AAATAA
1 AAATAAAACAAAATAAGAAATAA
560750 AAATAAAACAAAATAAGAAATA
1 AAATAAAACAAAATAAGAAATA
560772 CTAAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (23 bp):
AAATAAAACAAAATAAGAAATAA
Found at i:560815 original size:16 final size:16
Alignment explanation
Indices: 560725--560828 Score: 61
Period size: 16 Copynumber: 6.3 Consensus size: 16
560715 AAAGAAAATC
*
560725 AAAAAAT-AAAATAAG
1 AAAAAATAAAAATAAT
560740 ATAAAAATAAAAATAA-
1 A-AAAAATAAAAATAAT
*
560756 AACAAAATAAGAAATACT
1 AA-AAAATAA-AAATAAT
* **
560774 AAATAATTATAATCTAAT
1 AAA-AAATA-AAAATAAT
* *
560792 CAACAAATAATAATAAT
1 -AAAAAATAAAAATAAT
*
560809 AAAAAATAAATA-AAT
1 AAAAAATAAAAATAAT
560824 AAAAA
1 AAAAA
560829 TCTTTTATAT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
15 10 0.15
16 23 0.34
17 18 0.26
18 14 0.21
19 3 0.04
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAAATAAT
Found at i:561235 original size:20 final size:19
Alignment explanation
Indices: 561196--561232 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
561186 ATATGGCCAA
561196 AAAACTCGTCAAAAAATTC
1 AAAACTCGTCAAAAAATTC
* *
561215 AAAATTCGTCGAAAAATT
1 AAAACTCGTCAAAAAATT
561233 TCACCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (19 bp):
AAAACTCGTCAAAAAATTC
Found at i:561562 original size:10 final size:10
Alignment explanation
Indices: 561540--561569 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
561530 GCCGAAGAAG
561540 AATAAAAATAA
1 AATAAAAA-AA
561551 AATAAAAAAA
1 AATAAAAAAA
561561 AATAAAAAA
1 AATAAAAAA
561570 TAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:561587 original size:22 final size:22
Alignment explanation
Indices: 561543--561642 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
561533 GAAGAAGAAT
** * *
561543 AAAAATAAAATAAAAAAAAATA
1 AAAAATAAAATATTAATAGATA
561565 AAAAATAAAATATTAATAGATA
1 AAAAATAAAATATTAATAGATA
* *
561587 ATTAAAAGAAAATA--ATTAGATA
1 A--AAAATAAAATATTAATAGATA
*
561609 AATAA-AAAATATTAATAGATA
1 AAAAATAAAATATTAATAGATA
*
561630 AATAATAATAATA
1 AAAAATAA-AATA
561643 AACATATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.09
20 3 0.05
21 12 0.19
22 29 0.45
23 4 0.06
24 10 0.16
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAATAAAATATTAATAGATA
Found at i:561638 original size:14 final size:13
Alignment explanation
Indices: 561540--561766 Score: 61
Period size: 13 Copynumber: 17.5 Consensus size: 13
561530 GCCGAAGAAG
561540 AATAAA-AATAA-
1 AATAAATAATAAT
561551 AATAAA-AA-AA-
1 AATAAATAATAAT
*
561561 AATAAAAAATAA-
1 AATAAATAATAAT
*
561573 AAT-ATTAATAGAT
1 AATAAATAATA-AT
* *
561586 AATTAA-AAGAA-
1 AATAAATAATAAT
*
561597 AATAATTAGATAAAT
1 AATAAATA-AT-AAT
* *
561612 AAAAAATATTAAT
1 AATAAATAATAAT
561625 AGATAAATAATAAT
1 A-ATAAATAATAAT
561639 AATAAACATATATATATT
1 AAT-AA-ATA-ATA-A-T
*
561657 AATAGATAAATAAT
1 AATAAAT-AATAAT
* **
561671 AATATATGTTAAT
1 AATAAATAATAAT
561684 AGATAAAT-A-AAT
1 A-ATAAATAATAAT
* * *
561696 -ATATATGTATATT
1 AATAAAT-AATAAT
561709 AATAAATAATAAT
1 AATAAATAATAAT
*
561722 AGT-AATAATAAAT
1 AATAAATAAT-AAT
*
561735 AATTAAATAA-AAA
1 AA-TAAATAATAAT
* *
561748 AATAAAAAACAAT
1 AATAAATAATAAT
561761 AA-AAAT
1 AATAAAT
561767 GCATTGGACT
Statistics
Matches: 162, Mismatches: 29, Indels: 49
0.68 0.12 0.20
Matches are distributed among these distances:
10 13 0.08
11 19 0.12
12 27 0.17
13 38 0.23
14 35 0.22
15 15 0.09
16 8 0.05
17 3 0.02
18 4 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:561659 original size:24 final size:24
Alignment explanation
Indices: 561632--561720 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 24
561622 AATAGATAAA
561632 TAATA-ATAATAAACATATATATAT
1 TAATAGATAATAAA-ATATATATAT
* *
561656 TAATAGATAA-ATAATAATATATGT
1 TAATAGATAATAAAAT-ATATATAT
561680 TAATAGATAAATAAATATATATGTATAT
1 TAATAGAT-AATAAA-ATATA--TATAT
*
561708 TAATAAATAATAA
1 TAATAGATAATAA
561721 TAGTAATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.04
24 22 0.42
25 6 0.11
26 5 0.09
27 7 0.13
28 11 0.21
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (24 bp):
TAATAGATAATAAAATATATATAT
Found at i:561694 original size:28 final size:28
Alignment explanation
Indices: 561606--561740 Score: 93
Period size: 28 Copynumber: 4.8 Consensus size: 28
561596 AAATAATTAG
561606 ATAAATAA-AA-A-ATATTAATAGATAA
1 ATAAATAATAATATATATTAATAGATAA
* * *
561631 ATAATAATAATAAACATATATATATTA-ATAG
1 AT-A-AATAAT-AATATATAT-TAATAGATAA
*
561662 ATAAATAATAATATATGTTAATAGATAA
1 ATAAATAATAATATATATTAATAGATAA
* *
561690 ATAAAT-ATATATGTATATTAATAAAT-A
1 ATAAATAATA-ATATATATTAATAGATAA
*
561717 ATAATAGTAATAATAAATAATTAA
1 ATAA-A-TAATAATATAT-ATTAA
561741 ATAAAAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 17 0.20
28 30 0.35
29 13 0.15
30 10 0.12
31 9 0.10
32 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (28 bp):
ATAAATAATAATATATATTAATAGATAA
Found at i:561743 original size:8 final size:7
Alignment explanation
Indices: 561540--561753 Score: 61
Period size: 8 Copynumber: 29.9 Consensus size: 7
561530 GCCGAAGAAG
561540 AATAAA-
1 AATAAAT
561546 AATAAAAT
1 AAT-AAAT
* *
561554 AAAAAAA
1 AATAAAT
*
561561 AATAAAA
1 AATAAAT
561568 AATAAA-
1 AATAAAT
*
561574 ATATTAAT
1 A-ATAAAT
*
561582 AGATAATT
1 A-ATAAAT
*
561590 AA-AAGAA
1 AATAA-AT
*
561597 AATAATT
1 AATAAAT
561604 AGATAAAT
1 A-ATAAAT
*
561612 AAAAAAT
1 AATAAAT
*
561619 -ATTAAT
1 AATAAAT
561625 AGATAAAT
1 A-ATAAAT
561633 AAT-AAT
1 AATAAAT
561639 AATAAA-
1 AATAAAT
* *
561645 CATATAT
1 AATAAAT
*
561652 ATATTAAT
1 A-ATAAAT
561660 AGATAAAT
1 A-ATAAAT
561668 AATAATAT
1 AATAA-AT
* *
561676 ATGTTAAT
1 A-ATAAAT
561684 AGATAAAT
1 A-ATAAAT
*
561692 AAATATAT
1 -AATAAAT
* *
561700 ATGTATATT
1 A-ATA-AAT
561709 AATAAAT
1 AATAAAT
561716 AAT-AAT
1 AATAAAT
*
561722 AGT-AAT
1 AATAAAT
561728 AATAAAT
1 AATAAAT
561735 AATTAAAT
1 AA-TAAAT
561743 AA-AAA-
1 AATAAAT
561748 AATAAA
1 AATAAA
561754 AAACAATAAA
Statistics
Matches: 152, Mismatches: 36, Indels: 40
0.67 0.16 0.18
Matches are distributed among these distances:
5 2 0.01
6 36 0.24
7 50 0.33
8 59 0.39
9 5 0.03
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:564392 original size:45 final size:45
Alignment explanation
Indices: 564328--564420 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
564318 GACCTCATAA
564328 ATGACCTAGCTCAATCCGTTTCCAGAGAAACATGCTTCAATTTGG
1 ATGACCTAGCTCAATCCGTTTCCAGAGAAACATGCTTCAATTTGG
564373 ATGACCTAGCTCAATCCGTTTCCAGAGAAACATGCTTCAATTTGG
1 ATGACCTAGCTCAATCCGTTTCCAGAGAAACATGCTTCAATTTGG
564418 ATG
1 ATG
564421 GAGACAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (45 bp):
ATGACCTAGCTCAATCCGTTTCCAGAGAAACATGCTTCAATTTGG
Found at i:572858 original size:2 final size:2
Alignment explanation
Indices: 572851--572876 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
572841 GAGGTGAAAC
572851 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
572877 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:572881 original size:2 final size:2
Alignment explanation
Indices: 572876--572917 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
572866 TCTCTCTCTC
572876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
572917 T
1 T
572918 GCAGAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:580678 original size:23 final size:23
Alignment explanation
Indices: 580651--580711 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 23
580641 TCGTATCAGA
580651 TTTAAAATTAATAAAATATTA-TT
1 TTTAAAATT-ATAAAATATTATTT
580674 TTT-AAA-TATAAAATATTATTT
1 TTTAAAATTATAAAATATTATTT
580695 TTTAAAA-TAT-AAATATT
1 TTTAAAATTATAAAATATT
580712 TAAATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.31
21 13 0.36
22 9 0.25
23 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAAATTATAAAATATTATTT
Found at i:580686 original size:20 final size:20
Alignment explanation
Indices: 580660--580711 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
580650 ATTTAAAATT
580660 AATAAAATATTA-TTTTTAA
1 AATAAAATATTATTTTTTAA
580679 ATATAAAATATTATTTTTTAA
1 A-ATAAAATATTATTTTTTAA
580700 AATATAAATATT
1 AATA-AAATATT
580712 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 15 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAAAATATTATTTTTTAA
Found at i:580697 original size:22 final size:20
Alignment explanation
Indices: 580651--580711 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 20
580641 TCGTATCAGA
580651 TTTAAAATTAATAAAATATTAT
1 TTTAAAA-T-ATAAAATATTAT
*
580673 TTTTAAATATAAAATATTATTT
1 TTTAAAATATAAAATATTA--T
580695 TTTAAAATAT-AAATATT
1 TTTAAAATATAAAATATT
580712 TAAATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 11 0.31
21 8 0.23
22 16 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAATATAAAATATTAT
Found at i:580722 original size:16 final size:16
Alignment explanation
Indices: 580695--580733 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
580685 AATATTATTT
580695 TTTAAA-ATATAAATA
1 TTTAAATATATAAATA
*
580710 TTTAAATATATAATTA
1 TTTAAATATATAAATA
*
580726 TATAAATA
1 TTTAAATA
580734 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAATATATAAATA
Found at i:580758 original size:13 final size:14
Alignment explanation
Indices: 580732--580761 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
580722 ATTATATAAA
580732 TAAAAAATTAATTT
1 TAAAAAATTAATTT
*
580746 TAAAAAATTATTTT
1 TAAAAAATTAATTT
580760 TA
1 TA
580762 TATAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAAAATTAATTT
Found at i:589339 original size:15 final size:15
Alignment explanation
Indices: 589306--589338 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
589296 ACACCACTTT
*
589306 CCCCTGCCCCACCCC
1 CCCCTACCCCACCCC
589321 CCCCTACCCC-CCCC
1 CCCCTACCCCACCCC
589335 CCCC
1 CCCC
589339 CCAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.06, C:0.85, G:0.03, T:0.06
Consensus pattern (15 bp):
CCCCTACCCCACCCC
Found at i:599897 original size:13 final size:13
Alignment explanation
Indices: 599879--599903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
599869 ATTTTCATCA
599879 TATATATATATAT
1 TATATATATATAT
599892 TATATATATATA
1 TATATATATATA
599904 GCAGCAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATATATATAT
Found at i:603876 original size:28 final size:28
Alignment explanation
Indices: 603836--603892 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
603826 TGAAGTTGAT
603836 TGAAAGAGAATCAACACTCCCCTCTATG
1 TGAAAGAGAATCAACACTCCCCTCTATG
603864 TGAAAGAGAATCAACACTCCCCTCTATG
1 TGAAAGAGAATCAACACTCCCCTCTATG
603892 T
1 T
603893 AATTAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (28 bp):
TGAAAGAGAATCAACACTCCCCTCTATG
Found at i:605605 original size:17 final size:17
Alignment explanation
Indices: 605583--605617 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
605573 ACCAGCAATC
*
605583 AAAATTAAACCTAAATA
1 AAAATTAAACCCAAATA
*
605600 AAAATTAGACCCAAATA
1 AAAATTAAACCCAAATA
605617 A
1 A
605618 GGATTTCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.14, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAATTAAACCCAAATA
Found at i:609413 original size:3 final size:3
Alignment explanation
Indices: 609407--609433 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
609397 AGAAGAAACC
609407 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
609434 GTAAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:609595 original size:2 final size:2
Alignment explanation
Indices: 609583--609614 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
609573 AACTTATTAA
609583 AT AT A- AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
609615 GCTTTAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:610396 original size:6 final size:6
Alignment explanation
Indices: 610381--610411 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
610371 CATATACTGT
*
610381 CAAATG CAAATA CAAATA CAAATA CAAATA C
1 CAAATA CAAATA CAAATA CAAATA CAAATA C
610412 CCCTGTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.16
Consensus pattern (6 bp):
CAAATA
Found at i:617637 original size:31 final size:30
Alignment explanation
Indices: 617577--617638 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
617567 TAAAATTTTT
*
617577 ATTAAATAATATAAATTATTATTATAAATTA
1 ATTAAATAATAT-AATTATTATTAAAAATTA
*
617608 ATTAAATTAATAT-ATTTTTATTGAAAAATTA
1 ATTAAA-TAATATAATTATTATT-AAAAATTA
617639 TATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.30
31 13 0.48
32 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
ATTAAATAATATAATTATTATTAAAAATTA
Found at i:618405 original size:13 final size:12
Alignment explanation
Indices: 618380--618404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
618370 ATTTAAATTA
618380 TAAATAATTTTT
1 TAAATAATTTTT
618392 TAAATAATTTTT
1 TAAATAATTTTT
618404 T
1 T
618405 TTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATAATTTTT
Done.