Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 169 of 202
Found at i:52811866 original size:26 final size:26
Alignment explanation
Indices: 52811837--52811901 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
52811827 AATATAAAAG
52811837 TATATATTTAATATATTATTATTTAA
1 TATATATTTAATATATTATTATTTAA
52811863 TATATATTTAATATATTATTATTTAA
1 TATATATTTAATATATTATTATTTAA
52811889 -ATATATTTAATAT
1 TATATATTTAATAT
52811902 TTTTTGGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 13 0.33
26 26 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATATATTTAATATATTATTATTTAA
Found at i:52811870 original size:11 final size:11
Alignment explanation
Indices: 52811837--52811901 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 11
52811827 AATATAAAAG
52811837 TATATATTTAATA
1 TATATATTT-A-A
52811850 TATTATTATTTAA
1 TA-TA-TATTTAA
52811863 TATATATTTAATA
1 TATATATTT-A-A
52811876 TATTATTATTTAA
1 TA-TA-TATTTAA
52811889 -ATATATTTAA
1 TATATATTTAA
52811899 TAT
1 TAT
52811902 TTTTTGGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
10 7 0.16
11 9 0.20
12 4 0.09
13 9 0.20
14 6 0.13
15 10 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATATTTAA
Found at i:52814521 original size:4 final size:4
Alignment explanation
Indices: 52814512--52814539 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
52814502 AATGGAAACG
52814512 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
52814540 GAAAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:52817021 original size:18 final size:16
Alignment explanation
Indices: 52816992--52817025 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
52816982 TCAAAGTAAA
52816992 TATTATTTATTAAATT
1 TATTATTTATTAAATT
52817008 TATTATATTAATTAAATT
1 TATTAT-TT-ATTAAATT
52817026 AATTTCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTATTAAATT
Found at i:52819059 original size:17 final size:19
Alignment explanation
Indices: 52819028--52819064 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52819018 GTATATTAGT
52819028 AAATTAATAAAAAA-TAAA
1 AAATTAATAAAAAATTAAA
*
52819046 AAATT-ATAATAAATTAAA
1 AAATTAATAAAAAATTAAA
52819064 A
1 A
52819065 GGTAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATTAATAAAAAATTAAA
Found at i:52820104 original size:45 final size:45
Alignment explanation
Indices: 52819980--52820335 Score: 197
Period size: 45 Copynumber: 7.9 Consensus size: 45
52819970 CTAGCTTGAA
* * * * *
52819980 TGAAACG-GATAAGACCATAGTTGAAAGACATTATGACATTATACC
1 TGAAACGAG-TAAGACCATAGCTGAAAAACGTTATGACATCATACT
* ** * * *
52820025 GGAATTGAATAAGACCATAGTTGAAAGAA-ATTATGACATCATACT
1 TGAAACGAGTAAGACCATAGCTGAAA-AACGTTATGACATCATACT
* * * * *
52820070 AGAAACGAGTAAAACCATAGCTGAAAAACGTTATGGCATCACAAT
1 TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGACATCATACT
** * * * * *
52820115 TTTAACAAGTAAGACCATAGATGAAAGACGTTATGGCATCACGA-T
1 TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGACATCA-TACT
** * * *
52820160 TTTAACGAGTAAGACCATAGCTGAAATACGTTATGACATCACGAGT
1 TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGACATCA-TACT
* * * *
52820206 T-TAATGAGTAAGACCATAGCT-AAAAGACATTATGACATCACGA-T
1 TGAAACGAGTAAGACCATAGCTGAAAA-ACGTTATGACATCA-TACT
** * * * *
52820250 TCTAACGAGTAAGACCATAGTTGAAAGACGCTAT-AGCATCACGA-T
1 TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGA-CATCA-TACT
** * * *
52820295 TCTAACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCA
1 TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGACATCA
52820336 CGATCTAACA
Statistics
Matches: 262, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.03
45 247 0.94
46 7 0.03
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (45 bp):
TGAAACGAGTAAGACCATAGCTGAAAAACGTTATGACATCATACT
Found at i:52820134 original size:90 final size:90
Alignment explanation
Indices: 52820034--52820379 Score: 381
Period size: 90 Copynumber: 3.9 Consensus size: 90
52820024 CGGAATTGAA
* * * *** *
52820034 TAAGACCATAGTTGAAAGAAATTATGACATCA-TACTAGAAACGAGTAAAACCATAGCTGAAAAA
1 TAAGACCATAGCTGAAAGACATTATGACATCACGA-TTCTAACGAGTAAGACCATAGCTGAAAAA
* *
52820098 CGTTATGGCATCACAATTTTAACAAG
65 CGTTATGGCATCACGATTTTAACGAG
* * * * *
52820124 TAAGACCATAGATGAAAGACGTTATGGCATCACGATTTTAACGAGTAAGACCATAGCTGAAATAC
1 TAAGACCATAGCTGAAAGACATTATGACATCACGATTCTAACGAGTAAGACCATAGCTGAAAAAC
* * *
52820189 GTTATGACATCACGAGTTTAATGAG
66 GTTATGGCATCACGATTTTAACGAG
* * *
52820214 TAAGACCATAGCTAAAAGACATTATGACATCACGATTCTAACGAGTAAGACCATAGTTGAAAGAC
1 TAAGACCATAGCTGAAAGACATTATGACATCACGATTCTAACGAGTAAGACCATAGCTGAAAAAC
* * *
52820279 GCTATAGCATCACGATTCTAACGAG
66 GTTATGGCATCACGATTTTAACGAG
** * * ** * *
52820304 TAAGACCATAGCTGAAAGACGCTATGGCATCACGA-TCTAACAAGTAAGAATATAGCTGAAAGAT
1 TAAGACCATAGCTGAAAGACATTATGACATCACGATTCTAACGAGTAAGACCATAGCTGAAAAAC
*
52820368 GCTATGGCATCA
66 GTTATGGCATCA
52820380 TGAATCAGAC
Statistics
Matches: 217, Mismatches: 38, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
89 35 0.16
90 181 0.83
91 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (90 bp):
TAAGACCATAGCTGAAAGACATTATGACATCACGATTCTAACGAGTAAGACCATAGCTGAAAAAC
GTTATGGCATCACGATTTTAACGAG
Found at i:52820336 original size:45 final size:45
Alignment explanation
Indices: 52820073--52820423 Score: 386
Period size: 45 Copynumber: 7.8 Consensus size: 45
52820063 TCATACTAGA
* * * * *
52820073 AACGAGTAAAACCATAGCTGAAAAACGTTATGGCATCACAATTTT
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
* * * *
52820118 AACAAGTAAGACCATAGATGAAAGACGTTATGGCATCACGATTTT
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
* * *
52820163 AACGAGTAAGACCATAGCTGAAATACGTTATGACATCACGAGTT-T
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGA-TTCT
* * ** *
52820208 AATGAGTAAGACCATAGCTAAAAGACATTATGACATCACGATTCT
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
* *
52820253 AACGAGTAAGACCATAGTTGAAAGACGCTATAGCATCACGATTCT
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
52820298 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGA-TCT
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
* ** * * *
52820342 AACAAGTAAGAATATAGCTGAAAGATGCTATGGCATCATGAATC-
1 AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
* * * *
52820386 AGACGAATAAGATCAT-GATTGAAAGACACTATGGCATC
1 A-ACGAGTAAGACCATAG-CTGAAAGACGCTATGGCATC
52820424 CTTCAACCTT
Statistics
Matches: 267, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
44 43 0.16
45 222 0.83
46 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (45 bp):
AACGAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCT
Found at i:52829427 original size:43 final size:43
Alignment explanation
Indices: 52829365--52829459 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
52829355 AACACATAGA
*
52829365 ATACCCAAAAGAGATAGTCGTAAATTGCTCAACTGTAACTATT
1 ATACCCAAAAGAGAGAGTCGTAAATTGCTCAACTGTAACTATT
52829408 ATACCCAAAAGAGAGAGTCGTAAATTGCTCAACTGTAACTATT
1 ATACCCAAAAGAGAGAGTCGTAAATTGCTCAACTGTAACTATT
*
52829451 ATACTCAAA
1 ATACCCAAA
52829460 CATCTATACC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (43 bp):
ATACCCAAAAGAGAGAGTCGTAAATTGCTCAACTGTAACTATT
Found at i:52834333 original size:49 final size:51
Alignment explanation
Indices: 52834168--52834345 Score: 245
Period size: 52 Copynumber: 3.5 Consensus size: 51
52834158 CAGATACCCG
* * * *
52834168 GTGGCCTGCACATAGTACCACCCTTG-AAGCCAAAGCTACCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCTTCTTCACAAA
52834219 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-TTCTTCACAAA
* * *
52834271 GTGGCCTTCACATAGTACCACACTTGTGATC-AAGTTATC-TCTTCTCAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCACAAA
*
52834320 GTGGCCGTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
52834346 AGTCGCTAAT
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
49 34 0.29
51 41 0.35
52 42 0.36
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTCTTCACAAA
Found at i:52839159 original size:21 final size:21
Alignment explanation
Indices: 52839121--52839160 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52839111 GCTTCTTGGC
* *
52839121 AAGTGGATATTGCGATACCCA
1 AAGTGGATATCGCAATACCCA
*
52839142 AAGTGGTTATCGCAATACC
1 AAGTGGATATCGCAATACC
52839161 ACTGAAGGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (21 bp):
AAGTGGATATCGCAATACCCA
Found at i:52851488 original size:11 final size:11
Alignment explanation
Indices: 52851472--52851497 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52851462 TTCGAAATTC
52851472 AATTAATTAAT
1 AATTAATTAAT
52851483 AATTAATTAAT
1 AATTAATTAAT
52851494 AATT
1 AATT
52851498 TGAAAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTAATTAAT
Found at i:52861913 original size:6 final size:6
Alignment explanation
Indices: 52861898--52861933 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
52861888 CAATGGTATA
* *
52861898 TATATC TATATG TATATC TACATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC
52861934 CAGTGTTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (6 bp):
TATATC
Found at i:52865621 original size:153 final size:153
Alignment explanation
Indices: 52865343--52865651 Score: 600
Period size: 153 Copynumber: 2.0 Consensus size: 153
52865333 ATTGTGTGAA
*
52865343 CCTTAACTGTTGCCAGATCTCTTTTGTGTGCAAACACTCTTGAAAAACATGTTCAATTGTTTCCA
1 CCTTAACTGTTGCCAGATCTCTTTTGTGTGCAAACACTCTTGAAAAACATGTTCAACTGTTTCCA
*
52865408 CACCATTGTGACAGCGGTGACAGTTCGCAGAGTTCATCAACCTCCTGTAGCATAGGTTTGCATAA
66 CACCATTGTAACAGCGGTGACAGTTCGCAGAGTTCATCAACCTCCTGTAGCATAGGTTTGCATAA
52865473 GTAGGCACATAGTTGTTCATAAT
131 GTAGGCACATAGTTGTTCATAAT
52865496 CCTTAACTGTTGCCAGATCTCTTTTGTGTGCAAACACTCTTGAAAAACATGTTCAACTGTTTCCA
1 CCTTAACTGTTGCCAGATCTCTTTTGTGTGCAAACACTCTTGAAAAACATGTTCAACTGTTTCCA
52865561 CACCATTGTAACAGCGGTGACAGTTCGCAGAGTTCATCAACCTCCTGTAGCATAGGTTTGCATAA
66 CACCATTGTAACAGCGGTGACAGTTCGCAGAGTTCATCAACCTCCTGTAGCATAGGTTTGCATAA
52865626 GTAGGCACATAGTTGTTCATAAT
131 GTAGGCACATAGTTGTTCATAAT
52865649 CCT
1 CCT
52865652 CCATGTTGTA
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (153 bp):
CCTTAACTGTTGCCAGATCTCTTTTGTGTGCAAACACTCTTGAAAAACATGTTCAACTGTTTCCA
CACCATTGTAACAGCGGTGACAGTTCGCAGAGTTCATCAACCTCCTGTAGCATAGGTTTGCATAA
GTAGGCACATAGTTGTTCATAAT
Found at i:52873384 original size:9 final size:10
Alignment explanation
Indices: 52873364--52873392 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
52873354 ATTGCATGTT
52873364 TGAATAGAAA
1 TGAATAGAAA
52873374 TGAAT-GAAA
1 TGAATAGAAA
52873383 TGAATAGAAA
1 TGAATAGAAA
52873393 AAGAGAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:52873494 original size:6 final size:6
Alignment explanation
Indices: 52873479--52873531 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
52873469 AAGTTTCCAC
* * *
52873479 AAATGG AAATGA AAATGG AAATGG AAATGA AAATGA AAATGA AAATGGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAAT-GA
52873528 AAAT
1 AAAT
52873532 TGCAATCCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (6 bp):
AAATGA
Found at i:52873502 original size:18 final size:18
Alignment explanation
Indices: 52873479--52873531 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
52873469 AAGTTTCCAC
*
52873479 AAATGGAAATGAAAATGG
1 AAATGGAAATGAAAATGA
52873497 AAATGGAAATGAAAATGA
1 AAATGGAAATGAAAATGA
*
52873515 AAATGAAAATGGAAAAT
1 AAATGGAAAT-GAAAAT
52873532 TGCAATCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (18 bp):
AAATGGAAATGAAAATGA
Found at i:52876522 original size:52 final size:48
Alignment explanation
Indices: 52876503--52876810 Score: 335
Period size: 46 Copynumber: 6.3 Consensus size: 48
52876493 TGACAAGTGG
* *
52876503 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
52876549 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
*
52876595 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-------AA
52876650 GTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 ----AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
52876706 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* ** *
52876752 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
52876798 AAAGTGATAAGTG
1 AAAGTGATAAGTG
52876811 GCTACACTTA
Statistics
Matches: 235, Mismatches: 11, Indels: 32
0.85 0.04 0.12
Matches are distributed among these distances:
46 143 0.61
52 44 0.19
53 2 0.01
56 1 0.00
59 45 0.19
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:52876824 original size:37 final size:37
Alignment explanation
Indices: 52876774--52876986 Score: 318
Period size: 37 Copynumber: 6.0 Consensus size: 37
52876764 AATAGCTTTA
*
52876774 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
52876811 GCTACACTTATCTGATCAAGAAACAAAGTG---A---
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
52876842 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
52876879 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
52876916 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* **
52876952 GCTACACTTATTTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
52876987 ATCATACGTA
Statistics
Matches: 164, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
31 30 0.18
34 2 0.01
35 11 0.07
36 38 0.23
37 83 0.51
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:52876882 original size:68 final size:69
Alignment explanation
Indices: 52876773--52876969 Score: 308
Period size: 68 Copynumber: 2.8 Consensus size: 69
52876763 TAATAGCTTT
*
52876773 AGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAA
1 AGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAA
52876838 GTG-
66 GTGA
52876841 AGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAA
1 AGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAA
52876906 GTGATA
66 GTG--A
* *
52876912 AGTGGCTACACTTATCTGATC-AGAAACAAAGTGATAGGTGGCTACACTTATTTGATCA
1 A---GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCA
52876970 GGGACAAGTG
Statistics
Matches: 120, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
68 67 0.56
71 1 0.01
73 35 0.29
74 17 0.14
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (69 bp):
AGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAA
GTGA
Found at i:52876898 original size:203 final size:197
Alignment explanation
Indices: 52876473--52876836 Score: 529
Period size: 203 Copynumber: 1.8 Consensus size: 197
52876463 GGTAGCTTTA
*
52876473 GCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCT
* * * * *
52876538 GATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGAT
66 GATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
** ** *
52876603 AAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGGAAAGTGATAAGTGA
131 AAG-GATAG---C-GCTACACTTATCTGATCAAGAAACAAGTGGAAAGTGGAAAGAAAAAAGTGA
52876668 TAGCTTCG
191 TAGC-TCG
*
52876676 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCT
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCT
*
52876741 GATCAAGAGACAAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGAT
66 GATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
52876806 AA-G-T-G-GCTACACTTATCTGATCAAGAAACAA
131 AAGGATAGCGCTACACTTATCTGATCAAGAAACAA
52876837 AGTGAGCTAC
Statistics
Matches: 151, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
194 24 0.16
199 1 0.01
200 1 0.01
201 1 0.01
203 124 0.82
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (197 bp):
GCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTAATAGCTTCGGCTATACTTATCT
GATCAAGAGACAAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGAT
AAGGATAGCGCTACACTTATCTGATCAAGAAACAAGTGGAAAGTGGAAAGAAAAAAGTGATAGCT
CG
Found at i:52879109 original size:57 final size:58
Alignment explanation
Indices: 52879040--52879153 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 58
52879030 TTTCCAAGTC
* *
52879040 ATTTTCATTTTGGAGAAAACCACATTCA-TTTCTAAATGATTC-CATATCTCTATTTTT
1 ATTTTCATTTTGGAGAAAACCACAATCATTTTC-AAATGATTCTCATATCTCCATTTTT
* * * *
52879097 ATTTTCGTTTTGGAGAAAACCATAATCATTTTCAAATGTTTCTCATTTCTCCATTTT
1 ATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCTCATATCTCCATTTT
52879154 CACCATTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
57 33 0.67
58 16 0.33
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (58 bp):
ATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCTCATATCTCCATTTTT
Found at i:52880354 original size:6 final size:6
Alignment explanation
Indices: 52880324--52880375 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
52880314 GGTTGCAAAA
* * * * *
52880324 GTGACAT GTGAAA GTGAAA GTGAAT GTGAAT GTGTAT GTGTAT GTGTAT
1 GTGA-AT GTGAAT GTGAAT GTGAAT GTGAAT GTGAAT GTGAAT GTGAAT
52880373 GTG
1 GTG
52880376 TAAATAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
6 38 0.90
7 4 0.10
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (6 bp):
GTGAAT
Found at i:52880376 original size:6 final size:6
Alignment explanation
Indices: 52880347--52880377 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
52880337 GTGAAAGTGA
*
52880347 ATGTGA ATGTGT ATGTGT ATGTGT ATGTGT A
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT A
52880378 AATAAAGATA
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:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (6 bp):
ATGTGT
Found at i:52894257 original size:50 final size:50
Alignment explanation
Indices: 52894177--52894650 Score: 329
Period size: 50 Copynumber: 9.5 Consensus size: 50
52894167 GCAATTCAAA
* * * *
52894177 AGATTGAAGCCACAATGGCAAATCTTACTTCCCAGGCGATGCAGCGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAAC
* * * * * * ** *
52894227 AGATTGAAGCTACGACAGCGAATCTCACTTCCCCGAC-ATTGCAATTCAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAAC
* * * * * *
52894277 AGATTGAGGCCACAACGGTGAATCTTACTTTCCTA-GCGTTGCAATGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGTGGAAC
* * * * * * *
52894327 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC-ATTGCAAT-TAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAAC
* * * *
52894376 ATGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCGATGCAGCGGAAC
1 A-GATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAAC
* * * * * * ** *
52894427 AGATTGAAGCTACGACGGCGAATCTCACTTCCCCGAC-ATTACAATTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAAC
** * *
52894477 AGATCAAAGC--CAACGGCGAATCTTACTTCTCTGGCGATGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAAC
** * * * *
52894525 AGATTGAAGCTACAACGGCGAATCTCGCTTCCTC-GAC-ATTGCAAT-TAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCC-CAGGCGA-TGCAGTGGAAC
* * *
52894574 AGATTGAGGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAAC
* *
52894624 AGATTGAAGCTACGATGGCGAATCTTA
1 AGATTGAAGCTACAACGGCGAATCTTA
52894651 TTTTCTCGAT
Statistics
Matches: 316, Mismatches: 91, Indels: 34
0.72 0.21 0.08
Matches are distributed among these distances:
48 35 0.11
49 47 0.15
50 225 0.71
51 9 0.03
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAAC
Found at i:52894338 original size:100 final size:99
Alignment explanation
Indices: 52894165--52894703 Score: 654
Period size: 100 Copynumber: 5.4 Consensus size: 99
52894155 AAACCATGGT
* *
52894165 TTGCAATTCAAAAGATTGAAGCCACAATGGCAAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
*
52894230 TTGAAGCTACGACAGCGAATCTCACTTCCCCGACA
65 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * **
52894265 TTGCAATTCAAAAGATTGAGGCCACAACGGTGAATCTTACTTTCCTA-GCGTTGCAATGGAACAG
1 TTGCAATT-AAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGCGGAACAG
* * * * *
52894329 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
64 ATTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * *
52894365 TTGCAATTAAAATGATTGAAGCTACAACAGCGGATCTTACTTTCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTAAAA-GATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
52894430 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
65 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* ** * * *
52894465 TTACAATTTAAAAGATCAAAG-C-CAACGGCGAATCTTACTTCTCTGGCGATGCAGTGGAACAGA
1 TTGCAA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * *
52894528 TTGAAGCTACAACGGCGAATCTCGCTTCCTCGACA
65 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
*
52894563 TTGCAATTAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGAT
* * * * * *
52894628 TGAAGCTACGATGGCGAATCTTATTTTCTCGATA
66 TGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * *
52894662 TTACAACT-AAAGATTGAAGCCGCAATGGCGAATCTTATTTCC
1 TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCC
52894704 TCGGCGAGAC
Statistics
Matches: 373, Mismatches: 60, Indels: 14
0.83 0.13 0.03
Matches are distributed among these distances:
97 11 0.03
98 103 0.28
99 80 0.21
100 168 0.45
101 11 0.03
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (99 bp):
TTGCAATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGAT
TGAAGCTACGACGGCGAATCTCACTTCCCCGACA
Found at i:52896519 original size:18 final size:21
Alignment explanation
Indices: 52896498--52896538 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
52896488 TATTTATTGT
52896498 TTTAC-TTGT-ATCATT-TTA
1 TTTACATTGTCATCATTATTA
52896516 TTTACATTGTCATCATTATTA
1 TTTACATTGTCATCATTATTA
52896537 TT
1 TT
52896539 ATTTTACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 4 0.20
20 6 0.30
21 5 0.25
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTACATTGTCATCATTATTA
Found at i:52898566 original size:22 final size:22
Alignment explanation
Indices: 52898525--52898567 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52898515 TATCTAAATA
*
52898525 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGCAGCAAT
52898547 ATAATAACAAAAT-GACAGCAA
1 ATAATAACAAAATAG-CAGCAA
52898568 AACAATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAATAACAAAATAGCAGCAAT
Found at i:52901543 original size:6 final size:6
Alignment explanation
Indices: 52901527--52901570 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
52901517 ACGGTGGTGC
* * * *
52901527 TGGAGG GGGAGG TGGAGG TGGAGG AGGAGG CGGAGG AGGAGG TG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TG
52901571 CCTCTGGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.20, C:0.02, G:0.68, T:0.09
Consensus pattern (6 bp):
TGGAGG
Found at i:52902015 original size:6 final size:6
Alignment explanation
Indices: 52902006--52902037 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
52901996 TGGTGGTGGG
*
52902006 GGAGGA GGAGGT GGAGGT GGAGGT GGAGGT GG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GG
52902038 GGCTAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (6 bp):
GGAGGT
Found at i:52902203 original size:3 final size:3
Alignment explanation
Indices: 52902195--52902238 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
52902185 AGAGGTGGGA
* * * *
52902195 GGT GGT GGT GGC GGT GGT GGT GGA GGT GGA GGT GGG GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
52902239 AAGCTCTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.02, G:0.70, T:0.23
Consensus pattern (3 bp):
GGT
Found at i:52902210 original size:6 final size:6
Alignment explanation
Indices: 52902186--52902235 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
52902176 TGCAGGCATA
* * * *
52902186 GAGGTGG GAGGTG GTGGTG GCGGTG GTGGTG GAGGTG GAGGTG GGGGTG
1 GAGGT-G GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG GAGGTG
52902235 G
1 G
52902236 TGGAAGCTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.08, C:0.02, G:0.70, T:0.20
Consensus pattern (6 bp):
GAGGTG
Found at i:52902212 original size:12 final size:12
Alignment explanation
Indices: 52902192--52902238 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
52902182 CATAGAGGTG
52902192 GGAGGTGGTGGT
1 GGAGGTGGTGGT
*
52902204 GGCGGTGGTGGT
1 GGAGGTGGTGGT
*
52902216 GGAGGTGGAGGT
1 GGAGGTGGTGGT
*
52902228 GGGGGTGGTGG
1 GGAGGTGGTGG
52902239 AAGCTCTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.02, G:0.70, T:0.21
Consensus pattern (12 bp):
GGAGGTGGTGGT
Found at i:52902376 original size:18 final size:18
Alignment explanation
Indices: 52902355--52902390 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52902345 GGTGGTTCGA
* *
52902355 GTGGAGGTGGAGGCGGAG
1 GTGGAAGTGGAGGAGGAG
52902373 GTGGAAGTGGAGGAGGAG
1 GTGGAAGTGGAGGAGGAG
52902391 AAGGGGTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.64, T:0.11
Consensus pattern (18 bp):
GTGGAAGTGGAGGAGGAG
Found at i:52915910 original size:41 final size:41
Alignment explanation
Indices: 52915859--52916041 Score: 165
Period size: 41 Copynumber: 4.5 Consensus size: 41
52915849 TTTAAACAGA
* **
52915859 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCAG
1 TTCACCGGCACTT-AGCCTGATAGGCTTATAGCCTAATTCAG
* * *
52915900 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
* * * * *
52915941 TTCACCGGCACTTAGCCTGCTAGACATATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAG
* * * * * *
52915982 TTCACCGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAG
52916023 TTCACCGGCACTTAGCCTG
1 TTCACCGGCACTTAGCCTG
52916042 CTAGACGTAG
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 124 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
Found at i:52916042 original size:41 final size:41
Alignment explanation
Indices: 52915894--52916055 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
52915884 TTATAGTTTA
* * * *
52915894 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
* *
52915935 ATTCAGTTCACCGGCACTTAGCCTGCTAGACATATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
52915976 ATTCAATTCACCGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
52916017 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTAGAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
52916056 TGAATAATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 110 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:52916068 original size:82 final size:82
Alignment explanation
Indices: 52915900--52916073 Score: 226
Period size: 82 Copynumber: 2.1 Consensus size: 82
52915890 TTTAATTCAG
* * * *
52915900 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
* *
52915965 CATATAGTCCGATTCAA
66 CATAGAGTCCGAATCAA
*
52915982 TTCACCGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAATTCACCGGCACTTAGCCTGCTAG
* *
52916046 ACGTAGAGTCTGAAT-AA
65 ACATAGAGTCCGAATCAA
*
52916063 TTTCACTGGCA
1 -TTCACCGGCA
52916074 ATAAATCCGA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 2 0.03
82 76 0.95
83 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
CATAGAGTCCGAATCAA
Found at i:52920894 original size:41 final size:41
Alignment explanation
Indices: 52920720--52920881 Score: 245
Period size: 41 Copynumber: 4.0 Consensus size: 41
52920710 TTATAGTTTA
* * * *
52920720 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
* *
52920761 ATTCAGTTCACCGACACTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
52920802 ATTCAATTCACCGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
52920843 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
52920882 TGAATAATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 110 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:52920894 original size:82 final size:82
Alignment explanation
Indices: 52920726--52920899 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
52920716 TTTAATTCAG
* * * *
52920726 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGACACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGACACTTAGCCTGCTAGA
*
52920791 CGTATAGTCCGATTCAA
66 CGTATAGTCCGAATCAA
* *
52920808 TTCACCGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCACCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAATTCACCGACACTTAGCCTGCTAG
*
52920872 ACGTATAGTCTGAAT-AA
65 ACGTATAGTCCGAATCAA
*
52920889 TTTCACTGGCA
1 -TTCACCGGCA
52920900 ATAAATCCGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 2 0.02
82 77 0.95
83 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGACACTTAGCCTGCTAGA
CGTATAGTCCGAATCAA
Found at i:52928679 original size:41 final size:41
Alignment explanation
Indices: 52928506--52928666 Score: 229
Period size: 41 Copynumber: 4.0 Consensus size: 41
52928496 TTATAGTTTA
* *
52928506 ATTCAGTTCACCGGCACTTAGCCTGCTAG--GCAT-GTGCCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGT-CC-G
* *
52928546 CTTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
52928587 ATTCAATTCACCGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
52928628 ATTCAATTCACCGGCACTTAGCCTGCTAGACCTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
52928667 TAAATAATTT
Statistics
Matches: 111, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
40 28 0.25
41 76 0.68
42 5 0.05
43 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:52928679 original size:82 final size:81
Alignment explanation
Indices: 52928512--52928684 Score: 208
Period size: 82 Copynumber: 2.1 Consensus size: 81
52928502 TTTAATTCAG
* *
52928512 TTCACCGGCACTTAGCCTGCTAGGCATGTGCCTGCTTCAGTTCACCGGCACTTAGCCTGCTAGAC
1 TTCACCGGCACTTAGCCTGCTAGGCATGTGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGAC
* * *
52928577 GTATAGTCCGATTCAA
66 CTATAGTCCAAATCAA
* *
52928593 TTCACCGGCATTTAGCCTGCTAGACGTATAGT-CC-GATTCAATTCACCGGCACTTAGCCTGCTA
1 TTCACCGGCACTTAGCCTGCTAG--GCAT-GTGCCTGATTCAATTCACCGGCACTTAGCCTGCTA
*
52928656 GACCTATAGTCTAAAT-AA
63 GACCTATAGTCCAAATCAA
*
52928674 TTTCACTGGCA
1 -TTCACCGGCA
52928685 ATAAATCCGA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
81 24 0.30
82 48 0.61
83 5 0.06
84 2 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (81 bp):
TTCACCGGCACTTAGCCTGCTAGGCATGTGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGAC
CTATAGTCCAAATCAA
Found at i:52929165 original size:2 final size:2
Alignment explanation
Indices: 52929158--52929186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52929148 TGTATATGCT
52929158 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 T
52929187 TCGGACCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52935217 original size:22 final size:21
Alignment explanation
Indices: 52935183--52935245 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
52935173 AAGGACATCA
*
52935183 TATTGAAATATATATAATAAAT
1 TATTGAAAAATATAT-ATAAAT
* *
52935205 TATTTAAAAATATATTTAAAT
1 TATTGAAAAATATATATAAAT
* *
52935226 TAAATGATAAAATATTTATA
1 T-ATTGA-AAAATATATATA
52935246 TTTATGTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.19
22 16 0.50
23 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (21 bp):
TATTGAAAAATATATATAAAT
Found at i:52935747 original size:17 final size:17
Alignment explanation
Indices: 52935725--52935763 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
52935715 TATAATCAAT
52935725 TTTAAAATTTTAATATA
1 TTTAAAATTTTAATATA
52935742 TTTAAAATTTTAATATA
1 TTTAAAATTTTAATATA
*
52935759 CTTAA
1 TTTAA
52935764 TATATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAATTTTAATATA
Found at i:52936098 original size:14 final size:15
Alignment explanation
Indices: 52936068--52936099 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52936058 TCTCCAAATT
52936068 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
52936083 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
52936097 TTT
1 TTT
52936100 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:52936224 original size:14 final size:15
Alignment explanation
Indices: 52936194--52936225 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52936184 TCTCCAAATT
52936194 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
52936209 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
52936223 TTT
1 TTT
52936226 TTATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:52936226 original size:126 final size:126
Alignment explanation
Indices: 52936001--52936238 Score: 449
Period size: 126 Copynumber: 1.9 Consensus size: 126
52935991 AATGAAAAAT
*
52936001 AGGACTCGAAATTCCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAA
1 AGGACTCGAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAA
52936066 TTTTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAGTTACGATTAC
66 TTTTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAGTTACGATTAC
*
52936127 AGGACTCTAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAA
1 AGGACTCGAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAA
*
52936192 TTTTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTATAAATTT
66 TTTTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTT
52936239 TAAATTACAA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 109 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (126 bp):
AGGACTCGAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAA
TTTTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAGTTACGATTAC
Found at i:52937173 original size:13 final size:13
Alignment explanation
Indices: 52937155--52937179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52937145 ATTATTAATA
52937155 TTATTTTGTGTGT
1 TTATTTTGTGTGT
52937168 TTATTTTGTGTG
1 TTATTTTGTGTG
52937180 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:52938878 original size:41 final size:41
Alignment explanation
Indices: 52938833--52938994 Score: 245
Period size: 41 Copynumber: 4.0 Consensus size: 41
52938823 AAATTATTCA
*
52938833 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
* *
52938874 GACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
*
52938915 AACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATC-G
* * *
52938957 G-CTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAAT
52938995 TAAACTATAA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 111 0.99
42 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCG
Found at i:52939007 original size:41 final size:41
Alignment explanation
Indices: 52938834--52939029 Score: 232
Period size: 41 Copynumber: 4.8 Consensus size: 41
52938824 AATTATTCAG
* **
52938834 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCGG
1 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAA
* * *
52938875 ACTATACGTCTAGCAGGCTAAATGCCGGTGAATTGAATCGA
1 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAA
*
52938916 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAA
* * * * *
52938957 GCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAATTAA
1 ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAA
* * * *
52938998 ACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 ACTATACGTCTAGCAGGCT-AAGTGCCGGTGAA
52939030 TCTGTTTAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 1 0.01
41 137 0.99
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (41 bp):
ACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAATCAA
Found at i:52945523 original size:3 final size:3
Alignment explanation
Indices: 52945483--52945545 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
52945473 TTTAGCAATT
* * * *
52945483 TTA TTA TT- TTG TTCA TTA TT- TTA ATG TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52945527 TTA TTA TTAA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA
52945546 GTTTTATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.82
4 5 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52945834 original size:2 final size:2
Alignment explanation
Indices: 52945823--52945879 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
52945813 GTACACCTTT
52945823 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52945864 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
52945880 CTTACGTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:52945923 original size:33 final size:33
Alignment explanation
Indices: 52945885--52945962 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
52945875 ATATACTTAC
*
52945885 GTATTCTTTATACTTTGAAAATATATTTTGTTT
1 GTATTCTTTATACTTTCAAAATATATTTTGTTT
52945918 GTATTCTTTATACTTTCAAAATATATTTTGTTT
1 GTATTCTTTATACTTTCAAAATATATTTTGTTT
* *
52945951 ATATTCATTATA
1 GTATTCTTTATA
52945963 TTTTATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (33 bp):
GTATTCTTTATACTTTCAAAATATATTTTGTTT
Found at i:52945978 original size:16 final size:16
Alignment explanation
Indices: 52945948--52945981 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
52945938 ATATATTTTG
52945948 TTTATATTCATTATAT
1 TTTATATTCATTATAT
52945964 TTTATGATTCATATATAT
1 TTTAT-ATTCAT-TATAT
52945982 ACCTACTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATATTCATTATAT
Found at i:52949227 original size:35 final size:34
Alignment explanation
Indices: 52949172--52949247 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
52949162 TTCTTTGACG
52949172 AAATATT-CCTACAAGAAAAGACG-AGTGAACAGT
1 AAATATTCCCTACAAGAAAAGACGCA-TGAACAGT
* * *
52949205 AAATATTCCCTTACAAGGAAAGATGCATGAATAGT
1 AAATATTCCC-TACAAGAAAAGACGCATGAACAGT
52949240 AAATATTC
1 AAATATTC
52949248 TCTGTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 7 0.19
34 2 0.05
35 27 0.73
36 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (34 bp):
AAATATTCCCTACAAGAAAAGACGCATGAACAGT
Found at i:52949480 original size:19 final size:19
Alignment explanation
Indices: 52949439--52949487 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
52949429 TCAAAACTCA
*
52949439 TTTCTCCAAAGTTTCAAAG
1 TTTCTCCAAAATTTCAAAG
*
52949458 TTTCTCCAAAATTT-TAAG
1 TTTCTCCAAAATTTCAAAG
52949476 TTT-T-CAAAATTT
1 TTTCTCCAAAATTT
52949488 AAGTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 6 0.21
19 13 0.46
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTCTCCAAAATTTCAAAG
Found at i:52949504 original size:16 final size:16
Alignment explanation
Indices: 52949464--52949502 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
52949454 AAAGTTTCTC
52949464 CAAAATTTTAAGTTTT
1 CAAAATTTTAAGTTTT
52949480 CAAAA-TTTAAGTTTT
1 CAAAATTTTAAGTTTT
52949495 -AAAATTTT
1 CAAAATTTT
52949503 TATTACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 13 0.59
16 5 0.23
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
CAAAATTTTAAGTTTT
Found at i:52949626 original size:14 final size:15
Alignment explanation
Indices: 52949596--52949627 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52949586 TCTCCAAATT
52949596 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
52949611 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
52949625 TTT
1 TTT
52949628 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:52949630 original size:126 final size:126
Alignment explanation
Indices: 52949405--52949653 Score: 471
Period size: 126 Copynumber: 2.0 Consensus size: 126
52949395 TGAAAAACAT
52949405 GACTCGAAATACCCATTTCAGAAATCAAAACTCATTTCTCCAAAGTTTCAAAGTTTCTCCAAAAT
1 GACTCGAAATACCCATTTCAGAAATCAAAACTCATTTCTCCAAAGTTTCAAAGTTTCTCCAAAAT
52949470 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
66 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
* * *
52949531 GACTCTAAATACCCATTTCAGAAATCAAAACTCGTTTCTCCAAAGTTTCAAAGTTTCTCCAAATT
1 GACTCGAAATACCCATTTCAGAAATCAAAACTCATTTCTCCAAAGTTTCAAAGTTTCTCCAAAAT
52949596 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
66 TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTA
52949654 TCATATATTT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (126 bp):
GACTCGAAATACCCATTTCAGAAATCAAAACTCATTTCTCCAAAGTTTCAAAGTTTCTCCAAAAT
TTTAAGTTTTCAAAATTTAAGTTTTAAAATTTTTATTACAAATTTCAAATTACGATTACAG
Found at i:52949703 original size:18 final size:18
Alignment explanation
Indices: 52949682--52949747 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 18
52949672 TAATTTTTTT
52949682 AAAATTTTAAATATATTA
1 AAAATTTTAAATATATTA
* *
52949700 AAAATGTTAAGTATA--A
1 AAAATTTTAAATATATTA
** *
52949716 CCAATTTTAAA-ATTTTA
1 AAAATTTTAAATATATTA
52949733 AAAA-TTT-AATATATT
1 AAAATTTTAAATATATT
52949748 TTTAATAGGT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
15 4 0.11
16 15 0.43
17 3 0.09
18 13 0.37
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAATTTTAAATATATTA
Found at i:52949806 original size:7 final size:8
Alignment explanation
Indices: 52949785--52949815 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
52949775 TTTAATATAT
*
52949785 TTAAAAAT
1 TTAAAAAC
52949793 TTAAAAAC
1 TTAAAAAC
52949801 TTAAAAAC
1 TTAAAAAC
52949809 TTAAAAA
1 TTAAAAA
52949816 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAC
Found at i:52955083 original size:18 final size:16
Alignment explanation
Indices: 52955060--52955118 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 16
52955050 AACATTTTCC
52955060 TTTAATTAATTTAGAAAA
1 TTTAATTAA-TTA-AAAA
52955078 TTTAATTAATT--AAA
1 TTTAATTAATTAAAAA
52955092 TTTAATTAATTAAAAA
1 TTTAATTAATTAAAAA
* *
52955108 ATCAATTAATT
1 TTTAATTAATT
52955119 TAGTTGGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
14 14 0.38
16 12 0.32
17 2 0.05
18 9 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTAATTAATTAAAAA
Found at i:52955859 original size:25 final size:25
Alignment explanation
Indices: 52955825--52955873 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
52955815 CTTGGATATG
52955825 TTAGTTTTAATTTTT-TATTTAAAAT
1 TTAGTTTTAATTTTTCT-TTTAAAAT
52955850 TTAGTTTTAATTTTTCTTTTAAAA
1 TTAGTTTTAATTTTTCTTTTAAAA
52955874 ATTATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
TTAGTTTTAATTTTTCTTTTAAAAT
Found at i:52957271 original size:44 final size:46
Alignment explanation
Indices: 52957183--52957275 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
52957173 GAGCTGTTGT
*
52957183 AATGGAATAGAACTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATCAGTAATTCAATTGTTTGGTTGAATGG
* *
52957229 AATGGAATAGAACTATAAT-GGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTATAATCAGTAATTCAAT-TGTTTGGTTGAATGG
52957273 AAT
1 AAT
52957276 AATGTTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 2 0.05
46 18 0.42
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAACTATAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:52960343 original size:68 final size:68
Alignment explanation
Indices: 52960248--52960374 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 68
52960238 TAAATTTAAT
* * * *
52960248 AATAAATAATTTACTTATATTTTAATATAATTATTA-CCAAATAT-AATTTAATAAAAATAAAAA
1 AATAAATAATTTAATAACATTTTAATATAATTATTATCAAAATATGAA-TTAATAAAAATAAAAA
52960311 TAAA
65 TAAA
*
52960315 AATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATTAATAAAAAT
1 AATAAATAATTTAATAACATT-TTAATATAATTATTATCAAAATATGAATTAATAAAAAT
52960375 CATAACATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
67 18 0.35
68 15 0.29
69 17 0.33
70 2 0.04
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (68 bp):
AATAAATAATTTAATAACATTTTAATATAATTATTATCAAAATATGAATTAATAAAAATAAAAAT
AAA
Found at i:52967538 original size:40 final size:40
Alignment explanation
Indices: 52967494--52967589 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
52967484 CAGACGAACG
* *
52967494 ATACCTACTGAATCTACTGAAACGTATGCGCTTTCGAGCC
1 ATACCTACTGAATCTACTGAAACGTATGCGCTCTCAAGCC
*
52967534 ATACCTACTGAATTTACTGAAACGTATGCGCTCTCAAGCC
1 ATACCTACTGAATCTACTGAAACGTATGCGCTCTCAAGCC
*
52967574 ATACCTACTAAATCTA
1 ATACCTACTGAATCTA
52967590 TTCAAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (40 bp):
ATACCTACTGAATCTACTGAAACGTATGCGCTCTCAAGCC
Found at i:52968919 original size:32 final size:32
Alignment explanation
Indices: 52968870--52969116 Score: 257
Period size: 32 Copynumber: 7.7 Consensus size: 32
52968860 TACAATAATG
* *
52968870 TGATTGGCACAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * * * * *
52968902 TGATCGACACACAGCCATGAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * *
52968934 TGATCCGCACAAAGCCATCAGTAGCTGTGATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * *
52968966 TGATCGGCACACATCCATCAGTAACAGTGAAA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
* * * *
52968998 TGATCGGCACACAGCCATCGGTAACGGTAATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGATA
52969030 TGATCGGCACAAAGCCATCAGTAACAGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACAGTGA-TA
*
52969062 TGATCGACACAAAGCCATCAGTAAC-GAT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACAG-TGA-TA
* *
52969094 TGATTGGCACAAAGCCATTAGTA
1 TGATCGGCACAAAGCCATCAGTA
52969117 GCATCGCAGC
Statistics
Matches: 179, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
31 2 0.01
32 177 0.99
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (32 bp):
TGATCGGCACAAAGCCATCAGTAACAGTGATA
Found at i:52969040 original size:96 final size:96
Alignment explanation
Indices: 52968870--52969086 Score: 303
Period size: 96 Copynumber: 2.3 Consensus size: 96
52968860 TACAATAATG
* * *
52968870 TGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATGAGTAACGGTAACAT
1 TGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGACACACAGCCATGAGTAACGGTAACAT
* *
52968935 GATCCGCACAAAGCCATCAGTAGCTGTGA-TA
66 GATCCGCACAAAGCCATCAGTAACAGT-ACTA
* * * *
52968966 TGATCGGCACACATCCATCAGTAACAGTGAAATGATCGGCACACAGCCATCG-GTAACGGTAATA
1 TGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGACACACAGCCAT-GAGTAACGGTAACA
*
52969030 TGATCGGCACAAAGCCATCAGTAACAGTACTA
65 TGATCCGCACAAAGCCATCAGTAACAGTACTA
*
52969062 TGATCGACACAAAGCCATCAGTAAC
1 TGATCGGCACAAAGCCATCAGTAAC
52969087 GATACTATGA
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
95 1 0.01
96 104 0.98
97 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (96 bp):
TGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGACACACAGCCATGAGTAACGGTAACAT
GATCCGCACAAAGCCATCAGTAACAGTACTA
Found at i:52969097 original size:96 final size:96
Alignment explanation
Indices: 52968877--52969116 Score: 299
Period size: 96 Copynumber: 2.5 Consensus size: 96
52968867 ATGTGATTGG
* *
52968877 CACAAAGCCATCAGTAGCAGTGATATGATCGACACACAGCCATGAGTAACGGTAACATGATCCGC
1 CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATGAGTAACGGTAACATGATCCGC
* * *
52968942 ACAAAGCCATCAGTAGCTGTGATATGATCGG
66 ACAAAGCCATCAGTAACAGTGATATGATCGA
* * * * *
52968973 CACACATCCATCAGTAACAGTGAAATGATCGGCACACAGCCATCG-GTAACGGTAATATGATCGG
1 CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCAT-GAGTAACGGTAACATGATCCG
52969037 CACAAAGCCATCAGTAACAGT-ACTATGATCGA
65 CACAAAGCCATCAGTAACAGTGA-TATGATCGA
* * *
52969069 CACAAAGCCATCAGTAAC-GAT-ACTATGATTGGCACAAAGCCATTAGTA
1 CACAAAGCCATCAGTAACAG-TGA-TATGATCGGCACACAGCCATGAGTA
52969117 GCATCGCAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
95 3 0.02
96 119 0.97
97 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (96 bp):
CACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATGAGTAACGGTAACATGATCCGC
ACAAAGCCATCAGTAACAGTGATATGATCGA
Found at i:52969151 original size:26 final size:26
Alignment explanation
Indices: 52969122--52969172 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
52969112 TAGTAGCATC
52969122 GCAGCAAAGCTGCCAGCAACAGTATT
1 GCAGCAAAGCTGCCAGCAACAGTATT
* *
52969148 GCAGCAAAGCTGCCAGTAATAGTAT
1 GCAGCAAAGCTGCCAGCAACAGTAT
52969173 ATGTGGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGCAACAGTATT
Found at i:52969190 original size:27 final size:27
Alignment explanation
Indices: 52969160--52969219 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
52969150 AGCAAAGCTG
*
52969160 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
52969187 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
52969214 CCAGTA
1 CCAGTA
52969220 CAATACTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:52969426 original size:27 final size:27
Alignment explanation
Indices: 52969368--52969799 Score: 329
Period size: 27 Copynumber: 16.1 Consensus size: 27
52969358 GGAAAAAATA
52969368 GTCA-TTTACCC-ACCA-GGGCATTACG
1 GTCATTTTACCCTA-CAGGGGCATTACG
* * *
52969393 GTTATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
52969420 ATCATTTGACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
52969447 GTCATTTTATCCTACAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
52969474 GTCATTTTATCCTATAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
52969501 GTCATTTTACCCTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
52969528 GTCATTTTACCCTATAGAGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
** **
52969555 ACCATTTTACCCTACAGGGATATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
52969582 GTCATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * **
52969609 GTTATTTTACCCTACAAGGGTATTATA
1 GTCATTTTACCCTACAGGGGCATTACG
* * **
52969636 GTCATTTTATCCTACAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * *
52969663 GT-ATTCTACCCTACGGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
52969689 GTTATTTTACCATA-TGGGAGCATTTCA
1 GTCATTTTACCCTACAGGG-GCATTACG
** * *
52969716 GTTTTTTTACCC-ATC-GAGGGTATTTCG
1 GTCATTTTACCCTA-CAG-GGGCATTACG
* * ** * *
52969743 ATTATTTTACCCTATGGGGGCATTTCA
1 GTCATTTTACCCTACAGGGGCATTACG
* *
52969770 GTCATTTTATCCTACCGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
52969797 GTC
1 GTC
52969800 CAGATATTGA
Statistics
Matches: 332, Mismatches: 65, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
25 3 0.01
26 34 0.10
27 291 0.88
28 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:52972919 original size:9 final size:9
Alignment explanation
Indices: 52972905--52972964 Score: 84
Period size: 9 Copynumber: 6.4 Consensus size: 9
52972895 TTTGGTTAAA
*
52972905 AATTACTCG
1 AATTACCCG
52972914 AATTACCCG
1 AATTACCCG
52972923 AAAATTACCCG
1 --AATTACCCG
*
52972934 AATTACCTG
1 AATTACCCG
52972943 AATTACCCG
1 AATTACCCG
52972952 AATTACCCG
1 AATTACCCG
52972961 AATT
1 AATT
52972965 GTATCACTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 37 0.80
11 9 0.20
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:52972994 original size:17 final size:17
Alignment explanation
Indices: 52972972--52973032 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
52972962 ATTGTATCAC
52972972 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
52972989 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
52973009 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
52973026 TACATAA
1 TACATAA
52973033 GTCTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 20 0.61
20 13 0.39
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:52973013 original size:37 final size:37
Alignment explanation
Indices: 52972967--52973037 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
52972957 CCCGAATTGT
52972967 ATCACTACATAATTAAAAACATTACATAAGTCTTTGA
1 ATCACTACATAATTAAAAACATTACATAAGTCTTTGA
52973004 ATCACTACATAATTAAAAACATTACATAAGTCTT
1 ATCACTACATAATTAAAAACATTACATAAGTCTT
52973038 GAAATTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.32
Consensus pattern (37 bp):
ATCACTACATAATTAAAAACATTACATAAGTCTTTGA
Found at i:52973051 original size:37 final size:37
Alignment explanation
Indices: 52972970--52973054 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 37
52972960 GAATTGTATC
*
52972970 ACTACATAATTAAAAACATTACATAAGTCTTTGAATC
1 ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
52973007 ACTACATAATTAAAAACATTACATAAGTC-TTGAAATTA
1 ACTACATAATTAAAAACATTACATAAGTCTTTG-AA-TA
52973045 AC-ACATAATT
1 ACTACATAATT
52973055 GAAATGTAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
36 3 0.07
37 39 0.87
38 3 0.07
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (37 bp):
ACTACATAATTAAAAACATTACATAAGTCTTTGAATA
Found at i:52975312 original size:235 final size:234
Alignment explanation
Indices: 52974901--52975366 Score: 803
Period size: 235 Copynumber: 2.0 Consensus size: 234
52974891 TTCATCTAAA
52974901 TACAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACACGCCAC
1 TACAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACACGCCAC
* *
52974966 AAACATAAAATTTTTAAAACCTTCACTTTCAACAAACTTGAAAGGTCATTTATCAATCACAATCA
66 AAACATAAAATTTTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCA
52975031 TTTGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCTTTCCCCC
131 TTTGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCTTT-CCCC
* *
52975096 CCTTCAACTCCCTTTCTAGGTAAAACTAGTTGTCCTTTCC
195 CATTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTTTCC
*
52975136 TACAATTGATAAACAGT-CCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACATGCCA
1 TACAATTGATAAACA-TCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACACGCCA
* *
52975200 CAAACAT-AAGTTTCTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAGT
65 CAAACATAAAATTT-TTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAAT
*
52975264 CATTTGTGCTAA-TCTTTTCCTACATGCTTCTTGATCAAATCTCCAAGTTGAAAGATTCCTTTCC
129 CATTTGTGCTAATTC-TTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCTTTCC
52975328 CCCATTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTT
193 CCCATTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTT
52975367 GACTAGGGTC
Statistics
Matches: 220, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
234 46 0.21
235 173 0.79
236 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (234 bp):
TACAATTGATAAACATCCCTAGTCATAGTAGTTCGTGAAGGAATATGAAACCTAGGACACGCCAC
AAACATAAAATTTTTAAAACCTTCACTTTCAACAAACTTGAAAGGTAATTCATCAATCACAATCA
TTTGTGCTAATTCTTTCCTACATGCTTCTCGATCAAATCTCCAAGTTGAAAGATTCCTTTCCCCC
ATTCAACTCCCTTTCTAGGTAAAACTAGTTGCCCTTTCC
Found at i:52985497 original size:25 final size:25
Alignment explanation
Indices: 52985469--52985523 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
52985459 AGCTCCTCTC
*
52985469 AGCTGAATAACGGTAAGCTCATACG
1 AGCTGAATAACGGTAAGCTCATAAG
* **
52985494 AGCTGAGTATTGGTAAGCTCATAAG
1 AGCTGAATAACGGTAAGCTCATAAG
52985519 AGCTG
1 AGCTG
52985524 GAATTGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
AGCTGAATAACGGTAAGCTCATAAG
Found at i:52985835 original size:5 final size:5
Alignment explanation
Indices: 52985825--52985850 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52985815 TTTAATCTTT
52985825 ATTCA ATTCA ATTCA ATTCA ATTCA A
1 ATTCA ATTCA ATTCA ATTCA ATTCA A
52985851 AAATCATGTT
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:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:52987728 original size:28 final size:28
Alignment explanation
Indices: 52987688--52987743 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
52987678 GTGATTAGGG
* *
52987688 TTGCTCACACAAGTTGACATTTATGAAT
1 TTGCTCACACAAGGTGACATTTAGGAAT
52987716 TTGCTCACACAAGGTGACATTTAGGAAT
1 TTGCTCACACAAGGTGACATTTAGGAAT
52987744 GTTCTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (28 bp):
TTGCTCACACAAGGTGACATTTAGGAAT
Found at i:52989480 original size:8 final size:8
Alignment explanation
Indices: 52989467--52989492 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
52989457 GGTCATGAAT
52989467 AATAAACA
1 AATAAACA
52989475 AATAAACA
1 AATAAACA
52989483 AATAAACA
1 AATAAACA
52989491 AA
1 AA
52989493 CAATAAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAACA
Found at i:52991853 original size:31 final size:33
Alignment explanation
Indices: 52991817--52991881 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
52991807 GTCATTGTAT
52991817 ACATGAAAC-TTGAATTGTGATTT-A-TATATAC
1 ACATGAAACTTTG-ATTGTGATTTAATTATATAC
*
52991848 ACATGAAACTTTGATTTTGATTTAATTATATAC
1 ACATGAAACTTTGATTGTGATTTAATTATATAC
52991881 A
1 A
52991882 TTTAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 18 0.60
32 4 0.13
33 8 0.27
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (33 bp):
ACATGAAACTTTGATTGTGATTTAATTATATAC
Found at i:52993453 original size:21 final size:21
Alignment explanation
Indices: 52993428--52993467 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52993418 GGTCCCCTTG
52993428 TTTTTACATTT-TTTTAAATCA
1 TTTTT-CATTTCTTTTAAATCA
*
52993449 TTTTTTATTTCTTTTAAAT
1 TTTTTCATTTCTTTTAAAT
52993468 TTTGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTCATTTCTTTTAAATCA
Found at i:52993666 original size:2 final size:2
Alignment explanation
Indices: 52993659--52993683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52993649 TTTATCATTT
52993659 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52993684 TTTAAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52993942 original size:2 final size:2
Alignment explanation
Indices: 52993937--52993962 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52993927 TTTTGTATTT
52993937 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
52993963 CACGTTTTCA
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):
TA
Found at i:53001446 original size:90 final size:91
Alignment explanation
Indices: 53001258--53001485 Score: 291
Period size: 90 Copynumber: 2.5 Consensus size: 91
53001248 GAAGATTCTG
* *
53001258 GCGTGTTATCGGTTGGAAAACTCTTATGAGCAATCTAGCGTGTTATCAGGGGCGAATATTTAGCC
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATTTAGCGTGTTATCAGGGGCGAATATTTAGCC
*
53001323 TATAAGCTTAACACTATGTGCATCTA
66 TACAAGCTTAACACTATGTGCATCTA
* * * *
53001349 GCATGTTATTGGTTGGAAAGCTCTTATAAGCAATTT-GACGTGTTGTC-GAGGG-GAATATTTAG
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATTTAG-CGTGTTATCAG-GGGCGAATATTTAG
** * * *
53001411 CCTACGGGCTTAGCACTATGTGCATTTT
64 CCTACAAGCTTAACACTATGTGCATCTA
* *
53001439 GCGTGTTATCAGTTGGAAAGCTCTTATGAGCAATTTAGTGTGTTATC
1 GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATTTAGCGTGTTATC
53001486 GGATGGTCAC
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
90 73 0.63
91 43 0.37
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (91 bp):
GCGTGTTATCGGTTGGAAAGCTCTTATGAGCAATTTAGCGTGTTATCAGGGGCGAATATTTAGCC
TACAAGCTTAACACTATGTGCATCTA
Found at i:53017453 original size:43 final size:43
Alignment explanation
Indices: 53017389--53017510 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
53017379 ATACATATTG
* *
53017389 AAGCAATTGTACTGGCACACACAGTGCATCATCTGACAAGCCGA
1 AAGCAATTATACTGGCACACACAGTGCATCATCGGACAAGCC-A
* *
53017433 AA-CAATTATACTGACACACACAGTACATCATCGGACAAGCCA
1 AAGCAATTATACTGGCACACACAGTGCATCATCGGACAAGCCA
* *
53017475 AAGCAATTATATTGGCACACACGGTGCATCATCGGA
1 AAGCAATTATACTGGCACACACAGTGCATCATCGGA
53017511 TAAACCGAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
42 3 0.04
43 64 0.93
44 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (43 bp):
AAGCAATTATACTGGCACACACAGTGCATCATCGGACAAGCCA
Found at i:53026834 original size:5 final size:5
Alignment explanation
Indices: 53026814--53026852 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
53026804 GAAGATACCT
* *
53026814 TATAA TATGTA TATAA TATAA TATAA TATAA TATTA TAT
1 TATAA TAT-AA TATAA TATAA TATAA TATAA TATAA TAT
53026853 GTATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (5 bp):
TATAA
Found at i:53026844 original size:15 final size:16
Alignment explanation
Indices: 53026814--53026859 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
53026804 GAAGATACCT
*
53026814 TATAATATGTATATAA
1 TATAATATGAATATAA
53026830 TATAATAT-AATATAA
1 TATAATATGAATATAA
* *
53026845 TATTATATGTATATA
1 TATAATATGAATATA
53026860 TAATGATCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
TATAATATGAATATAA
Found at i:53031081 original size:209 final size:198
Alignment explanation
Indices: 53030763--53031228 Score: 549
Period size: 209 Copynumber: 2.3 Consensus size: 198
53030753 ATGCATACCC
* * * *
53030763 GTGTGATAGGATTTTTAGTATTGATAATGTATTTGATTGAGTTGATGTCAAAAGTTAAACTATTT
1 GTGTGATAGGATTTTCAGTATTAATAATG-ATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
* *
53030828 TTCATTTTAATTTCATGCATATTGCACATATGGTGCTGTTATTATTATTATTACTAGTTTCAAAT
65 TTCATTTTAATTTCATACATATTGCACATAT-G-G-TG---TTATTATTA-T--TAGTTTCAAAC
* * *
53030893 CTTACGTCTCATTATTTATTTTATGTTATTTTTAAACATACATTTTTATTCAAAATTTATGGCTT
121 CTTACGTCTCATTATTTATTATATGTTA-TTTTAAACACACATTTTTATTCAAAATTTATAGCTT
**
53030958 CAACACGA-ATAGGT
185 CAACAC-ACATACAT
53030972 GTGTGATAGGATTTTCAGTATTAATAATGAATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
1 GTGTGATAGGATTTTCAGTATTAATAATG-ATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
* * * * * *
53031037 TTCATTTTAATTTCGTACGTATTGCATATGTGTTGTTATTATTATTAGTTTCAAACCTTACGTTT
65 TTCATTTTAATTTCATACATATTGCACATATGGTGTTATTATTATTAGTTTCAAACCTTACGTCT
* * * *
53031102 CATTATTTATTATATGTTATTTTAAACACATATTTTTATTCAAAATTTGTAGTTTCCACACACAT
130 CATTATTTATTATATGTTATTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACACACAT
53031167 ACAT
195 ACAT
* * * * *
53031171 GTGTGGTA-GAATTCCTAGTATTAATAATGTTGTTAATTGAGTTGGTGTCACAAGTTAA
1 GTGTGATAGGATTTTC-AGTATTAATAATGAT-TTGATTGAGTTGGTGTCACAAGTTAA
53031229 CTCGACATTA
Statistics
Matches: 227, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
198 7 0.03
199 85 0.37
200 36 0.16
202 1 0.00
203 9 0.04
206 2 0.01
208 1 0.00
209 86 0.38
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (198 bp):
GTGTGATAGGATTTTCAGTATTAATAATGATTTGATTGAGTTGGTGTCACAAGTTAAACTATTTT
TCATTTTAATTTCATACATATTGCACATATGGTGTTATTATTATTAGTTTCAAACCTTACGTCTC
ATTATTTATTATATGTTATTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACACACATA
CAT
Found at i:53031224 original size:199 final size:203
Alignment explanation
Indices: 53030763--53031228 Score: 559
Period size: 199 Copynumber: 2.3 Consensus size: 203
53030753 ATGCATACCC
* * * * *
53030763 GTGTGATAGGATTTTTAGTATTGATAATGTATTTGATTGAGTTGATGTCAAAAGTTAAACTATTT
1 GTGTGATA-GAATTCTAGTATTAATAATGT-TTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
* *
53030828 TTCATTTTAATTTCATGCATATTGCACATATGGTGCTGTTATTATTATTATTACTAGTTTCAAAT
64 TTCATTTTAATTTCATACATATTG-ACATA--GTGCTGTTATTATTATTATTA-TAGTTTCAAAC
* * *
53030893 CTTACGTCTCATTATTTATTTTATGTTATTTTTAAACATACATTTTTATTCAAAATTTATGGCTT
125 CTTACGTCTCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTT
**
53030958 CAACACGAATAGGT
190 CAACACGAATACAT
* * *
53030972 GTGTGATAGGATTTTCAGTATTAATAATGAATTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
1 GTGTGATAGAATTCT-AGTATTAATAATG-TTTTGATTGAGTTGGTGTCACAAGTTAAACTATTT
* * *
53031037 TTCATTTTAATTTCGTACGTATTG-CATA-TG-TGTTGTTATTATTA-T-TAGTTTCAAACCTTA
64 TTCATTTTAATTTCATACATATTGACATAGTGCTGTTATTATTATTATTATAGTTTCAAACCTTA
* * * * *
53031097 CGTTTCATTATTTATTATATGTTA-TTTTAAACACATATTTTTATTCAAAATTTGTAGTTTCCAC
129 CGTCTCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAAC
53031161 AC-ACATACAT
194 ACGA-ATACAT
* *
53031171 GTGTGGTAGAATTCCTAGTATTAATAATGTTGTTAATTGAGTTGGTGTCACAAGTTAA
1 GTGTGATAGAATT-CTAGTATTAATAATGTT-TTGATTGAGTTGGTGTCACAAGTTAA
53031229 CTCGACATTA
Statistics
Matches: 226, Mismatches: 26, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
198 2 0.01
199 89 0.39
200 37 0.16
202 1 0.00
203 13 0.06
204 2 0.01
207 4 0.02
208 5 0.02
209 73 0.32
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (203 bp):
GTGTGATAGAATTCTAGTATTAATAATGTTTTGATTGAGTTGGTGTCACAAGTTAAACTATTTTT
CATTTTAATTTCATACATATTGACATAGTGCTGTTATTATTATTATTATAGTTTCAAACCTTACG
TCTCATTATTTATTATATGTTATTTTTAAACACACATTTTTATTCAAAATTTATAGCTTCAACAC
GAATACAT
Found at i:53035012 original size:16 final size:16
Alignment explanation
Indices: 53034991--53035021 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53034981 AATTAATTTA
*
53034991 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
53035007 AATTAAATAATTTTC
1 AATTAAATAATTTTC
53035022 TCAGTCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:53049869 original size:49 final size:49
Alignment explanation
Indices: 53049814--53049913 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
53049804 ACGTAACTCA
53049814 TAAAATAAAACATATTTAGAAAATGGTAATAACAAGAGTAACATAGTAT
1 TAAAATAAAACATATTTAGAAAATGGTAATAACAAGAGTAACATAGTAT
*
53049863 TAAAATAAAACATATTTAGCAAATGGTAATAACAAGAGTAACATAGTAT
1 TAAAATAAAACATATTTAGAAAATGGTAATAACAAGAGTAACATAGTAT
53049912 TA
1 TA
53049914 GCAAAAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (49 bp):
TAAAATAAAACATATTTAGAAAATGGTAATAACAAGAGTAACATAGTAT
Found at i:53051331 original size:16 final size:17
Alignment explanation
Indices: 53051309--53051346 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
53051299 AACTAAATAG
*
53051309 CTAAAATAAATAAACAA
1 CTAAAATAAACAAACAA
53051326 -TAAAATAAACAAACAA
1 CTAAAATAAACAAACAA
53051342 CTAAA
1 CTAAA
53051347 CAAATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (17 bp):
CTAAAATAAACAAACAA
Found at i:53054546 original size:24 final size:24
Alignment explanation
Indices: 53054519--53054564 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53054509 ATGACTATAT
*
53054519 ATAAAATTTTAATAA-ATAAAATAG
1 ATAAAATTATAA-AATATAAAATAG
53054543 ATAAAATTATAAAATATAAAAT
1 ATAAAATTATAAAATATAAAAT
53054565 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAAAATTATAAAATATAAAATAG
Found at i:53054563 original size:15 final size:14
Alignment explanation
Indices: 53054543--53054572 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
53054533 AATAAAATAG
53054543 ATAAAATTATAAAAT
1 ATAAAATTA-AAAAT
53054558 ATAAAATTAAAAAT
1 ATAAAATTAAAAAT
53054572 A
1 A
53054573 ATATAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATTAAAAAT
Found at i:53055093 original size:14 final size:14
Alignment explanation
Indices: 53055074--53055103 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53055064 AACCGTTACA
53055074 GATTTTCAAATTAG
1 GATTTTCAAATTAG
53055088 GATTTTCAAATTAG
1 GATTTTCAAATTAG
53055102 GA
1 GA
53055104 GTAAACGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
GATTTTCAAATTAG
Found at i:53055908 original size:30 final size:30
Alignment explanation
Indices: 53055867--53055927 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
53055857 GGGGGTGGGA
*
53055867 TGGGAAGGGAGTAAAAGTTTTGGGGGGAAAG
1 TGGGAAGGGAGTAAAAGTATT-GGGGGAAAG
*
53055898 TGGG-AGGGAGTAAAAGTATTGTGGGAAAG
1 TGGGAAGGGAGTAAAAGTATTGGGGGAAAG
53055927 T
1 T
53055928 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.32
30 15 0.54
31 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.46, T:0.21
Consensus pattern (30 bp):
TGGGAAGGGAGTAAAAGTATTGGGGGAAAG
Found at i:53056305 original size:20 final size:20
Alignment explanation
Indices: 53056269--53056306 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53056259 TACATTTATT
*
53056269 TTTTATTTAATTTTTAATTA
1 TTTTATTTAATTATTAATTA
53056289 TTTTATTTTAA-TATTAAT
1 TTTTA-TTTAATTATTAAT
53056307 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTAATTATTAATTA
Found at i:53056851 original size:18 final size:19
Alignment explanation
Indices: 53056828--53056878 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
53056818 TAATGTAAAG
53056828 TAATATTATTTAAAAT-T-T
1 TAATA-TATTTAAAATATGT
*
53056846 TAATATAATTAAAATATGT
1 TAATATATTTAAAATATGT
53056865 TAATA-ATTTTAAAA
1 TAATATA-TTTAAAA
53056879 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATATATTTAAAATATGT
Found at i:53056885 original size:26 final size:27
Alignment explanation
Indices: 53056837--53056888 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
53056827 GTAATATTAT
53056837 TTAAAATTTTAATATAATTAAAATATG
1 TTAAAATTTTAATATAATTAAAATATG
53056864 TTAATAATTTTAA-A-AATTAAAATAT
1 TTAA-AATTTTAATATAATTAAAATAT
53056889 TACAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.46
27 5 0.21
28 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TTAAAATTTTAATATAATTAAAATATG
Found at i:53056895 original size:26 final size:28
Alignment explanation
Indices: 53056841--53056897 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
53056831 TATTATTTAA
*
53056841 AATTTTAATATAATTAAAATATGTTAAT
1 AATTTTAATATAATTAAAATATGTCAAT
53056869 AATTTTAA-A-AATTAAAATAT-TACAAT
1 AATTTTAATATAATTAAAATATGT-CAAT
53056895 AAT
1 AAT
53056898 AAAAAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 17 0.63
27 1 0.04
28 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
AATTTTAATATAATTAAAATATGTCAAT
Found at i:53059857 original size:15 final size:15
Alignment explanation
Indices: 53059834--53059868 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53059824 TTATATTAAA
*
53059834 TTTTGATTTGATAAT
1 TTTTAATTTGATAAT
53059849 TTTTAATTTGATAAT
1 TTTTAATTTGATAAT
*
53059864 CTTTA
1 TTTTA
53059869 CAGAGTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (15 bp):
TTTTAATTTGATAAT
Found at i:53061239 original size:25 final size:25
Alignment explanation
Indices: 53061199--53061257 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
53061189 TAGCTATTTG
* * * *
53061199 AGGCATGTATGCTTAATTCTAGTGA
1 AGGCATGAATGCTTAATGCTAATCA
*
53061224 AGGCATGAATGGTTAATGCTAATCA
1 AGGCATGAATGCTTAATGCTAATCA
53061249 A-GCATGAAT
1 AGGCATGAAT
53061258 TGGTAAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (25 bp):
AGGCATGAATGCTTAATGCTAATCA
Found at i:53067219 original size:22 final size:20
Alignment explanation
Indices: 53067179--53067219 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
53067169 CCACGGCCTA
*
53067179 AGCACACGAGTGTGTGATAT
1 AGCACACGAGTGTGGGATAT
53067199 AGCACACGAGCATGTGGGATA
1 AGCACACGAG--TGTGGGATA
53067220 GCCACATAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.20
Consensus pattern (20 bp):
AGCACACGAGTGTGGGATAT
Found at i:53068644 original size:70 final size:71
Alignment explanation
Indices: 53068552--53068714 Score: 172
Period size: 71 Copynumber: 2.3 Consensus size: 71
53068542 TTAGGCAATT
* * * * *
53068552 AAAAAAGGTAAAATTCCTTTTGGCGC-C-CAAAGTTTTTAACATCATT-AAATTGTTCTTGTATC
1 AAAAAATGTAAAATTACATTTGGC-CACTCAAAGTTTTTAACAT-ATTAAAATAGTCCTTGTATC
53068614 ATTACTTA
64 ATTACTTA
* * *
53068622 AAAAAATGTAAAATTAGATTTGGCCACTCAAAGTTTTTAATATTTTAAAATAGTCCTTGTATCAT
1 AAAAAATGTAAAATTACATTTGGCCACTCAAAGTTTTTAACATATTAAAATAGTCCTTGTATCAT
*
53068687 TATTTA
66 TACTTA
* *
53068693 AAAATAATAT-AAATTATATTTG
1 AAAA-AATGTAAAATTACATTTG
53068715 ACCCTTCCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
69 1 0.01
70 23 0.29
71 50 0.64
72 4 0.05
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (71 bp):
AAAAAATGTAAAATTACATTTGGCCACTCAAAGTTTTTAACATATTAAAATAGTCCTTGTATCAT
TACTTA
Found at i:53068683 original size:71 final size:71
Alignment explanation
Indices: 53068579--53068714 Score: 177
Period size: 71 Copynumber: 1.9 Consensus size: 71
53068569 TTTTGGCGCC
* * *
53068579 CAAAGTTTTTAACATCATTAAATTGTTCTTGTATCATTACTTAAAAA-AATGTAAAATTAGATTT
1 CAAAGTTTTTAACATCATTAAATAGTCCTTGTATCATTACTTAAAAATAATAT-AAATTAGATTT
53068643 GGCCACT
65 GGCCACT
* * * *
53068650 CAAAGTTTTTAATAT-TTTAAAATAGTCCTTGTATCATTATTTAAAAATAATATAAATTATATTT
1 CAAAGTTTTTAACATCATT-AAATAGTCCTTGTATCATTACTTAAAAATAATATAAATTAGATTT
53068714 G
65 G
53068715 ACCCTTCCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 2 0.04
71 50 0.89
72 4 0.07
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (71 bp):
CAAAGTTTTTAACATCATTAAATAGTCCTTGTATCATTACTTAAAAATAATATAAATTAGATTTG
GCCACT
Found at i:53075602 original size:15 final size:16
Alignment explanation
Indices: 53075582--53075612 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53075572 AACAACAAAG
53075582 AAAATTTT-AGGGATA
1 AAAATTTTAAGGGATA
53075597 AAAATTTTAAGGGATA
1 AAAATTTTAAGGGATA
53075613 GACATTCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (16 bp):
AAAATTTTAAGGGATA
Found at i:53077743 original size:22 final size:22
Alignment explanation
Indices: 53077715--53077758 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53077705 TATATTGTAA
53077715 TTTTTATCTAATTAAAAATAAT
1 TTTTTATCTAATTAAAAATAAT
53077737 TTTTTATCTAATTAAAAATAAT
1 TTTTTATCTAATTAAAAATAAT
53077759 AACGTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTATCTAATTAAAAATAAT
Found at i:53077773 original size:26 final size:22
Alignment explanation
Indices: 53077712--53077781 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 22
53077702 ATCTATATTG
53077712 TAATTT-TTATCTAATTAAAAA
1 TAATTTATTATCTAATTAAAAA
*
53077733 TAATTTTTTATCTAATTAAAAA
1 TAATTTATTATCTAATTAAAAA
*
53077755 TAATAACGTTATTATCTAATTACAAA
1 TAAT----TTATTATCTAATTAAAAA
53077781 T
1 T
53077782 TCATTTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 6 0.14
22 19 0.45
26 17 0.40
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATTTATTATCTAATTAAAAA
Found at i:53079939 original size:23 final size:22
Alignment explanation
Indices: 53079896--53079939 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
53079886 TTCTAAGTCG
53079896 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
53079919 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
53079940 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:53080048 original size:45 final size:45
Alignment explanation
Indices: 53079984--53080077 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
53079974 AACAGATACT
* *
53079984 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
53080029 CGGTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
53080074 CGGT
1 CGGT
53080078 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:53085313 original size:14 final size:14
Alignment explanation
Indices: 53085290--53085342 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
53085280 TTCAATGTTT
*
53085290 ATATTGCAACGATC
1 ATATTCCAACGATC
53085304 ATATTCCAACGATC
1 ATATTCCAACGATC
**
53085318 ATATTGTAAC-AGTC
1 ATATTCCAACGA-TC
53085332 ATATTCCAACG
1 ATATTCCAACG
53085343 GCCATATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 1 0.03
14 31 0.97
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (14 bp):
ATATTCCAACGATC
Found at i:53085348 original size:14 final size:14
Alignment explanation
Indices: 53085290--53085350 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
53085280 TTCAATGTTT
* *
53085290 ATATTGCAACGATC
1 ATATTCCAACGGTC
*
53085304 ATATTCCAACGATC
1 ATATTCCAACGGTC
** *
53085318 ATATTGTAACAGTC
1 ATATTCCAACGGTC
*
53085332 ATATTCCAACGGCC
1 ATATTCCAACGGTC
53085346 ATATT
1 ATATT
53085351 TTTGCATTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (14 bp):
ATATTCCAACGGTC
Found at i:53095020 original size:29 final size:26
Alignment explanation
Indices: 53094967--53095027 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
53094957 ACGTCCCTCT
53094967 CCTCCCAAAGTTCATCATTAATCTCC
1 CCTCCCAAAGTTCATCATTAATCTCC
*
53094993 CCTCCCAAAGTTCATCATTAATCTTC
1 CCTCCCAAAGTTCATCATTAATCTCC
*
53095019 TCTCCCAAA
1 CCTCCCAAA
53095028 CTAAGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.38, G:0.03, T:0.31
Consensus pattern (26 bp):
CCTCCCAAAGTTCATCATTAATCTCC
Found at i:53096707 original size:44 final size:44
Alignment explanation
Indices: 53096640--53096754 Score: 139
Period size: 44 Copynumber: 2.6 Consensus size: 44
53096630 TGTCATTAGG
*
53096640 ATTTATATTCA-AAAGGTATTATGT-CCAGGTGTT-GGCTACT-TGCC
1 ATTTATATTCAGCAA-GTATTATGTACCA-GTGTTAGG-TA-TGTGCC
* *
53096684 ATTTATATTCAGCAAGTACTATGTACCAGTGTTAGGTATGTTCC
1 ATTTATATTCAGCAAGTATTATGTACCAGTGTTAGGTATGTGCC
53096728 ATTTATATTCAGCAAGTATTATGTACC
1 ATTTATATTCAGCAAGTATTATGTACC
53096755 GATGTTGCAG
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.02
44 55 0.87
45 7 0.11
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (44 bp):
ATTTATATTCAGCAAGTATTATGTACCAGTGTTAGGTATGTGCC
Found at i:53098661 original size:18 final size:17
Alignment explanation
Indices: 53098640--53098674 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
53098630 AGTCCCACGT
53098640 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
53098658 GCCCGTGTGGCCCACAC
1 GCCCATGTGGCCCACAC
53098675 AGCCTGGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:53098740 original size:17 final size:18
Alignment explanation
Indices: 53098708--53098745 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
53098698 CCGTGTGGCT
*
53098708 TGCTCATGTGGGCCCACA
1 TGCTCATATGGGCCCACA
53098726 TGCTCATAT-GGCCCACA
1 TGCTCATATGGGCCCACA
53098743 TGC
1 TGC
53098746 CCAATCTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (18 bp):
TGCTCATATGGGCCCACA
Found at i:53108728 original size:21 final size:21
Alignment explanation
Indices: 53108696--53108745 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
53108686 TGACATTTTT
53108696 AATTAA-ATAAAAATATTTAA
1 AATTAACATAAAAATATTTAA
53108716 AATTAACATAAAAATATTTAA
1 AATTAACATAAAAATATTTAA
53108737 AATTAACAT
1 AATTAACAT
53108746 TAAGTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTAACATAAAAATATTTAA
Found at i:53109618 original size:9 final size:9
Alignment explanation
Indices: 53109606--53109630 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53109596 TATTTTCTAA
53109606 TTTTTAATT
1 TTTTTAATT
53109615 TTTTTAATT
1 TTTTTAATT
53109624 TTTTTAA
1 TTTTTAA
53109631 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Done.