Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 120 of 135
Found at i:36145198 original size:2 final size:2
Alignment explanation
Indices: 36145191--36145262 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
36145181 TATTCAACAC
36145191 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
* * * *
36145233 AG AG GG AG AG GG AG AG GG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
36145263 GTATGATCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36146117 original size:17 final size:16
Alignment explanation
Indices: 36146089--36146137 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
36146079 TTATTAATTG
36146089 TTAAAAATATAAATAA
1 TTAAAAATATAAATAA
36146105 TTAAAATATATAAATAA
1 TTAAAA-ATATAAATAA
*
36146122 TTTTAAAATA-AAATAA
1 -TTAAAAATATAAATAA
36146138 ACTAAAAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 12 0.40
17 13 0.43
18 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAAATATAAATAA
Found at i:36146129 original size:19 final size:19
Alignment explanation
Indices: 36146083--36146131 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
36146073 TAAAAGTTAT
36146083 TAATTGTTAAAA-ATATAAA
1 TAATT-TTAAAATATATAAA
36146102 TAA--TTAAAATATATAAA
1 TAATTTTAAAATATATAAA
36146119 TAATTTTAAAATA
1 TAATTTTAAAATA
36146132 AAATAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 10 0.37
19 11 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATTTTAAAATATATAAA
Found at i:36146379 original size:25 final size:26
Alignment explanation
Indices: 36146348--36146420 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
36146338 TCTTTTATTT
36146348 TATGAAATTATTAAAAATATGTATAA
1 TATGAAATTATTAAAAATATGTATAA
* * **
36146374 TA-GAAAATT-TT-AAATTATTTTATTT
1 TATG-AAATTATTAAAAATA-TGTATAA
36146399 TATGAAATTATTAAAAATATGT
1 TATGAAATTATTAAAAATATGT
36146421 GAATTTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
24 5 0.14
25 14 0.39
26 12 0.33
27 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (26 bp):
TATGAAATTATTAAAAATATGTATAA
Found at i:36146405 original size:26 final size:26
Alignment explanation
Indices: 36146334--36146413 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
36146324 CATTAGGTTC
*
36146334 AAATTCTTTTATTTTATGAAATTATT
1 AAATTATTTTATTTTATGAAATTATT
* * **
36146360 AAA-AATATGTATAATA-GAAAATT-TT
1 AAATTAT-TTTATTTTATG-AAATTATT
36146385 AAATTATTTTATTTTATGAAATTATT
1 AAATTATTTTATTTTATGAAATTATT
36146411 AAA
1 AAA
36146414 AATATGTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (26 bp):
AAATTATTTTATTTTATGAAATTATT
Found at i:36147044 original size:82 final size:82
Alignment explanation
Indices: 36146958--36147119 Score: 209
Period size: 82 Copynumber: 2.0 Consensus size: 82
36146948 TAAGTGACAC
* *
36146958 ATTTTGTTAATAAAAAAGTAAATTTTAATAATATTAAGTATAATTGAAAATATTAAAAC-TAATA
1 ATTTTGTAAATAAAAAAGTAAATTTTAATAATATTAAATATAATTGAAAATATT-AAACTTAATA
36147022 ATCCGTATTTTATTTGGT
65 ATCCGTATTTTATTTGGT
* * ** * * *
36147040 ATTTTGTAAATAATAAATTATTTTTTATTGATATTAAATATTATTGAAAATATTAAACTTAATAA
1 ATTTTGTAAATAAAAAAGTAAATTTTAATAATATTAAATATAATTGAAAATATTAAACTTAATAA
**
36147105 TTTGTATTTTATTTG
66 TCCGTATTTTATTTG
36147120 AGGCGGGTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 4 0.06
82 64 0.94
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (82 bp):
ATTTTGTAAATAAAAAAGTAAATTTTAATAATATTAAATATAATTGAAAATATTAAACTTAATAA
TCCGTATTTTATTTGGT
Found at i:36149312 original size:74 final size:74
Alignment explanation
Indices: 36149182--36149321 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 74
36149172 ATTTGATATA
* *
36149182 TACACAATTGAGATATGATAAAATAATTGCAACAATAGTTATTAAGATTAAAAAAGCTTATATTT
1 TACACAATTGAGATATGATAAAATAATTGCAACAATAGTTATTAAGATTAAAAAAGCATAAATTT
36149247 TACTTTTTT
66 TACTTTTTT
* * * *
36149256 TACACAATTGAGATATGATAAAATGATTGCAACAATAGTTATTGAGATTTAGAAAGCATAAATTT
1 TACACAATTGAGATATGATAAAATAATTGCAACAATAGTTATTAAGATTAAAAAAGCATAAATTT
36149321 T
66 T
36149322 GATGAAAGGG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (74 bp):
TACACAATTGAGATATGATAAAATAATTGCAACAATAGTTATTAAGATTAAAAAAGCATAAATTT
TACTTTTTT
Found at i:36155701 original size:14 final size:14
Alignment explanation
Indices: 36155682--36155709 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36155672 ATCTCAATCT
36155682 TAAATCTTAAACCC
1 TAAATCTTAAACCC
36155696 TAAATCTTAAACCC
1 TAAATCTTAAACCC
36155710 AAACTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:36155849 original size:118 final size:118
Alignment explanation
Indices: 36155641--36155876 Score: 445
Period size: 118 Copynumber: 2.0 Consensus size: 118
36155631 ATAATTTTGG
* * *
36155641 TAATTTTTTTACCCTGAACACTGAATCTAGAATCTCAATCTTAAATCTTAAACCCTAAATCTTAA
1 TAATTTTTTTACCCAGAACACTGAATCTAGAATCCCAATCTTAAACCTTAAACCCTAAATCTTAA
36155706 ACCCAAACTCATAACTCATAACCCCAAACCCTTAAACATTGAACCTCAAACTC
66 ACCCAAACTCATAACTCATAACCCCAAACCCTTAAACATTGAACCTCAAACTC
36155759 TAATTTTTTTACCCAGAACACTGAATCTAGAATCCCAATCTTAAACCTTAAACCCTAAATCTTAA
1 TAATTTTTTTACCCAGAACACTGAATCTAGAATCCCAATCTTAAACCTTAAACCCTAAATCTTAA
36155824 ACCCAAACTCATAACTCATAACCCCAAACCCTTAAACATTGAACCTCAAACTC
66 ACCCAAACTCATAACTCATAACCCCAAACCCTTAAACATTGAACCTCAAACTC
36155877 GTAACACCGA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.39, C:0.30, G:0.03, T:0.28
Consensus pattern (118 bp):
TAATTTTTTTACCCAGAACACTGAATCTAGAATCCCAATCTTAAACCTTAAACCCTAAATCTTAA
ACCCAAACTCATAACTCATAACCCCAAACCCTTAAACATTGAACCTCAAACTC
Found at i:36157669 original size:3 final size:3
Alignment explanation
Indices: 36157661--36157685 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36157651 TCAGAAGCAC
36157661 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
36157686 AGTATTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:36163609 original size:113 final size:113
Alignment explanation
Indices: 36163411--36163643 Score: 466
Period size: 113 Copynumber: 2.1 Consensus size: 113
36163401 ACTTTGGGAT
36163411 GGAGAAATTTGATTTAAGCTTCTATTTGGATGCATGCGAAATCTGATTCTGGTATGACGTATGTT
1 GGAGAAATTTGATTTAAGCTTCTATTTGGATGCATGCGAAATCTGATTCTGGTATGACGTATGTT
36163476 AAAGATCCTAAGCTGGCTAATTGTATTTATGATGCAGCACCAACCGAA
66 AAAGATCCTAAGCTGGCTAATTGTATTTATGATGCAGCACCAACCGAA
36163524 GGAGAAATTTGATTTAAGCTTCTATTTGGATGCATGCGAAATCTGATTCTGGTATGACGTATGTT
1 GGAGAAATTTGATTTAAGCTTCTATTTGGATGCATGCGAAATCTGATTCTGGTATGACGTATGTT
36163589 AAAGATCCTAAGCTGGCTAATTGTATTTATGATGCAGCACCAACCGAA
66 AAAGATCCTAAGCTGGCTAATTGTATTTATGATGCAGCACCAACCGAA
36163637 GGAGAAA
1 GGAGAAA
36163644 ACTGGAAGCT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (113 bp):
GGAGAAATTTGATTTAAGCTTCTATTTGGATGCATGCGAAATCTGATTCTGGTATGACGTATGTT
AAAGATCCTAAGCTGGCTAATTGTATTTATGATGCAGCACCAACCGAA
Found at i:36167335 original size:2 final size:2
Alignment explanation
Indices: 36167328--36167352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36167318 TGCAGTAAGT
36167328 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
36167353 TTTTTTTTTT
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:36167548 original size:12 final size:12
Alignment explanation
Indices: 36167531--36167556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36167521 GTAGAAATCT
36167531 TTGTGGCTAAAG
1 TTGTGGCTAAAG
36167543 TTGTGGCTAAAG
1 TTGTGGCTAAAG
36167555 TT
1 TT
36167557 TAAACTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (12 bp):
TTGTGGCTAAAG
Found at i:36183489 original size:13 final size:11
Alignment explanation
Indices: 36183457--36183499 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
36183447 CCATTTTCTA
*
36183457 AATAAAATAAT
1 AATAAAATATT
36183468 AAT-AAATATTT
1 AATAAAATA-TT
36183479 AAGTAAAATATT
1 AA-TAAAATATT
36183491 AATAAAATA
1 AATAAAATA
36183500 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:36183529 original size:27 final size:26
Alignment explanation
Indices: 36183464--36183530 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
36183454 CTAAATAAAA
* *
36183464 TAATAATAAATATTTAAGTAAAATAT
1 TAATAAAAAATATTTAACTAAAATAT
*
36183490 TAATAAAATAATATTTAACT-AATTAAT
1 TAATAAAA-AATATTTAACTAAAAT-AT
36183517 TAATGAAAAAATAT
1 TAAT-AAAAAATAT
36183531 CTCCAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.29
27 21 0.60
28 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (26 bp):
TAATAAAAAATATTTAACTAAAATAT
Found at i:36200047 original size:20 final size:19
Alignment explanation
Indices: 36200024--36200075 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
36200014 AAATTGTCAA
36200024 AAGTACAATTAAATACTACC
1 AAGTACAATTAAATACTA-C
* *
36200044 AAGTAAAAAATT-AATACTAT
1 AAGT--ACAATTAAATACTAC
36200064 AAGTACAATTAA
1 AAGTACAATTAA
36200076 GGAGCTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 8 0.31
21 7 0.27
22 5 0.19
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.27
Consensus pattern (19 bp):
AAGTACAATTAAATACTAC
Found at i:36202170 original size:16 final size:17
Alignment explanation
Indices: 36202141--36202173 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
36202131 AATAAAATAA
36202141 TTTATAAATGTGATAAAT
1 TTTATAAA-GTGATAAAT
36202159 TTTATAAA-TGATAAA
1 TTTATAAAGTGATAAA
36202174 CATATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTATAAAGTGATAAAT
Found at i:36203506 original size:29 final size:29
Alignment explanation
Indices: 36203482--36203539 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
36203472 ATCATGTCAG
* *
36203482 AGATACAGTTACAGATGTAGACATGATAC
1 AGATACAGTTACAAATGCAGACATGATAC
* *
36203511 AGATACCGTTACAAATGCAGACGTGATAC
1 AGATACAGTTACAAATGCAGACATGATAC
36203540 CCCCATCCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (29 bp):
AGATACAGTTACAAATGCAGACATGATAC
Found at i:36203687 original size:40 final size:40
Alignment explanation
Indices: 36203597--36203741 Score: 148
Period size: 40 Copynumber: 3.6 Consensus size: 40
36203587 TCGGTATGAC
* * **
36203597 ATGTTGCAGTGTTTATAGTGTCACTGCTA-GTTAAGTGGTA
1 ATGTTGCAGTGTTTACAGTGTCACTGC-AGGTTCAGTTATA
** *
36203637 ACCTTGCAGTGTTTATAGTGTCACTGCAGGTTCAGTTATA
1 ATGTTGCAGTGTTTACAGTGTCACTGCAGGTTCAGTTATA
* * * * * *
36203677 ATGTTACAGTGTTTACAGTGCCACTACCGGGTCAATTATA
1 ATGTTGCAGTGTTTACAGTGTCACTGCAGGTTCAGTTATA
*
36203717 ATATTGCAGTGTTTACAGTGTCACT
1 ATGTTGCAGTGTTTACAGTGTCACT
36203742 ACCAACTCAG
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 86 0.99
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (40 bp):
ATGTTGCAGTGTTTACAGTGTCACTGCAGGTTCAGTTATA
Found at i:36204300 original size:55 final size:55
Alignment explanation
Indices: 36204238--36204342 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
36204228 CACACACTCG
* * *
36204238 TGTGCCAGCCCGTGTGCTTCTAAACAGTATAGACACACACCCTAACACACGTCCA
1 TGTGCCAGCCCGTGTGCCTCCAAACAGTATACACACACACCCTAACACACGTCCA
*
36204293 TGTGCCAGCCCGTGTGCCTCCAAACAGTTTACACACACACCCTAACACAC
1 TGTGCCAGCCCGTGTGCCTCCAAACAGTATACACACACACCCTAACACAC
36204343 CTTGTGTGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.29, C:0.37, G:0.15, T:0.19
Consensus pattern (55 bp):
TGTGCCAGCCCGTGTGCCTCCAAACAGTATACACACACACCCTAACACACGTCCA
Found at i:36206206 original size:29 final size:30
Alignment explanation
Indices: 36206158--36206214 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
36206148 GAATTTAATC
*
36206158 AAATCAAAATTTCATATATAAAATTACATA
1 AAATCAAAAGTTCATATATAAAATTACATA
* *
36206188 AAATC-AAAGTTCATGTATACAATTACA
1 AAATCAAAAGTTCATATATAAAATTACA
36206215 CATTGAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATAAAATTACATA
Found at i:36212951 original size:17 final size:17
Alignment explanation
Indices: 36212929--36212967 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
36212919 AGGTGGAGAA
* *
36212929 CTTGTTCGTAGTGAGTT
1 CTTGTTCGTAGAGAATT
36212946 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
36212963 CTTGT
1 CTTGT
36212968 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:36213053 original size:23 final size:22
Alignment explanation
Indices: 36213009--36213057 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
36212999 GAATTCTTAT
* *
36213009 TAAAATAAAATACAGTGGCAAAA
1 TAAAATAAAATAAAGT-GCCAAA
36213032 TAAAATAAAAGTAAAGT-CCAAA
1 TAAAATAAAA-TAAAGTGCCAAA
36213054 TAAA
1 TAAA
36213058 CTAGACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 10 0.43
24 5 0.22
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.18
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCCAAA
Found at i:36216134 original size:13 final size:13
Alignment explanation
Indices: 36216116--36216140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36216106 CAAATTATGT
36216116 TAAAAATTAAATA
1 TAAAAATTAAATA
36216129 TAAAAATTAAAT
1 TAAAAATTAAAT
36216141 CTCAAATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATTAAATA
Found at i:36222707 original size:6 final size:6
Alignment explanation
Indices: 36222696--36222722 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
36222686 AGAAGCTAAA
36222696 CCATCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCA
36222723 ACCGCTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATCT
Found at i:36234480 original size:13 final size:14
Alignment explanation
Indices: 36234462--36234490 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36234452 AATTTAAAAC
36234462 AAAGAAGA-AGAAA
1 AAAGAAGAGAGAAA
36234475 AAAGAAGAGAGAAA
1 AAAGAAGAGAGAAA
36234489 AA
1 AA
36234491 TAATCATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAGAAGAGAGAAA
Found at i:36238075 original size:18 final size:18
Alignment explanation
Indices: 36238032--36238086 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
36238022 TGCTAGTTTT
36238032 TTTTAATTATTTATAATA
1 TTTTAATTATTTATAATA
36238050 TATTTAATATATTTATAA-A
1 T-TTTAAT-TATTTATAATA
36238069 TTTTAATTATTTCATAAT
1 TTTTAATTATTT-ATAAT
36238087 TTATTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 5 0.15
18 11 0.33
19 8 0.24
20 9 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAATTATTTATAATA
Found at i:36257609 original size:14 final size:14
Alignment explanation
Indices: 36257590--36257618 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
36257580 TTTCAAATGG
36257590 ATTAATATAGAGAT
1 ATTAATATAGAGAT
36257604 ATTAATATAGAGAT
1 ATTAATATAGAGAT
36257618 A
1 A
36257619 CTTGAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
ATTAATATAGAGAT
Found at i:36273193 original size:16 final size:16
Alignment explanation
Indices: 36273172--36273216 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
36273162 ATAACACGAA
* *
36273172 GAATGAATGATTATAC
1 GAATGAATAAATATAC
36273188 GAATGAATAAATATAC
1 GAATGAATAAATATAC
36273204 GAA--AATAAATATA
1 GAATGAATAAATATA
36273217 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 10 0.37
16 17 0.63
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (16 bp):
GAATGAATAAATATAC
Found at i:36273212 original size:14 final size:14
Alignment explanation
Indices: 36273183--36273233 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
36273173 AATGAATGAT
36273183 TATACGAATGAATAAA
1 TATACGAA--AATAAA
36273199 TATACGAAAATAAA
1 TATACGAAAATAAA
**
36273213 TATAAAAAAATAAA
1 TATACGAAAATAAA
36273227 -ATACGAA
1 TATACGAA
36273234 TCAGGAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 5 0.16
14 18 0.58
16 8 0.26
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.22
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:36273388 original size:29 final size:29
Alignment explanation
Indices: 36273356--36273635 Score: 86
Period size: 29 Copynumber: 9.8 Consensus size: 29
36273346 TTTCAAAGAG
*
36273356 TTAGGGATTAAAATATAATTTTGAAAAGT
1 TTAGGGATAAAAATATAATTTTGAAAAGT
* **
36273385 TTAGGGGA-AAAAATGTAATTTTAGGGAAGT
1 TTA-GGGATAAAAATATAATTTT-GAAAAGT
* *
36273415 TT-GGGGTAAAAATATGATTTTTGAAAAGT
1 TTAGGGATAAAAATAT-AATTTTGAAAAGT
** * *
36273444 TT-GGG-GCAAAATGTAATTTTGGGAAAG-
1 TTAGGGATAAAAATATAATTTT-GAAAAGT
** * * *
36273471 TTCCGGA-AAAATTGTAAATTTTGAGAAGT
1 TTAGGGATAAAAATAT-AATTTTGAAAAGT
* * * * *
36273500 TCAAGGG-TAAAAATGTGATTTTTAGAAGT
1 T-TAGGGATAAAAATATAATTTTGAAAAGT
** *
36273529 TT-GGG-GCAAAATGA-AATTTTTGAGAAGT
1 TTAGGGATAAAAAT-ATAA-TTTTGAAAAGT
* *
36273557 TTGAGGG-T-AAAATGTGATTTTTG-AAAGT
1 TT-AGGGATAAAAATAT-AATTTTGAAAAGT
* *
36273585 TTAAGGG-CAAAAATAAAATTTTTGAAAAGT
1 TT-AGGGATAAAAATATAA-TTTTGAAAAGT
* *
36273615 TTAGGG-TTAAAATGTAATTTT
1 TTAGGGATAAAAATATAATTTT
36273636 AGGAAATTTT
Statistics
Matches: 187, Mismatches: 44, Indels: 41
0.69 0.16 0.15
Matches are distributed among these distances:
27 16 0.09
28 53 0.28
29 82 0.44
30 36 0.19
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
TTAGGGATAAAAATATAATTTTGAAAAGT
Found at i:36273425 original size:57 final size:56
Alignment explanation
Indices: 36273365--36273648 Score: 197
Period size: 58 Copynumber: 5.0 Consensus size: 56
36273355 GTTAGGGATT
36273365 AAAATATAATTTTGAAAAGTTTAGGGGAAAAAATGTAATTTTAGGGAAGTTTGGGGTA
1 AAAATATAATTTTGAAAAGTTTAGGGG-AAAAATGTAATTTTAGGGAAGTTTGGGG-A
* * **
36273423 AAAATATGATTTTTGAAAAGTTT-GGGGCAAAATGTAATTTT-GGGAAAG-TTCCGGA
1 AAAATAT-AATTTTGAAAAGTTTAGGGGAAAAATGTAATTTTAGGG-AAGTTTGGGGA
* * * * * *
36273478 AAAATTGTAAATTTTGAGAAGTTCAAGGGTAAAAATGTGATTTTTA--GAAGTTTGGGGC
1 AAAA-TAT-AATTTTGAAAAGTT-TAGGGGAAAAATGT-AATTTTAGGGAAGTTTGGGGA
* * * * * *
36273536 AAAATGA-AATTTTTGAGAAGTTT-GAGGGTAAAATGTGATTTT-TGAAAGTTTAAGGGCA
1 AAAAT-ATAA-TTTTGAAAAGTTTAG-GGGAAAAATGTAATTTTAGGGAAGTTT--GGGGA
* ** * *
36273594 AAAATAAAATTTTTGAAAAGTTTAGGGTTAAAATGTAATTTTAGGAAATTTTGGG
1 AAAATATAA-TTTTGAAAAGTTTAGGGGAAAAATGTAATTTTAGGGAAGTTTGGG
36273649 TTCAAAATGG
Statistics
Matches: 179, Mismatches: 29, Indels: 37
0.73 0.12 0.15
Matches are distributed among these distances:
55 10 0.06
56 38 0.21
57 36 0.20
58 68 0.38
59 27 0.15
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
AAAATATAATTTTGAAAAGTTTAGGGGAAAAATGTAATTTTAGGGAAGTTTGGGGA
Found at i:36273665 original size:58 final size:56
Alignment explanation
Indices: 36273374--36273657 Score: 213
Period size: 57 Copynumber: 4.9 Consensus size: 56
36273364 TAAAATATAA
* * * *
36273374 TTTTGAAAAGTTTAGGGGAAAAAATGTAATTTTAGGGAAGTTTGGGGTAAAAAT-ATGAT
1 TTTTGAAAAGTTTA-GGGTAAAAATGTAATTTTAGGAAAGTTT-GGG-CAAAATGA-AAT
** * ** *
36273433 TTTTGAAAAGTTT-GGGGCAAAATGTAATTTTGGGAAAGTTCCGGAAAAATTGTAAA-
1 TTTTGAAAAGTTTAGGGTAAAAATGTAATTTTAGGAAAGTTTGGGCAAAA-TG-AAAT
* * *
36273489 TTTTGAGAAGTTCAAGGGTAAAAATGTGATTTTTA-G-AAGTTTGGGGCAAAATGAAAT
1 TTTTGAAAAGTT-TAGGGTAAAAATGT-AATTTTAGGAAAGTTT-GGGCAAAATGAAAT
* * * *
36273546 TTTTGAGAAGTTTGAGGGT-AAAATGTGATTTT-TGAAAGTTTAAGGGCAAAAATAAAAT
1 TTTTGAAAAGTTT-AGGGTAAAAATGTAATTTTAGGAAAGTTT--GGGC-AAAATGAAAT
* *
36273604 TTTTGAAAAGTTTAGGGTTAAAATGTAATTTTAGGAAATTTTGGGTTCAAAATG
1 TTTTGAAAAGTTTAGGGTAAAAATGTAATTTTAGGAAAGTTTGGG--CAAAATG
36273658 GGATTTTTAA
Statistics
Matches: 182, Mismatches: 26, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
55 10 0.05
56 30 0.16
57 60 0.33
58 56 0.31
59 26 0.14
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
TTTTGAAAAGTTTAGGGTAAAAATGTAATTTTAGGAAAGTTTGGGCAAAATGAAAT
Found at i:36277156 original size:22 final size:22
Alignment explanation
Indices: 36277131--36277179 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
36277121 CTTAGCAAGC
36277131 AAAATGATAGCAAAACAATAGA
1 AAAATGATAGCAAAACAATAGA
* * *
36277153 AAAATGGTGGCAAAACAATAGC
1 AAAATGATAGCAAAACAATAGA
36277175 AAAAT
1 AAAAT
36277180 TTTTTAGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (22 bp):
AAAATGATAGCAAAACAATAGA
Found at i:36283880 original size:14 final size:14
Alignment explanation
Indices: 36283861--36283924 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
36283851 AAATTTAGTC
36283861 AAAATAAAATTAAG
1 AAAATAAAATTAAG
*
36283875 AAAATAACAACTT-TG
1 AAAATAA-AA-TTAAG
* * *
36283890 AATAT-AATTTAATC
1 AAAATAAAATTAA-G
36283904 AAAATAAAATTAAG
1 AAAATAAAATTAAG
36283918 AAAATAA
1 AAAATAA
36283925 CAACTTTGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
12 2 0.05
13 1 0.03
14 19 0.51
15 13 0.35
16 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (14 bp):
AAAATAAAATTAAG
Found at i:36283900 original size:43 final size:42
Alignment explanation
Indices: 36283848--36283937 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 42
36283838 GCTTAAAATA
*
36283848 AATAAATTTAGTCAAAATAAAATTAAGAAAATAACAACTTTG
1 AATAAATTTAATCAAAATAAAATTAAGAAAATAACAACTTTG
36283890 AATATAATTTAATCAAAATAAAATTAAGAAAATAACAACTTTG
1 AATA-AATTTAATCAAAATAAAATTAAGAAAATAACAACTTTG
36283933 AATAA
1 AATAA
36283938 GCTTATTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 5 0.11
43 41 0.89
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.29
Consensus pattern (42 bp):
AATAAATTTAATCAAAATAAAATTAAGAAAATAACAACTTTG
Found at i:36299194 original size:11 final size:12
Alignment explanation
Indices: 36299169--36299197 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
36299159 GATAATGCTT
36299169 AATTCTTTCTGA
1 AATTCTTTCTGA
36299181 AATTCTTT-TGA
1 AATTCTTTCTGA
36299192 AATTCT
1 AATTCT
36299198 ATCATTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (12 bp):
AATTCTTTCTGA
Found at i:36301720 original size:69 final size:69
Alignment explanation
Indices: 36301609--36301750 Score: 248
Period size: 69 Copynumber: 2.1 Consensus size: 69
36301599 GACTCGACTC
* * * *
36301609 TATTGAATGCCCATTCCTACCAATAGCTCCTCTCCAATCCTTAAATAAGAGGATAGTTAACTTAA
1 TATTGAATGCCCATTCCTACCAATAGCTCATCTCCAATCCTTAAATAAGAAGATAGTGAACTCAA
36301674 AATG
66 AATG
36301678 TATTGAATGCCCATTCCTACCAATAGCTCATCTCCAATCCTTAAATAAGAAGATAGTGAACTCAA
1 TATTGAATGCCCATTCCTACCAATAGCTCATCTCCAATCCTTAAATAAGAAGATAGTGAACTCAA
36301743 AATG
66 AATG
36301747 TATT
1 TATT
36301751 TAAATCACGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (69 bp):
TATTGAATGCCCATTCCTACCAATAGCTCATCTCCAATCCTTAAATAAGAAGATAGTGAACTCAA
AATG
Found at i:36303553 original size:31 final size:31
Alignment explanation
Indices: 36303517--36303605 Score: 74
Period size: 31 Copynumber: 2.9 Consensus size: 31
36303507 AGTATTTAAT
*
36303517 TTTTTTGTCCAATTTAATAATTAAACTTGACA
1 TTTTTTCT-CAATTTAATAATTAAACTTGACA
* ** *
36303549 TTTTTTCTTAATTTGGTACTTAAACTTGACA
1 TTTTTTCTCAATTTAATAATTAAACTTGACA
* * *
36303580 CCTTTTT-T-AAGTTGATAATTAAACTT
1 -TTTTTTCTCAATTTAATAATTAAACTT
36303606 TTGGGTCCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 15 0.32
31 20 0.43
32 12 0.26
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTTTTCTCAATTTAATAATTAAACTTGACA
Found at i:36303604 original size:30 final size:31
Alignment explanation
Indices: 36303533--36303605 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
36303523 GTCCAATTTA
** *
36303533 ATAATTAAACTTGACATTTTTTCTTAATTTG
1 ATAATTAAACTTGACACCTTTTCTTAAGTTG
* *
36303564 GTACTTAAACTTGACACCTTTT-TTAAGTTG
1 ATAATTAAACTTGACACCTTTTCTTAAGTTG
36303594 ATAATTAAACTT
1 ATAATTAAACTT
36303606 TTGGGTCCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 17 0.49
31 18 0.51
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
ATAATTAAACTTGACACCTTTTCTTAAGTTG
Found at i:36303928 original size:60 final size:59
Alignment explanation
Indices: 36303827--36303999 Score: 186
Period size: 59 Copynumber: 2.9 Consensus size: 59
36303817 AATTGAATTT
* * * * *
36303827 AAAAAAAGCTTATGTACAAAATTAGGAAAAAAATGCCAAGTTCAAGTATCAAATTGGATCC
1 AAAAAAAGTTTAAGTACAAAATTA-GAAAAAAATGTCAAGTTCAGGTATCAAATTGGAT-A
* * * *
36303888 AAAAAAAGTTTAGGTATC-AAATTAGAAAAAATTGTCAAGTTCAGGAATCAAATTGGGTA
1 AAAAAAAGTTTAAGTA-CAAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGGATA
* * * * *
36303947 AAAAAAAGTTCAAGTACTAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAAT
1 AAAAAAAGTTTAAGTACAAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAAT
36304000 ATTATATTGA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.01
59 45 0.47
60 29 0.30
61 20 0.21
62 1 0.01
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (59 bp):
AAAAAAAGTTTAAGTACAAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGGATA
Found at i:36304633 original size:59 final size:58
Alignment explanation
Indices: 36304540--36304721 Score: 231
Period size: 59 Copynumber: 3.1 Consensus size: 58
36304530 TTTATATATT
* *
36304540 AAAAAATAAAAAAATAATATTATATTAGTGGAGGGCTATTAAATGGAGGCATTACATGGG
1 AAAAAAT-AAAAAATAATATTATATTAGTGGAGGGTTATCAAATGGAGGCATTACA-GGG
* * ** **
36304600 AAAAAATAAAAAATAATATTATATTAATAGAGGGTTATCAAA-CAACGGCACCACAGGG
1 AAAAAATAAAAAATAATATTATATTAGTGGAGGGTTATCAAATGGA-GGCATTACAGGG
* *
36304658 AAAAAAATAAAAAATAATATTATATTAGTGGAGGGTTATCAAATGGCGGCATTACAGAG
1 -AAAAAATAAAAAATAATATTATATTAGTGGAGGGTTATCAAATGGAGGCATTACAGGG
36304717 AAAAA
1 AAAAA
36304722 TTATACAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
58 9 0.09
59 87 0.84
60 7 0.07
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.24
Consensus pattern (58 bp):
AAAAAATAAAAAATAATATTATATTAGTGGAGGGTTATCAAATGGAGGCATTACAGGG
Found at i:36304813 original size:11 final size:11
Alignment explanation
Indices: 36304778--36305012 Score: 73
Period size: 11 Copynumber: 21.0 Consensus size: 11
36304768 AAAATACACA
36304778 AAAAATTAAA-T
1 AAAAA-TAAATT
*
36304789 AACAAATCAATT
1 AA-AAATAAATT
*
36304801 AAAAATAACTT
1 AAAAATAAATT
*
36304812 AAAAATTAAATA
1 AAAAA-TAAATT
36304824 AAAAATAAA--
1 AAAAATAAATT
* *
36304833 AATATTAAA-T
1 AAAAATAAATT
36304843 AACAAATAAATT
1 AA-AAATAAATT
36304855 AAAAATTAAATTT
1 AAAAA-TAAA-TT
* * *
36304868 ACTCAACTAAATA
1 A--AAAATAAATT
36304881 AAAACATTAAA-T
1 AAAA-A-TAAATT
*
36304893 AACAAATCAATT
1 AA-AAATAAATT
36304905 AAAAATTAAA-T
1 AAAAA-TAAATT
36304916 AACAAATAAA--
1 AA-AAATAAATT
* *
36304926 AACATTAAA-T
1 AAAAATAAATT
*
36304936 AACAAATCAATT
1 AA-AAATAAATT
*
36304948 AAAAATAACTT
1 AAAAATAAATT
*
36304959 AAAATTAAA-T
1 AAAAATAAATT
36304969 AACAAATAAA--
1 AA-AAATAAATT
* *
36304979 AATATTAAA-T
1 AAAAATAAATT
*
36304989 AACAAATCAATT
1 AA-AAATAAATT
36305001 AAAAATTAAATT
1 AAAAA-TAAATT
36305013 TACTCAATTA
Statistics
Matches: 167, Mismatches: 33, Indels: 47
0.68 0.13 0.19
Matches are distributed among these distances:
9 17 0.10
10 13 0.08
11 75 0.45
12 45 0.27
13 11 0.07
14 4 0.02
15 2 0.01
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:36304849 original size:27 final size:27
Alignment explanation
Indices: 36304777--36304852 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
36304767 TAAAATACAC
* *
36304777 AAAAA-ATTAAATAACAAAT--CAATT
1 AAAAATATTAAATAACAAATAAAAAAT
*
36304801 AAAAATAACTTAAA-AATTAAATAAAAAAT
1 AAAAAT-A-TTAAATAA-CAAATAAAAAAT
36304830 AAAAATATTAAATAACAAATAAA
1 AAAAATATTAAATAACAAATAAA
36304853 TTAAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
24 5 0.12
26 3 0.07
27 21 0.51
28 3 0.07
29 9 0.22
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAAATATTAAATAACAAATAAAAAAT
Found at i:36304857 original size:43 final size:43
Alignment explanation
Indices: 36304803--36304953 Score: 194
Period size: 43 Copynumber: 3.3 Consensus size: 43
36304793 AATCAATTAA
* *
36304803 AAATAACTTAAAAATTAAATAAAAAATAAAAATATTAAATAAC
1 AAATAAATTAAAAATTAAATAAAAAATAAAAACATTAAATAAC
36304846 AAATAAATTAAAAATTAAATTTACTCAACTAAATAAAAACATTAAATAAC
1 AAATAAATTAAAAATTAAA--TA---AA--AAATAAAAACATTAAATAAC
* *
36304896 AAATCAATTAAAAATTAAATAACAAATAAAAACATTAAATAAC
1 AAATAAATTAAAAATTAAATAAAAAATAAAAACATTAAATAAC
*
36304939 AAATCAATTAAAAAT
1 AAATAAATTAAAAAT
36304954 AACTTAAAAT
Statistics
Matches: 97, Mismatches: 4, Indels: 14
0.84 0.03 0.12
Matches are distributed among these distances:
43 53 0.55
45 3 0.03
48 4 0.04
50 37 0.38
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (43 bp):
AAATAAATTAAAAATTAAATAAAAAATAAAAACATTAAATAAC
Found at i:36304890 original size:50 final size:48
Alignment explanation
Indices: 36304826--36305062 Score: 304
Period size: 50 Copynumber: 4.9 Consensus size: 48
36304816 ATTAAATAAA
* *
36304826 AAATAAAAATATTAAATAACAAATAAATTAAAAATTAAATTTACTCAAC
1 AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT-AAC
36304875 TAAATAAAAACATTAAATAACAAATCAATTAAAAATT-AA---A-TAAC
1 -AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACTAAC
* *
36304919 AAATAAAAACATTAAATAACAAATCAATTAAAAATAACTTAAAATTAAATAAC
1 AAATAAAAACATTAAATAACAAATCAATT--AAA-AA-TT-AAATTTACTAAC
* *
36304972 AAATAAAAATATTAAATAACAAATCAATTAAAAATTAAATTTACTCAATT
1 AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACT-AA-C
36305022 AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATT
1 AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATT
36305063 AAACAAAACA
Statistics
Matches: 168, Mismatches: 7, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
43 29 0.17
44 3 0.02
45 4 0.02
46 3 0.02
47 2 0.01
48 7 0.04
49 8 0.05
50 76 0.45
51 3 0.02
52 1 0.01
53 32 0.19
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (48 bp):
AAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTTACTAAC
Found at i:36304966 original size:53 final size:52
Alignment explanation
Indices: 36304896--36305065 Score: 213
Period size: 53 Copynumber: 3.2 Consensus size: 52
36304886 ATTAAATAAC
36304896 AAATCAATTAAAAATTAAATAACAAATAAAAACATTAAATAACAAATCAATTAA
1 AAAT-AATT-AAAATTAAATAACAAATAAAAACATTAAATAACAAATCAATTAA
*
36304950 AAATAACTTAAAATTAAATAACAAATAAAAATATTAAATAACAAATCAATT--
1 AAATAA-TTAAAATTAAATAACAAATAAAAACATTAAATAACAAATCAATTAA
* * *
36305001 AAA-AATT-AAATTTACTCAATTAAATAAAAACATTAAATAACAAATCAATTAA
1 AAATAATTAAAATTAAAT-AA-CAAATAAAAACATTAAATAACAAATCAATTAA
36305053 AAATTAAATTAAA
1 AAA-T-AATTAAA
36305066 CAAAACAAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
48 7 0.07
49 4 0.04
50 30 0.29
51 3 0.03
52 3 0.03
53 43 0.42
54 6 0.06
55 4 0.04
56 2 0.02
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (52 bp):
AAATAATTAAAATTAAATAACAAATAAAAACATTAAATAACAAATCAATTAA
Found at i:36304993 original size:146 final size:146
Alignment explanation
Indices: 36304777--36305061 Score: 527
Period size: 146 Copynumber: 2.0 Consensus size: 146
36304767 TAAAATACAC
36304777 AAAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAAAAAATAAAAATATTAAA
1 AAAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAAAAAATAAAAATATTAAA
36304842 TAACAAATAAATTAAAAATTAAATTTACTCAACTAAATAAAAACATTAAATAACAAATCAATTAA
66 TAACAAATAAATTAAAAATTAAATTTACTCAACTAAATAAAAACATTAAATAACAAATCAATTAA
36304907 AAATTAAATAACAAAT
131 AAATTAAATAACAAAT
*
36304923 AAAAACATTAAATAACAAATCAATTAAAAATAACTT-AAAATTAAATAACAAATAAAAATATTAA
1 AAAAA-ATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAAAAAATAAAAATATTAA
* *
36304987 ATAACAAATCAATTAAAAATTAAATTTACTCAATTAAATAAAAACATTAAATAACAAATCAATTA
65 ATAACAAATAAATTAAAAATTAAATTTACTCAACTAAATAAAAACATTAAATAACAAATCAATTA
36305052 AAAATTAAAT
130 AAAATTAAAT
36305062 TAAACAAAAC
Statistics
Matches: 135, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
146 105 0.78
147 30 0.22
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (146 bp):
AAAAAATTAAATAACAAATCAATTAAAAATAACTTAAAAATTAAATAAAAAATAAAAATATTAAA
TAACAAATAAATTAAAAATTAAATTTACTCAACTAAATAAAAACATTAAATAACAAATCAATTAA
AAATTAAATAACAAAT
Found at i:36305069 original size:25 final size:23
Alignment explanation
Indices: 36304959--36305061 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 23
36304949 AAAATAACTT
36304959 AAAATTAAATAACAAAT-AA--A
1 AAAATTAAATAACAAATCAATTA
*
36304979 AATATTAAATAACAAATCAATTA
1 AAAATTAAATAACAAATCAATTA
* * * *
36305002 AAAATTAAATTTACTCAATTAAATAA
1 AAAATTAAA--TA-ACAAATCAATTA
36305028 AAACATTAAATAACAAATCAATTA
1 AAA-ATTAAATAACAAATCAATTA
36305052 AAAATTAAAT
1 AAAATTAAAT
36305062 TAAACAAAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 16 0.24
21 2 0.03
23 16 0.24
24 11 0.17
25 4 0.06
26 11 0.17
27 6 0.09
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTAAATAACAAATCAATTA
Found at i:36305075 original size:30 final size:32
Alignment explanation
Indices: 36305039--36305103 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
36305029 AACATTAAAT
*
36305039 AACAAATCAA-TTAAAA-ATTAAAT-TAAACAA
1 AACAAAT-AACTTAAAACAATAAATATAAACAA
36305069 AACAAATAACTTAAAACAATAAATACTAAACAA
1 AACAAATAACTTAAAACAATAAATA-TAAACAA
36305102 AA
1 AA
36305104 TATAACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (32 bp):
AACAAATAACTTAAAACAATAAATATAAACAA
Found at i:36305129 original size:103 final size:102
Alignment explanation
Indices: 36304825--36305093 Score: 258
Period size: 103 Copynumber: 2.7 Consensus size: 102
36304815 AATTAAATAA
* * **
36304825 AAAATAAAAATATTAAATAACAAATAAATTAAAAATTAAATT----TACTCAACTAAATAAAAAC
1 AAAATAAAAACATTAAATAACAAATCAATTAAAAA-TAAATTAAAATAAACAAC-AAATAAAAAC
* *
36304886 ATTAAATAACAAATCAATTAAAAATT-AA---A-T-AA-
64 AATAAATAACAAATCAAATAAAAATTAAATTTACTCAAT
* * * *
36304918 CAAATAAAAACATTAAATAACAAATCAATTAAAAATAACTTAAAATTAAATAACAAATAAAAATA
1 AAAATAAAAACATTAAATAACAAATCAATTAAAAATAAATTAAAA-TAAACAACAAATAAAAACA
* *
36304983 TTAAATAACAAATCAATTAAAAATTAAATTTACTCAAT
65 ATAAATAACAAATCAAATAAAAATTAAATTTACTCAAT
* *
36305021 TAAATAAAAACATTAAATAACAAATCAATTAAAAATTAAATTAAACA-AAACAA-ATAACTTAAA
1 AAAATAAAAACATTAAATAACAAATCAATTAAAAA-TAAATTAAA-ATAAACAACA-AA-TAAAA
36305084 ACAATAAATA
62 ACAATAAATA
36305094 CTAAACAAAA
Statistics
Matches: 146, Mismatches: 14, Indels: 21
0.81 0.08 0.12
Matches are distributed among these distances:
92 5 0.03
93 32 0.22
96 35 0.24
97 7 0.05
100 1 0.01
101 1 0.01
102 3 0.02
103 41 0.28
104 20 0.14
105 1 0.01
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (102 bp):
AAAATAAAAACATTAAATAACAAATCAATTAAAAATAAATTAAAATAAACAACAAATAAAAACAA
TAAATAACAAATCAAATAAAAATTAAATTTACTCAAT
Found at i:36305348 original size:21 final size:21
Alignment explanation
Indices: 36305323--36305391 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
36305313 ATTCGTTATT
36305323 TTTTTCATGTATTTTGTATAA
1 TTTTTCATGTATTTTGTATAA
*** **
36305344 TTTTTCAGTGT-TCAAGTATTT
1 TTTTTCA-TGTATTTTGTATAA
**
36305365 TTTTTTGTGTATTTTGTATAA
1 TTTTTCATGTATTTTGTATAA
36305386 TTTTTC
1 TTTTTC
36305392 CTTGTAGTGC
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.64
Consensus pattern (21 bp):
TTTTTCATGTATTTTGTATAA
Found at i:36305600 original size:97 final size:92
Alignment explanation
Indices: 36305396--36305607 Score: 241
Period size: 93 Copynumber: 2.2 Consensus size: 92
36305386 TTTTTCCTTG
* * * * * *
36305396 TAGTGCCGTCATTTGATAA-CCTTCCATTAATATAATATTATTTTTTTATTTTTTAATATATAAA
1 TAGTGCCGCCATTTGATAATCCTTCCACTAATATAATATTATTTTTTAATATATAAATATATAAA
* *
36305460 TGTAAAAAAATTCATGTTAAAAAACTC
66 AGTAAAAAAATTCATGTCAAAAAACTC
*
36305487 TGGAGTGCCGCCATTTGATAATTC-TCCACTAATATAATATTATTTTTTAATATATAAATATAAT
1 T--AGTGCCGCCATTTGATAATCCTTCCACTAATATAATATTATTTTTTAATATATAAATAT-AT
36305551 AAAAGAATTAAAAAAATT-ATGTCAGAAAAACCTAC
63 AAAAG---TAAAAAAATTCATGTCA-AAAAA-CT-C
36305586 TAGTGCCGCCATTTGATAATCC
1 TAGTGCCGCCATTTGATAATCC
36305608 ATCACCTAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
91 1 0.01
93 49 0.49
94 7 0.07
96 5 0.05
97 35 0.35
98 2 0.02
99 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (92 bp):
TAGTGCCGCCATTTGATAATCCTTCCACTAATATAATATTATTTTTTAATATATAAATATATAAA
AGTAAAAAAATTCATGTCAAAAAACTC
Found at i:36306076 original size:16 final size:18
Alignment explanation
Indices: 36306043--36306090 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
36306033 AGCTTAGCTA
36306043 CTCCTTTCTTTTCCTTCCC
1 CTCCTTTCTTTT-CTTCCC
36306062 CTCCTTT-TTTT-TTCCC
1 CTCCTTTCTTTTCTTCCC
36306078 TCTCTCTTTCTTT
1 -CTC-CTTTCTTT
36306091 GTCTCCAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.19
17 3 0.12
18 8 0.31
19 10 0.38
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (18 bp):
CTCCTTTCTTTTCTTCCC
Found at i:36309305 original size:5 final size:5
Alignment explanation
Indices: 36309297--36309324 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
36309287 AAACTTTGTT
36309297 TTGGG TTGGG TTGGG TTGGG TTGGG TTG
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTG
36309325 CGTGGGTGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (5 bp):
TTGGG
Found at i:36324716 original size:25 final size:25
Alignment explanation
Indices: 36324682--36324729 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
36324672 ATTATTTTAT
*
36324682 TATATAAATA-ATTTTAAAATATGA
1 TATATAAATACATTTAAAAATATGA
36324706 TATATCAAATACATTTAAAAATAT
1 TATAT-AAATACATTTAAAAATAT
36324730 TAAAACAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
TATATAAATACATTTAAAAATATGA
Found at i:36337474 original size:22 final size:22
Alignment explanation
Indices: 36337432--36337474 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
36337422 AATCATTAAT
* *
36337432 AAATATTTTAAAAGTATAAAAG
1 AAATATTTTAAAAGAAAAAAAG
36337454 AAATA-TTTAAAATGAAAAAAA
1 AAATATTTTAAAA-GAAAAAAA
36337475 AACTTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
AAATATTTTAAAAGAAAAAAAG
Found at i:36337495 original size:20 final size:20
Alignment explanation
Indices: 36337473--36337511 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36337463 AAATGAAAAA
36337473 AAAACTT-GTAAAAAATATT
1 AAAACTTAGTAAAAAATATT
*
36337492 AAAATTTAGTAAAAAATATT
1 AAAACTTAGTAAAAAATATT
36337512 TATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAACTTAGTAAAAAATATT
Found at i:36337526 original size:22 final size:20
Alignment explanation
Indices: 36337480--36337526 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
36337470 AAAAAAACTT
*
36337480 GTAAAAAATATTAAAATTTA
1 GTAAAAAATATTAAAAATTA
36337500 GTAAAAAATATTTATAAAATTA
1 GTAAAAAATA-TTA-AAAATTA
*
36337522 TTAAA
1 GTAAA
36337527 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
22 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
GTAAAAAATATTAAAAATTA
Found at i:36337622 original size:32 final size:32
Alignment explanation
Indices: 36337568--36337634 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
36337558 TAAAAATATT
* *
36337568 AAAATGTTGTAAAAATTCTTTAAAATTGTAAA
1 AAAATGTTGAAAAAATTCTTTAAAATGGTAAA
* *
36337600 AAAATGTT-AAAAAATTATTTTAAAATGGTTAA
1 AAAATGTTGAAAAAATT-CTTTAAAATGGTAAA
36337632 AAA
1 AAA
36337635 TTATTAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (32 bp):
AAAATGTTGAAAAAATTCTTTAAAATGGTAAA
Found at i:36337624 original size:22 final size:21
Alignment explanation
Indices: 36337600--36337639 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
36337590 AAATTGTAAA
36337600 AAAAT-GTTAAAAAATTATTTT
1 AAAATGGTT-AAAAATTATTTT
36337621 AAAATGGTTAAAAATTATT
1 AAAATGGTTAAAAATTATT
36337640 AATTACCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATGGTTAAAAATTATTTT
Found at i:36341910 original size:35 final size:35
Alignment explanation
Indices: 36341864--36341935 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
36341854 GGGAATATTG
*
36341864 ATTTTCACCTTTCGAAATGTCTCTAAAATTTCTTT
1 ATTTTCACCTTTCAAAATGTCTCTAAAATTTCTTT
36341899 ATTTTCACCTTTCAAAATGTCTCTAAAATTTCTTT
1 ATTTTCACCTTTCAAAATGTCTCTAAAATTTCTTT
36341934 AT
1 AT
36341936 CTTCTCACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (35 bp):
ATTTTCACCTTTCAAAATGTCTCTAAAATTTCTTT
Found at i:36347667 original size:6 final size:6
Alignment explanation
Indices: 36347656--36347681 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
36347646 TGAAAGAAGA
36347656 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
36347682 TACCACGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:36353895 original size:23 final size:22
Alignment explanation
Indices: 36353856--36353901 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
36353846 AGATCCGCCC
*
36353856 ATATTATTATTATTTAAATATTT
1 ATATTATTATTAGTT-AATATTT
36353879 ATATTATT-TTAAGTTAATATTT
1 ATATTATTATT-AGTTAATATTT
36353901 A
1 A
36353902 ATCATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATTATTATTAGTTAATATTT
Found at i:36355206 original size:21 final size:20
Alignment explanation
Indices: 36355182--36355252 Score: 88
Period size: 22 Copynumber: 3.3 Consensus size: 20
36355172 ATATTGTTGC
36355182 TTTGGTGCTTTTTTTTACTGT
1 TTTGGTG-TTTTTTTTACTGT
*
36355203 TTTGGTTGTTATTTTTTACTAT
1 TTTGG-TGTT-TTTTTTACTGT
36355225 TTTGGTGTTATTTTTTTACTGT
1 TTTGGTG-T-TTTTTTTACTGT
36355247 TTTGGT
1 TTTGGT
36355253 TATTAATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.20
22 34 0.77
23 1 0.02
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.68
Consensus pattern (20 bp):
TTTGGTGTTTTTTTTACTGT
Found at i:36355220 original size:22 final size:23
Alignment explanation
Indices: 36355191--36355253 Score: 103
Period size: 22 Copynumber: 2.8 Consensus size: 23
36355181 CTTTGGTGCT
36355191 TTTTTTTACTGTTTTGGTTGTTA
1 TTTTTTTACTGTTTTGGTTGTTA
*
36355214 -TTTTTTACTATTTTGG-TGTTA
1 TTTTTTTACTGTTTTGGTTGTTA
36355235 TTTTTTTACTGTTTTGGTT
1 TTTTTTTACTGTTTTGGTT
36355254 ATTAATTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.14
22 30 0.83
23 1 0.03
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.70
Consensus pattern (23 bp):
TTTTTTTACTGTTTTGGTTGTTA
Found at i:36355301 original size:12 final size:12
Alignment explanation
Indices: 36355277--36355359 Score: 66
Period size: 12 Copynumber: 7.2 Consensus size: 12
36355267 TTTTTTATTG
*
36355277 TTTTGATGTTAT
1 TTTTGCTGTTAT
* *
36355289 TTTTGTTGCTA-
1 TTTTGCTGTTAT
*
36355300 TTTT--TGTTGT
1 TTTTGCTGTTAT
36355310 -TTTGCTGTTAT
1 TTTTGCTGTTAT
36355321 TTTTGCTGTTAT
1 TTTTGCTGTTAT
* *
36355333 TTTTGCTGCTGT
1 TTTTGCTGTTAT
* *
36355345 TTTGGTTGTTAT
1 TTTTGCTGTTAT
36355357 TTT
1 TTT
36355360 GACTGTTTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
9 6 0.11
11 9 0.16
12 41 0.73
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.67
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:36355360 original size:12 final size:12
Alignment explanation
Indices: 36355304--36355366 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
36355294 TTGCTATTTT
*
36355304 TGTTGTTTT-GC
1 TGTTATTTTGGC
*
36355315 TGTTATTTTTGC
1 TGTTATTTTGGC
*
36355327 TGTTATTTTTGC
1 TGTTATTTTGGC
* * *
36355339 TGCTGTTTTGGT
1 TGTTATTTTGGC
*
36355351 TGTTATTTTGAC
1 TGTTATTTTGGC
36355363 TGTT
1 TGTT
36355367 TGGATGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 8 0.19
12 34 0.81
ACGTcount: A:0.06, C:0.08, G:0.22, T:0.63
Consensus pattern (12 bp):
TGTTATTTTGGC
Found at i:36355531 original size:23 final size:25
Alignment explanation
Indices: 36355494--36355541 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
36355484 ATATAAAGAA
36355494 TTTTAATTGTATTTTAAATTTATTT
1 TTTTAATTGTATTTTAAATTTATTT
36355519 TTTTAA-TGT-TTTTAAATTTATTT
1 TTTTAATTGTATTTTAAATTTATTT
36355542 GATATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
24 3 0.13
25 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTAATTGTATTTTAAATTTATTT
Found at i:36356107 original size:26 final size:26
Alignment explanation
Indices: 36356078--36356128 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
36356068 CAAATCTTTA
36356078 ACCAAATTTTTCAAAAGCACTTTTCC
1 ACCAAATTTTTCAAAAGCACTTTTCC
* *
36356104 ACCACATTTTTTAAAAGCACTTTTC
1 ACCAAATTTTTCAAAAGCACTTTTC
36356129 AAAAGCAATG
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:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (26 bp):
ACCAAATTTTTCAAAAGCACTTTTCC
Found at i:36361296 original size:9 final size:9
Alignment explanation
Indices: 36361282--36361332 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
36361272 TGTTTTGACT
36361282 TAAAAATTA
1 TAAAAATTA
36361291 TAAAAAATTA
1 T-AAAAATTA
*
36361301 AAAAAATTA
1 TAAAAATTA
**
36361310 TGTAAATTA
1 TAAAAATTA
*
36361319 TAAAAATTT
1 TAAAAATTA
36361328 TAAAA
1 TAAAA
36361333 TTTTTTATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:36363162 original size:21 final size:21
Alignment explanation
Indices: 36363138--36363179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36363128 CATATAGTAC
36363138 AAAT-AATAAATAAATTATTAT
1 AAATCAATAAATAAA-TATTAT
*
36363159 AAATCAATACATAAATATTAT
1 AAATCAATAAATAAATATTAT
36363180 GTCTATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATCAATAAATAAATATTAT
Found at i:36369986 original size:31 final size:31
Alignment explanation
Indices: 36369948--36370009 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
36369938 TCAACCAAAC
36369948 CTAAATATATAAAAATAAAAAAAATAGTGTT
1 CTAAATATATAAAAATAAAAAAAATAGTGTT
* * *
36369979 CTAAATATATAAAATTTAAAAAAATTGTGTT
1 CTAAATATATAAAAATAAAAAAAATAGTGTT
36370010 GTTATAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.34
Consensus pattern (31 bp):
CTAAATATATAAAAATAAAAAAAATAGTGTT
Found at i:36388559 original size:6 final size:6
Alignment explanation
Indices: 36388548--36388573 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
36388538 GATGGATGGT
36388548 GGTGAA GGTGAA GGTGAA GGTGAA GG
1 GGTGAA GGTGAA GGTGAA GGTGAA GG
36388574 CATGAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGTGAA
Found at i:36397599 original size:4 final size:4
Alignment explanation
Indices: 36397590--36397621 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
36397580 GATTACAAAC
36397590 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
36397622 TGCACGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:36402111 original size:29 final size:30
Alignment explanation
Indices: 36402052--36402117 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
36402042 CTCAAAAATC
*
36402052 ATAAAAGTTTTATAATTTTTTTTTGAAGATT
1 ATAAAAGTTTTATAA-TTTTTTTTAAAGATT
36402083 ATAAAAGTTTTATAA-TTTTTTTAAAGATT
1 ATAAAAGTTTTATAATTTTTTTTAAAGATT
36402112 ATAAAA
1 ATAAAA
36402118 AATTTAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (30 bp):
ATAAAAGTTTTATAATTTTTTTTAAAGATT
Found at i:36402121 original size:22 final size:23
Alignment explanation
Indices: 36402096--36402148 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
36402086 AAAGTTTTAT
36402096 AATTTTTTTA-AAGATTATAAAA
1 AATTTTTTTATAAGATTATAAAA
**
36402118 AA-TTTAATATAAGATTATAAAA
1 AATTTTTTTATAAGATTATAAAA
36402140 ATATTTTTT
1 A-ATTTTTT
36402149 ATATTTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.21
22 15 0.62
23 1 0.04
24 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTTTTTTATAAGATTATAAAA
Found at i:36402288 original size:3 final size:3
Alignment explanation
Indices: 36402280--36402306 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36402270 CAAACTAACA
36402280 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
36402307 TTAGGTATAA
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):
AAT
Found at i:36402584 original size:3 final size:3
Alignment explanation
Indices: 36402576--36402600 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36402566 CCTTTGGTGC
36402576 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
36402601 TATGGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:36409294 original size:5 final size:5
Alignment explanation
Indices: 36409240--36409280 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
36409230 CACGCCCCAC
*
36409240 TCCCC TCCCT TCCCT TCCCT TCCCT TCCCT TCCCT TCCCT T
1 TCCCT TCCCT TCCCT TCCCT TCCCT TCCCT TCCCT TCCCT T
36409281 TTCTTCTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
TCCCT
Found at i:36412141 original size:49 final size:48
Alignment explanation
Indices: 36412057--36412151 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 48
36412047 TTTTATTATA
* * * *
36412057 TAAAACAAATTTAAAAAATATATAATATATCAAATACACTTAAAAATAT
1 TAAAACAAATTTAAAAAATAAACAATATATAAAATA-AATTAAAAATAT
* *
36412106 TAAAATAAATATTAAAAAATAAACAA-ATTTAAAATAAATTAAAAAT
1 TAAAACAAAT-TTAAAAAATAAACAATATATAAAATAAATTAAAAAT
36412152 TAGTAGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
48 9 0.23
49 17 0.44
50 13 0.33
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (48 bp):
TAAAACAAATTTAAAAAATAAACAATATATAAAATAAATTAAAAATAT
Found at i:36412211 original size:21 final size:21
Alignment explanation
Indices: 36412187--36412229 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36412177 TAAGTTTTAC
* *
36412187 AATATTCAAATAATATTAAAA
1 AATATTCAAACAATAGTAAAA
*
36412208 AATATTGAAACAATAGTAAAA
1 AATATTCAAACAATAGTAAAA
36412229 A
1 A
36412230 CACATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AATATTCAAACAATAGTAAAA
Found at i:36412279 original size:20 final size:21
Alignment explanation
Indices: 36412226--36412284 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
36412216 AACAATAGTA
36412226 AAAACACATAAAAATAAC-GTTC
1 AAAACA-ATAAAAATAACAG-TC
**
36412248 -AAACAACCAAAATAACAG-C
1 AAAACAATAAAAATAACAGTC
*
36412267 AAAACAATAAAAACAACA
1 AAAACAATAAAAATAACA
36412285 AAATAGTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 23 0.77
21 6 0.20
ACGTcount: A:0.66, C:0.20, G:0.03, T:0.10
Consensus pattern (21 bp):
AAAACAATAAAAATAACAGTC
Found at i:36412331 original size:22 final size:23
Alignment explanation
Indices: 36412283--36412334 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
36412273 ATAAAAACAA
* *
36412283 CAAAATAGTAAAAAAACAGCAAT
1 CAAAACAGTAAAAAAACAGCAAC
*
36412306 CAAAACAGTAAAAAAATAGC-AC
1 CAAAACAGTAAAAAAACAGCAAC
36412328 CAAAACA
1 CAAAACA
36412335 ACAATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.65, C:0.17, G:0.08, T:0.10
Consensus pattern (23 bp):
CAAAACAGTAAAAAAACAGCAAC
Found at i:36414843 original size:30 final size:31
Alignment explanation
Indices: 36414797--36414854 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
36414787 TGCCAATTTT
36414797 TTTTTTATTATAAATTTTTAAGGGATTTCAA
1 TTTTTTATTATAAATTTTTAAGGGATTTCAA
*
36414828 TTTTTT-TTATCAATTTTTAAGGGATTT
1 TTTTTTATTATAAATTTTTAAGGGATTT
36414855 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (31 bp):
TTTTTTATTATAAATTTTTAAGGGATTTCAA
Found at i:36418637 original size:18 final size:18
Alignment explanation
Indices: 36418614--36418683 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
36418604 AAAATGCAGG
*
36418614 AAATGATGTTAACATTTT
1 AAATGATGTTAACATTTC
*
36418632 AAATGATGTTAACACTTC
1 AAATGATGTTAACATTTC
36418650 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACATTTC
36418668 AAATGATGTTAACATT
1 AAATGATGTTAACATT
36418684 GATGGAAACG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
17 2 0.04
18 43 0.91
19 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:36419206 original size:72 final size:71
Alignment explanation
Indices: 36419115--36419365 Score: 339
Period size: 72 Copynumber: 3.5 Consensus size: 71
36419105 AATGCTAAAC
36419115 TAGTTTTATCAATAGTTGTTTAAGTTTGATTTTTAGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTAAGTTTGATTTTT-GATATTGAATTTATGTTCTACTTATTTATG
36419180 TGTAATT
65 TGTAATT
* * * * *
36419187 TAGTTTTATCAATTGTTGTTTATGTTTGGTTCTTG-GA--GAATTTATGTTCTACTTATTTATGT
1 TAGTTTTATCAATAGTTGTTTAAGTTTGATTTTTGATATTGAATTTATGTTCTACTTATTTATGT
*
36419249 GTAATC
66 GTAATT
** *
36419255 TAGTTTTATCAATAGTTGTTTATTTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTAAGTTTGATTTTT-GATATTGAATTTATGTTCTACTTATTTATG
* *
36419320 AGTATTT
65 TGTAATT
*
36419327 TAGTTTTATCAATAGTTGTTTATA-TTTGATTTTGGATAT
1 TAGTTTTATCAATAGTTGTTTA-AGTTTGATTTTTGATAT
36419366 AAAATTTGTT
Statistics
Matches: 158, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
68 61 0.39
69 1 0.01
70 2 0.01
71 6 0.04
72 88 0.56
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.56
Consensus pattern (71 bp):
TAGTTTTATCAATAGTTGTTTAAGTTTGATTTTTGATATTGAATTTATGTTCTACTTATTTATGT
GTAATT
Found at i:36422096 original size:20 final size:20
Alignment explanation
Indices: 36422071--36422108 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36422061 TTAATAAATA
*
36422071 TTTAATTAAGCTTAATTTAT
1 TTTAATTAAACTTAATTTAT
36422091 TTTAATTAAACTTAATTT
1 TTTAATTAAACTTAATTT
36422109 GATTAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAATTAAACTTAATTTAT
Found at i:36428817 original size:15 final size:16
Alignment explanation
Indices: 36428779--36428819 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
36428769 TCCTAAATTT
36428779 AAAGAAAAATCTAAAA
1 AAAGAAAAATCTAAAA
*
36428795 ATTA-AAAAAT-TAAAA
1 A-AAGAAAAATCTAAAA
36428810 AAAGAAAAAT
1 AAAGAAAAAT
36428820 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 7 0.33
17 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAGAAAAATCTAAAA
Found at i:36429644 original size:4 final size:4
Alignment explanation
Indices: 36429635--36429665 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
36429625 CAAGTTCAAG
36429635 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
36429666 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:36432925 original size:2 final size:2
Alignment explanation
Indices: 36432864--36432907 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
36432854 TCTAGGATGC
* *
36432864 AT AT AT AA AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36432906 AT
1 AT
36432908 TAAAAAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:36435306 original size:13 final size:15
Alignment explanation
Indices: 36435266--36435311 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
36435256 ATAAGGATTG
36435266 AAATTTAAAAATATA
1 AAATTTAAAAATATA
*
36435281 AAATTTAAAAATATC
1 AAATTTAAAAATATA
36435296 AAA-TT-AAAATATA
1 AAATTTAAAAATATA
36435309 AAA
1 AAA
36435312 ACTAAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 10 0.34
14 2 0.07
15 17 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTTAAAAATATA
Found at i:36441053 original size:16 final size:15
Alignment explanation
Indices: 36441032--36441065 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
36441022 CAAAGTTTTT
36441032 AATATTAAACAGAGTC
1 AATATTAAACAGA-TC
36441048 AATATTAAACAGATC
1 AATATTAAACAGATC
36441063 AAT
1 AAT
36441066 TAATCAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (15 bp):
AATATTAAACAGATC
Found at i:36444363 original size:75 final size:72
Alignment explanation
Indices: 36444242--36444393 Score: 189
Period size: 75 Copynumber: 2.1 Consensus size: 72
36444232 TATGTTAATG
* * * *
36444242 ATGTTTTTAGATGACCATATTCAGAAGAATGTGAACATTTGTTTGACCACCTGCTAAATG-CCGA
1 ATGTTTTTAGATGACCATATTCAAAAGAATATGAACATCTATTTGACCACCTGCT-AATGCCCG-
36444306 AAGGTACCC
64 AAGGTACCC
* ** *
36444315 ATGTTTTTAGACTTGATCATATTCAAAATTATATGAACATCTATTTGACCACTTGCTAATGCCCG
1 ATGTTTTTAGA--TGACCATATTCAAAAGAATATGAACATCTATTTGACCACCTGCTAATGCCCG
36444380 AAGGTACCC
64 AAGGTACCC
36444389 ATGTT
1 ATGTT
36444394 CACACATTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
73 11 0.16
74 18 0.26
75 39 0.57
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (72 bp):
ATGTTTTTAGATGACCATATTCAAAAGAATATGAACATCTATTTGACCACCTGCTAATGCCCGAA
GGTACCC
Found at i:36445181 original size:17 final size:17
Alignment explanation
Indices: 36445119--36445181 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
36445109 GTAATGTGCA
36445119 ATATTATTAAATATAAAT
1 ATATTATTAAAT-TAAAT
* *
36445137 AT-TTATTTATATTTAAT
1 ATATTA-TTAAATTAAAT
*
36445154 A-ATATAATAAATTAAAT
1 ATAT-TATTAAATTAAAT
36445171 ATATTATTAAA
1 ATATTATTAAA
36445182 AAATATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
17 24 0.69
18 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTATTAAATTAAAT
Found at i:36447819 original size:15 final size:15
Alignment explanation
Indices: 36447799--36447828 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36447789 CAATTGGTAA
*
36447799 ATCATATTAAATAAT
1 ATCATATAAAATAAT
36447814 ATCATATAAAATAAT
1 ATCATATAAAATAAT
36447829 CATAATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
ATCATATAAAATAAT
Found at i:36451539 original size:18 final size:17
Alignment explanation
Indices: 36451516--36451561 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
36451506 GTTCAAGGTG
36451516 TAATTAATTTAAAAATTT
1 TAATTAATTTAAAAA-TT
36451534 TAATTAA-TT--AAATT
1 TAATTAATTTAAAAATT
*
36451548 TATTTAATTTAAAA
1 TAATTAATTTAAAA
36451562 TCTATTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
17 4 0.17
18 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAATTTAAAAATT
Found at i:36455189 original size:20 final size:17
Alignment explanation
Indices: 36455141--36455182 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
36455131 TCATTATTGA
36455141 ATATA-TAGACTAGCTG
1 ATATAGTAGACTAGCTG
*
36455157 ATATAGTAGACTAGTTG
1 ATATAGTAGACTAGCTG
36455174 ATATAGTAG
1 ATATAGTAG
36455183 TCTACTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (17 bp):
ATATAGTAGACTAGCTG
Found at i:36457989 original size:23 final size:23
Alignment explanation
Indices: 36457931--36458019 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
36457921 TTCAAAACAT
* * *
36457931 TGTTCGTGAACATATTCAATTATA
1 TGTTCATGAACATGTTCATTTA-A
*
36457955 TGTTCATAAACATGTTCATTTAA
1 TGTTCATGAACATGTTCATTTAA
*
36457978 TGTTCGTGAACATGTTCGA-TTAA
1 TGTTCATGAACATGTTC-ATTTAA
*
36458001 -GTTAAATGAACATGTTCAT
1 TGTT-CATGAACATGTTCAT
36458020 GAACATTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 4 0.07
23 31 0.57
24 19 0.35
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCATTTAA
Found at i:36458028 original size:23 final size:23
Alignment explanation
Indices: 36457984--36458030 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
36457974 TTAATGTTCG
* *
36457984 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
36458007 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
36458030 T
1 T
36458031 AAACGAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:36459968 original size:15 final size:15
Alignment explanation
Indices: 36459941--36460010 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
36459931 ATAAAAATAC
**
36459941 TCATTTAT-TTTTTT
1 TCATTTATATTTTAG
36459955 TCATATTATATTTTAG
1 TCAT-TTATATTTTAG
36459971 TCATTTATA-TTT-G
1 TCATTTATATTTTAG
**
36459984 AAATATTATATTTTAG
1 TCAT-TTATATTTTAG
*
36460000 TCACTTATATT
1 TCATTTATATT
36460011 ATCGTTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
13 3 0.07
14 12 0.27
15 19 0.43
16 10 0.23
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (15 bp):
TCATTTATATTTTAG
Found at i:36470654 original size:41 final size:42
Alignment explanation
Indices: 36470570--36470656 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
36470560 CATTAAAAGC
* ** * *
36470570 TAAAAAAAAATTAGACCCTTTAAAAGTTGGTAAAAAATTTTT
1 TAAAAAAAAATTAAACCCTTTAAAAACTGGAAAAAAATATTT
36470612 TAAAAAAAAATTAAACCC-TTAAAAACT-GAAAAATAATATTT
1 TAAAAAAAAATTAAACCCTTTAAAAACTGGAAAAA-AATATTT
36470653 TAAA
1 TAAA
36470657 CCCCTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.13
41 17 0.44
42 17 0.44
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (42 bp):
TAAAAAAAAATTAAACCCTTTAAAAACTGGAAAAAAATATTT
Found at i:36473269 original size:13 final size:13
Alignment explanation
Indices: 36473253--36473277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36473243 ATTTATATTA
36473253 AATTTAATAATAC
1 AATTTAATAATAC
36473266 AATTTAATAATA
1 AATTTAATAATA
36473278 TAAAAATATG
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTAATAATAC
Found at i:36478532 original size:28 final size:30
Alignment explanation
Indices: 36478485--36478568 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 30
36478475 TTTTTTTAAT
* *
36478485 TTTTAAGGGTTTCAATTTTTTTTAAAAAAC
1 TTTTAAGGGTCTCAAATTTTTTTAAAAAAC
**
36478515 TTTTATA-GGT-T-AAATTTTTTTAACCAAC
1 TTTTA-AGGGTCTCAAATTTTTTTAAAAAAC
36478543 TTTTAAGGGTCTCAAATTTTTTTAAA
1 TTTTAAGGGTCTCAAATTTTTTTAAA
36478569 GGGCCTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 22 0.48
29 2 0.04
30 20 0.43
31 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (30 bp):
TTTTAAGGGTCTCAAATTTTTTTAAAAAAC
Found at i:36478567 original size:19 final size:20
Alignment explanation
Indices: 36478543--36478585 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
36478533 TTTAACCAAC
*
36478543 TTTT-AAGGGTCTCAAATTT-
1 TTTTAAAGGGCCT-AAATTTA
36478562 TTTTAAAGGGCCTAAATTTA
1 TTTTAAAGGGCCTAAATTTA
36478582 TTTT
1 TTTT
36478586 TTTTACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTTAAAGGGCCTAAATTTA
Found at i:36480254 original size:21 final size:21
Alignment explanation
Indices: 36480207--36480256 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
36480197 CTTAGTGTCG
* **
36480207 CGACTTTACCAAGGTATATTG
1 CGACTTTGCCAAGGTATATCA
*
36480228 CAACTTTGCCAAGGTATATCA
1 CGACTTTGCCAAGGTATATCA
36480249 CGACTTTG
1 CGACTTTG
36480257 AAAGCAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (21 bp):
CGACTTTGCCAAGGTATATCA
Found at i:36481581 original size:2 final size:2
Alignment explanation
Indices: 36481574--36481613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
36481564 TGTTTCAAAC
36481574 AT AT AT AT AT 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 AT AT AT AT AT
36481614 GGTTTACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36482217 original size:175 final size:175
Alignment explanation
Indices: 36481925--36482279 Score: 602
Period size: 175 Copynumber: 2.0 Consensus size: 175
36481915 ATAATATTAG
*
36481925 TTTTCGCAAAGCACATGAAAACACAAAAAATTAGCATAACTTGTATTTTATTCATTTTAGTCCCT
1 TTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTCATTTTAGTCCCT
* * * * * *
36481990 TTATTCGAAATATTTGTATATTTTGGTGTATAATATCGAATCAAAGTCAGATTTCACATTCTTTT
66 ATATTCAAAATATTTGTATATTATGGTATATAATATCGAATCAAAATCAGATTTCACATTCTTTC
* *
36482055 ATTAGGGACCCCAAACTTTCGATTTGTAACATAATTTTCTAACAA
131 ATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAACAA
*
36482100 TTTTCGCCAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTCATTTTAGTCCCT
1 TTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTCATTTTAGTCCCT
*
36482165 ATATTCAAAATATTTGTATATTATGGTATATAGTATCGAATCAAAATCAGATTTCACATTCTTTC
66 ATATTCAAAATATTTGTATATTATGGTATATAATATCGAATCAAAATCAGATTTCACATTCTTTC
*
36482230 ATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAACAG
131 ATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAACAA
36482275 TTTTC
1 TTTTC
36482280 ACTTTATTCA
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 168 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (175 bp):
TTTTCGCAAAGCACATGAAAACACAAAAAATTAACATAACTTGTATTTTATTCATTTTAGTCCCT
ATATTCAAAATATTTGTATATTATGGTATATAATATCGAATCAAAATCAGATTTCACATTCTTTC
ATTAGGGACCCCAAACTTTCGATCTATAACATAATTTTCTAACAA
Found at i:36486159 original size:20 final size:20
Alignment explanation
Indices: 36486134--36486171 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36486124 AATGAGAATT
* *
36486134 GGGTTTTAGAAAGAAATTTG
1 GGGTTTGAGAAAAAAATTTG
36486154 GGGTTTGAGAAAAAAATT
1 GGGTTTGAGAAAAAAATT
36486172 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (20 bp):
GGGTTTGAGAAAAAAATTTG
Found at i:36486948 original size:19 final size:18
Alignment explanation
Indices: 36486910--36486948 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
36486900 AAATTTTAAC
* *
36486910 TTTTTTTCAAAAATATTT
1 TTTTTTTCAAAAACACTT
36486928 TTTTTTTCCAAAAACACTT
1 TTTTTTT-CAAAAACACTT
36486947 TT
1 TT
36486949 AAAACGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTTTCAAAAACACTT
Found at i:36487939 original size:2 final size:2
Alignment explanation
Indices: 36487932--36487959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36487922 CTTTGTTGCC
36487932 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
36487960 TGCTCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36493496 original size:19 final size:19
Alignment explanation
Indices: 36493472--36493512 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
36493462 AATCAAACTA
36493472 TAATACATGATAGATAGAT
1 TAATACATGATAGATAGAT
36493491 TAATACATGATAGATAGAT
1 TAATACATGATAGATAGAT
36493510 TAA
1 TAA
36493513 ATTCATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (19 bp):
TAATACATGATAGATAGAT
Found at i:36494444 original size:31 final size:29
Alignment explanation
Indices: 36494408--36494477 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
36494398 ATCTCAATAT
* *
36494408 TATACATGAACATTGATTTAATGTGCAATTA
1 TATACATGAACATTAATTT--GGTGCAATTA
*
36494439 TATACATGAACTTTAATTTGGTGCAATTA
1 TATACATGAACATTAATTTGGTGCAATTA
*
36494468 TACACATGAA
1 TATACATGAA
36494478 TTTTTAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (29 bp):
TATACATGAACATTAATTTGGTGCAATTA
Found at i:36494455 original size:26 final size:28
Alignment explanation
Indices: 36494430--36494487 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
36494420 TTGATTTAAT
*
36494430 GTGCAATTATATACATGAACTTTAATTTG
1 GTGCAATTATACACATGAACTTTAA-TTG
*
36494459 GTGCAATTATACACATGAATTTTTAATTG
1 GTGCAATTATACACATGAA-CTTTAATTG
36494488 TGGTTCGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (28 bp):
GTGCAATTATACACATGAACTTTAATTG
Found at i:36494462 original size:29 final size:30
Alignment explanation
Indices: 36494430--36494518 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
36494420 TTGATTTAAT
36494430 GTGCAATTATATACATGAA-CTTTAATTTG
1 GTGCAATTATATACATGAAGCTTTAATTTG
* **
36494459 GTGCAATTATACACATGAATTTTTAATTGTG
1 GTGCAATTATATACATGAAGCTTTAATT-TG
*
36494490 GTTCGC-A-TGTATACATGAAGCTTTAATTT
1 G-T-GCAATTATATACATGAAGCTTTAATTT
36494519 TGATTTAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 18 0.36
30 8 0.16
31 20 0.40
32 2 0.04
33 2 0.04
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (30 bp):
GTGCAATTATATACATGAAGCTTTAATTTG
Found at i:36495260 original size:15 final size:15
Alignment explanation
Indices: 36495240--36495270 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36495230 CAAGATTTTG
*
36495240 ATTTTTAATTTTTAT
1 ATTTTTAATTTATAT
36495255 ATTTTTAATTTATAT
1 ATTTTTAATTTATAT
36495270 A
1 A
36495271 ATTACATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTAATTTATAT
Found at i:36502190 original size:29 final size:30
Alignment explanation
Indices: 36502147--36502205 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
36502137 AAGTTGGATC
36502147 AAATCAAAATTTTATGTATA-AGATTATACA
1 AAATCAAAATTTTATGTATACAG-TTATACA
36502177 AAATCAAAA-TTTATGTATACAGTTATACA
1 AAATCAAAATTTTATGTATACAGTTATACA
36502206 TTAAACCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATACAGTTATACA
Found at i:36508542 original size:24 final size:24
Alignment explanation
Indices: 36508488--36508551 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
36508478 TTTATTTTAT
36508488 TTCATTTATTT-AAAAATAAATAAA
1 TTCATTT-TTTAAAAAATAAATAAA
* *
36508512 TTAATTTCTTTAAAAAATAAATTAA
1 TTCATTT-TTTAAAAAATAAATAAA
36508537 -TCATTTTATTAAAAA
1 TTCATTTT-TTAAAAA
36508552 TTTAATACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 12 0.35
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
TTCATTTTTTAAAAAATAAATAAA
Found at i:36508551 original size:25 final size:25
Alignment explanation
Indices: 36508491--36508551 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 25
36508481 ATTTTATTTC
* *
36508491 ATTTATT-TAAAAATAAATAAATTA
1 ATTTATTAAAAAAATAAATAAATCA
* * *
36508515 ATTTCTTTAAAAAATAAATTAATCA
1 ATTTATTAAAAAAATAAATAAATCA
*
36508540 TTTTATTAAAAA
1 ATTTATTAAAAA
36508552 TTTAATACAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTATTAAAAAAATAAATAAATCA
Found at i:36508816 original size:17 final size:17
Alignment explanation
Indices: 36508794--36508826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36508784 TTCTTAGATA
36508794 ATTTTAAATT-TATATTT
1 ATTTT-AATTATATATTT
36508811 ATTTTAATTATATATT
1 ATTTTAATTATATATT
36508827 AAACTTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAATTATATATTT
Done.