Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 92 of 185
Found at i:28842572 original size:21 final size:20
Alignment explanation
Indices: 28842542--28842586 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
28842532 GCACGATGTT
*
28842542 TCTTCTTCTTCCTCTTTTTC
1 TCTTCTTCTTCATCTTTTTC
* *
28842562 TCTTCCTTCTTGATCTTTTTG
1 TCTT-CTTCTTCATCTTTTTC
28842583 TCTT
1 TCTT
28842587 TGAAGCGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.64
Consensus pattern (20 bp):
TCTTCTTCTTCATCTTTTTC
Found at i:28851016 original size:16 final size:17
Alignment explanation
Indices: 28850995--28851027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28850985 AAATATTATG
28850995 AAATAAA-ATCAAACAA
1 AAATAAACATCAAACAA
28851011 AAATAAACATCAAACAA
1 AAATAAACATCAAACAA
28851028 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAACATCAAACAA
Found at i:28853225 original size:14 final size:14
Alignment explanation
Indices: 28853206--28853232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28853196 TAGCTTTAGT
28853206 TTTAATTAGTTTAA
1 TTTAATTAGTTTAA
28853220 TTTAATTAGTTTA
1 TTTAATTAGTTTA
28853233 TCATTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTAATTAGTTTAA
Found at i:28853313 original size:25 final size:25
Alignment explanation
Indices: 28853285--28853334 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28853275 TTCTAGTAGA
* *
28853285 CTAATAATTATTTTCTACAAGTAAC
1 CTAATAATAATTTTCTACAAATAAC
*
28853310 CTAATAATAATTTTCTCCAAATAAC
1 CTAATAATAATTTTCTACAAATAAC
28853335 AATCCATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (25 bp):
CTAATAATAATTTTCTACAAATAAC
Found at i:28859882 original size:25 final size:25
Alignment explanation
Indices: 28859853--28859902 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
28859843 AAAATGAAAC
* *
28859853 ATTAAGTGCACAAGATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
28859878 ATTAAGTGAACAAAATAGTGAAAGT
1 ATTAAGTGAACAAAATAGTGAAAGT
28859903 GAAAGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTAAGTGAACAAAATAGTGAAAGT
Found at i:28863215 original size:14 final size:14
Alignment explanation
Indices: 28863198--28863227 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28863188 AATACGAAGA
28863198 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
28863212 AAGAAATGTTTGAT
1 AAGAAATGTTTGAT
28863226 AA
1 AA
28863228 TCACAATGAT
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:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (14 bp):
AAGAAATGTTTGAT
Found at i:28863455 original size:48 final size:48
Alignment explanation
Indices: 28863384--28863483 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
28863374 ATGGGACTCT
**
28863384 TTCTCTGACCGGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
1 TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
*
28863432 TTCTCTGACAAGCTATTTGATGTTTGCAATATGTTATTGTCATTCACA
1 TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
28863480 TTCT
1 TTCT
28863484 TACAGCTCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (48 bp):
TTCTCTGACAAGCTATTTGATGTTTGCAATACGTTATTGTCATTCACA
Found at i:28865044 original size:28 final size:28
Alignment explanation
Indices: 28864973--28865054 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
28864963 AGTGGTGGAT
*
28864973 AATCCAAAGTACAAGCCAAAGTGACGAAC
1 AATCC-AAGTACAAGCCAAAGTGGCGAAC
* *
28865002 AGTCCAAGTATAAGCCAAAGTGGCGAAC
1 AATCCAAGTACAAGCCAAAGTGGCGAAC
* * *
28865030 AATCCCAGTGCAAGCCAATGTGGCG
1 AATCCAAGTACAAGCCAAAGTGGCG
28865055 GATAGTCCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 41 0.91
29 4 0.09
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (28 bp):
AATCCAAGTACAAGCCAAAGTGGCGAAC
Found at i:28867584 original size:43 final size:43
Alignment explanation
Indices: 28867520--28867637 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
28867510 CTGATAAGTG
* *
28867520 TTTTCGTGTAATAGCACGTCTGGGACATTGGCATCGACTTGT-A
1 TTTTCGTGTAAGA-CCCGTCTGGGACATTGGCATCGACTTGTGA
* *
28867563 TTTTCGTGTAAGACCCTGTCTGGGACAATGGCATCGATTTGTGA
1 TTTTCGTGTAAGACCC-GTCTGGGACATTGGCATCGACTTGTGA
* * *
28867607 -TTACATGTAAGACCACGTCTGGGACGTTGGC
1 TTTTCGTGTAAGACC-CGTCTGGGACATTGGC
28867638 GTTGTACGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 2 0.03
43 60 0.94
44 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (43 bp):
TTTTCGTGTAAGACCCGTCTGGGACATTGGCATCGACTTGTGA
Found at i:28870524 original size:29 final size:29
Alignment explanation
Indices: 28870473--28870570 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
28870463 AACAGTGGTG
*
28870473 GACAAGCCAAAAGTACAAGCCAAAGTGGCA
1 GACAATCC-AAAGTACAAGCCAAAGTGGCA
* *
28870503 GACAATCCAAAGTACAAGCCAAAATGG-T
1 GACAATCCAAAGTACAAGCCAAAGTGGCA
* * *
28870531 GAACAATCC-TAGTGCAAGCCAATGTGGCA
1 G-ACAATCCAAAGTACAAGCCAAAGTGGCA
* *
28870560 GATAGTCCAAA
1 GACAATCCAAA
28870571 TGTGGCGAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 20 0.37
29 27 0.50
30 7 0.13
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.13
Consensus pattern (29 bp):
GACAATCCAAAGTACAAGCCAAAGTGGCA
Found at i:28870574 original size:18 final size:18
Alignment explanation
Indices: 28870551--28870611 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
28870541 AGTGCAAGCC
28870551 AATGTGGCAGATAGTCCA
1 AATGTGGCAGATAGTCCA
* *
28870569 AATGTGGC-GAACAATCCA
1 AATGTGGCAG-ATAGTCCA
*
28870587 AATGTGGCAAATAGTCCA
1 AATGTGGCAGATAGTCCA
28870605 AATGTGG
1 AATGTGG
28870612 TGAACAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 35 0.97
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (18 bp):
AATGTGGCAGATAGTCCA
Found at i:28870630 original size:36 final size:36
Alignment explanation
Indices: 28870551--28870620 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
28870541 AGTGCAAGCC
*
28870551 AATGTGGCAGATAGTCCAAATGTGGCGAACAATCCA
1 AATGTGGCAAATAGTCCAAATGTGGCGAACAATCCA
*
28870587 AATGTGGCAAATAGTCCAAATGTGGTGAACAATC
1 AATGTGGCAAATAGTCCAAATGTGGCGAACAATC
28870621 TAAGAGTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (36 bp):
AATGTGGCAAATAGTCCAAATGTGGCGAACAATCCA
Found at i:28873896 original size:22 final size:20
Alignment explanation
Indices: 28873848--28873886 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28873838 TCATATAGTG
28873848 AAATATTTTATTTTATATAT
1 AAATATTTTATTTTATATAT
28873868 AAATATTTTATTTTATATA
1 AAATATTTTATTTTATATA
28873887 ATTAAGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAATATTTTATTTTATATAT
Found at i:28887871 original size:38 final size:38
Alignment explanation
Indices: 28887817--28887891 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
28887807 GGTGAAATTC
* * *
28887817 AGGCTTAGTGATTAGCAGGCTTTGTGCTGATGTTATTT
1 AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATTT
* *
28887855 AGGCTTAGTGCCTAGCAGGCTTGGTGCCGGTGTTATT
1 AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATT
28887892 AGTGCCGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.16, C:0.15, G:0.32, T:0.37
Consensus pattern (38 bp):
AGGCTTAGTGACTAGCAGGCTTGGTGCCGATGTTATTT
Found at i:28887898 original size:15 final size:15
Alignment explanation
Indices: 28887878--28887906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28887868 AGCAGGCTTG
28887878 GTGCCGGTGTTATTA
1 GTGCCGGTGTTATTA
28887893 GTGCCGGTGTTATT
1 GTGCCGGTGTTATT
28887907 CAGGCTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.34, T:0.41
Consensus pattern (15 bp):
GTGCCGGTGTTATTA
Found at i:28888191 original size:12 final size:12
Alignment explanation
Indices: 28888176--28888208 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28888166 AACAGAACCG
28888176 TAAATATTTTTA
1 TAAATATTTTTA
28888188 TAAATATTTTTA
1 TAAATATTTTTA
28888200 TAAATATTT
1 TAAATATTT
28888209 ACGGAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:28889056 original size:287 final size:287
Alignment explanation
Indices: 28888540--28889118 Score: 1095
Period size: 287 Copynumber: 2.0 Consensus size: 287
28888530 CATTGTTAAA
28888540 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
* *
28888605 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCGTTTTTGAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
*
28888670 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATTTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
*
28888735 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTGATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
*
28888800 AAATTGCTAAAGGAATAATAATTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
*
28888827 GACTTTGAAGCTTCGGCCAAGCTTTAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
1 GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
28888892 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
66 ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
28888957 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
131 TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
*
28889022 AGTATTTGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
196 AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
28889087 AAATTGCTAAAGGAATAATAAGTCAAG
261 AAATTGCTAAAGGAATAATAAGTCAAG
28889114 GACTT
1 GACTT
28889119 GATGTGAAAT
Statistics
Matches: 285, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
287 285 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (287 bp):
GACTTTGAAGCTTCGGCCAAGCTTCAATGTATTCATGTAAGTCCATTTTGAACCCGTTTCTCGTA
ATTTTTATGTTTTTGAGATCGTTGCAACTAGGTCCAGCTAGCCCGTACCTTCATTTTTAAATTTG
TTAAAGATTTTAAATGTTGCCATTGATGAATCTTTGTGATTTTAGATGTTAAGTGATGAATTTGA
AGTATTAGTTGTTATTTATAAGTATTTTGTTAAGTAATTTTTAATGATTTAAATGTTTAGGGATT
AAATTGCTAAAGGAATAATAAGTCAAG
Found at i:28897375 original size:38 final size:37
Alignment explanation
Indices: 28897323--28897553 Score: 219
Period size: 38 Copynumber: 6.1 Consensus size: 37
28897313 ATGAGGTCAA
* * * *
28897323 ATTCAAGCTTAGTGCCTAGTAAGCTTAGTCCCAGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
* ** *
28897361 ATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCGGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTG-CCGTGTT
* * *
28897399 ATTCAGACTTAGAGCTTAGCAGGCTTAGTGCCGATGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCG-TGTT
* * **
28897437 ATCCAGGCTTACTGCCTAATAGGCTTAGTGCCTGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
* * *
28897475 ATTCATGCTTAGTGTCTAGCAGGCTTAGTGTCGATGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCG-TGTT
* * *
28897513 ATTCTGGCTTAATGCCTAGCAGGTTTAGTGCCAGTGTT
1 ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCC-GTGTT
28897551 ATT
1 ATT
28897554 TAGACTTATT
Statistics
Matches: 155, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
37 3 0.02
38 149 0.96
39 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (37 bp):
ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCGTGTT
Found at i:28897453 original size:76 final size:76
Alignment explanation
Indices: 28897357--28897561 Score: 252
Period size: 76 Copynumber: 2.7 Consensus size: 76
28897347 TTAGTCCCAG
* * * *
28897357 TGTTATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCGGTGTTATTCAGACTTAGAG-CTTAGCAG
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTAGAGTC-TAGCAG
28897421 GCTTAGTGCCGA
65 GCTTAGTGCCGA
* * * *
28897433 TGTTATCCAGGCTTACTGCCTAATAGGCTTAGTGCCTGTGTTATTCATG-CTTAGTGTCTAGCAG
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCA-GACTTAGAGTCTAGCAG
*
28897497 GCTTAGTGTCGA
65 GCTTAGTGCCGA
* ** * *
28897509 TGTTATTCTGGCTTAATGCCTAGCAGGTTTAGTGCCAGTGTTATTTAGACTTA
1 TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTA
28897562 TTGCCACTGT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 108 0.97
77 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (76 bp):
TGTTATTCAGGCTTAATGCCTAATAGGCTTAGTGCCAGTGTTATTCAGACTTAGAGTCTAGCAGG
CTTAGTGCCGA
Found at i:28897533 original size:114 final size:114
Alignment explanation
Indices: 28897329--28897552 Score: 281
Period size: 114 Copynumber: 2.0 Consensus size: 114
28897319 TCAAATTCAA
* * *
28897329 GCTTAGTGCCTAGTAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAATAGGCTTAGTGTCG
1 GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
* *
28897394 GTGTTATTCAGACTTAGAGCTTAGCAGGCTTAGTGCC-GATGTTATCCAG
66 ATGTTATTCAGACTTAGAGCCTAGCAGGCTTAGTGCCAG-TGTTATCCAG
* * * * * * *
28897443 GCTTACTGCCTAATAGGCTTAGTGCCTGTGTTATTCATGCTTAGTGTCTAGCAGGCTTAGTGTCG
1 GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
* * *
28897508 ATGTTATTCTGGCTTA-ATGCCTAGCAGGTTTAGTGCCAGTGTTAT
66 ATGTTATTCAGACTTAGA-GCCTAGCAGGCTTAGTGCCAGTGTTAT
28897553 TTAGACTTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
113 1 0.01
114 91 0.98
115 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (114 bp):
GCTTACTGCCTAATAAGCTTAGTCCCAGTGTTATTCAGGCTCAGTGCCTAACAGGCTTAGTGTCG
ATGTTATTCAGACTTAGAGCCTAGCAGGCTTAGTGCCAGTGTTATCCAG
Found at i:28899907 original size:50 final size:50
Alignment explanation
Indices: 28899801--28900020 Score: 260
Period size: 50 Copynumber: 4.3 Consensus size: 50
28899791 GAAGATGTGA
*
28899801 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
28899857 TCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* **
28899907 TCTCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
28899957 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
28900007 TCCGATGTAAGACC
1 TCCCATGTAAGACC
28900021 GTATCTAGGA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
50 106 0.73
53 3 0.02
55 1 0.01
56 35 0.24
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:28900042 original size:100 final size:100
Alignment explanation
Indices: 28899849--28900043 Score: 230
Period size: 100 Copynumber: 1.9 Consensus size: 100
28899839 CATTGAGATT
* * * * **
28899849 ATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGAGGTCTCATG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTCATG
* * ***
28899914 TAAGACCATGTCTGGGACATGGTGTTGGCACCGAG
66 TAAGACCATATCTAGGACATGAAATTGGCACCGAG
* * *
28899949 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAAAACTC-CGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTC-AT
* *
28900013 GTAAGACCGTATCTAGGATATGAAATTGGCA
65 GTAAGACCATATCTAGGACATGAAATTGGCA
28900044 GTAAAGGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 1 0.01
100 77 0.99
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (100 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAAAACTCTCATG
TAAGACCATATCTAGGACATGAAATTGGCACCGAG
Found at i:28904158 original size:50 final size:50
Alignment explanation
Indices: 28904083--28904253 Score: 243
Period size: 50 Copynumber: 3.4 Consensus size: 50
28904073 TGATTTTCAG
*
28904083 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* **
28904133 ATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * **
28904183 ATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACC
1 ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
* * *
28904233 ATATCTAGGATATGGCATTGG
1 ATGTCTGGGACATGGCATTGG
28904254 TAGTAAACGA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
ATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACC
Found at i:28907167 original size:23 final size:22
Alignment explanation
Indices: 28907140--28907195 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
28907130 TAAATCTAAT
*
28907140 AAATTATAAAAAAATATTATATA
1 AAATTATAAAAAAA-ATTATAAA
28907163 AAATTAT-AAAAAAATTATAAA
1 AAATTATAAAAAAAATTATAAA
*
28907184 AAATCATAAAAA
1 AAATTATAAAAA
28907196 TGGAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 13 0.43
22 10 0.33
23 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTATAAAAAAAATTATAAA
Found at i:28907183 original size:19 final size:19
Alignment explanation
Indices: 28907140--28907381 Score: 80
Period size: 17 Copynumber: 12.7 Consensus size: 19
28907130 TAAATCTAAT
28907140 AAATTATAAAAAAATATTATATA
1 AAATTAT-AAAAAA-A-T-TATA
28907163 AAATTATAAAAAAATTATA
1 AAATTATAAAAAAATTATA
* * *
28907182 AAA-AATCATAAAAATGGA-A
1 AAATTAT-AAAAAAAT-TATA
* *
28907201 AAA-TAT-TAAAAA-TAGGA
1 AAATTATAAAAAAATTA-TA
* *
28907218 AAATTATTAAAAAATCATA
1 AAATTATAAAAAAATTATA
* *
28907237 AAATTAT--TAAAATTAAA
1 AAATTATAAAAAAATTATA
**
28907254 AAATTA-AAATTAA-TATA
1 AAATTATAAAAAAATTATA
*
28907271 AACTTAT-AAAAAATTATAA
1 AAATTATAAAAAAATTAT-A
**
28907290 TAAAAAATAATAAAAACTTATA
1 -AAATTATAA-AAAAA-TTATA
* *
28907312 AATATTATAAAAATATAAT-
1 AA-ATTATAAAAAAATTATA
28907331 AAA-TAT-AAAAAATTATA
1 AAATTATAAAAAAATTATA
* **
28907348 AAA-AATAATATAAACGTATAA
1 AAATTATAA-A-AAAATTAT-A
28907369 AAATTATAAAAAA
1 AAATTATAAAAAA
28907382 TAAAAAATAA
Statistics
Matches: 165, Mismatches: 31, Indels: 49
0.67 0.13 0.20
Matches are distributed among these distances:
15 1 0.01
16 8 0.05
17 43 0.26
18 12 0.07
19 37 0.22
20 19 0.12
21 13 0.08
22 21 0.13
23 11 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAAAATTATA
Found at i:28907184 original size:9 final size:9
Alignment explanation
Indices: 28907102--28907389 Score: 99
Period size: 9 Copynumber: 31.7 Consensus size: 9
28907092 AAAAGTAATA
28907102 AAAAATTAT
1 AAAAATTAT
* *
28907111 AAATATTTT
1 AAAAATTAT
28907120 AAAAATCTA-
1 AAAAAT-TAT
*
28907129 ATAAATCTA-
1 AAAAAT-TAT
*
28907138 ATAAATTAT
1 AAAAATTAT
28907147 AAAAAAATATTAT
1 ---AAAA-ATTAT
28907160 ATAAAATTAT
1 A-AAAATTAT
28907170 AAAAAAATTAT
1 --AAAAATTAT
*
28907181 AAAAAATCAT
1 -AAAAATTAT
**
28907191 AAAAA-TGG
1 AAAAATTAT
28907199 AAAAA-TATT
1 AAAAATTA-T
*
28907208 AAAAA-TAG
1 AAAAATTAT
*
28907216 GAAAATTATT
1 AAAAATTA-T
*
28907226 AAAAAATCAT
1 -AAAAATTAT
28907236 -AAAATTAT
1 AAAAATTAT
*
28907244 TAAAATTA-
1 AAAAATTAT
28907252 AAAAA-T-T
1 AAAAATTAT
28907259 -AAAATTAAT
1 AAAAATT-AT
*
28907268 ATAAACTTAT
1 A-AAAATTAT
28907278 AAAAAATTAT
1 -AAAAATTAT
28907288 ---AA-TA-
1 AAAAATTAT
*
28907292 AAAAATAAT
1 AAAAATTAT
28907301 AAAAACTTAT
1 AAAAA-TTAT
*
28907311 AAATATTAT
1 AAAAATTAT
28907320 AAAAA-TAT
1 AAAAATTAT
28907328 AATAAA-TAT
1 AA-AAATTAT
28907337 AAAAAATTAT
1 -AAAAATTAT
*
28907347 AAAAAATAAT
1 -AAAAATTAT
**
28907357 ATAAACGTAT
1 A-AAAATTAT
28907367 AAAAATTAT
1 AAAAATTAT
*
28907376 AAAAAATA-
1 AAAAATTAT
28907384 AAAAAT
1 AAAAAT
28907390 AAACTTGAAC
Statistics
Matches: 215, Mismatches: 33, Indels: 63
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.01
6 6 0.03
7 4 0.02
8 34 0.16
9 84 0.39
10 53 0.25
11 23 0.11
12 4 0.02
13 5 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28907248 original size:18 final size:18
Alignment explanation
Indices: 28907190--28907248 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
28907180 TAAAAAATCA
*
28907190 TAAAAAT-GGAAAAATAT
1 TAAAAATAGGAAAATTAT
28907207 TAAAAATAGGAAAATTAT
1 TAAAAATAGGAAAATTAT
*
28907225 TAAAAAATCA-TAAAATTAT
1 T-AAAAAT-AGGAAAATTAT
28907244 TAAAA
1 TAAAA
28907249 TTAAAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.19
18 14 0.38
19 15 0.41
20 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAAAATAGGAAAATTAT
Found at i:28907281 original size:33 final size:33
Alignment explanation
Indices: 28907234--28907339 Score: 101
Period size: 34 Copynumber: 3.2 Consensus size: 33
28907224 TTAAAAAATC
*
28907234 ATAAAATTATTAAAATTA-AAAAATTAAAATTAAT
1 ATAAACTTA-TAAAATTATAAAAA-TAAAATTAAT
*
28907268 ATAAACTTATAAAAAATTATAATAA-AAAA-TAAT
1 ATAAACTTAT--AAAATTATAAAAATAAAATTAAT
* * *
28907301 AAAAACTTATAAATATTATAAAAATATAATAAAT
1 ATAAACTTATAAA-ATTATAAAAATAAAATTAAT
28907335 ATAAA
1 ATAAA
28907340 AAATTATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
31 3 0.05
32 9 0.15
33 17 0.29
34 19 0.32
35 7 0.12
36 4 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (33 bp):
ATAAACTTATAAAATTATAAAAATAAAATTAAT
Found at i:28907294 original size:13 final size:13
Alignment explanation
Indices: 28907276--28907361 Score: 52
Period size: 13 Copynumber: 6.4 Consensus size: 13
28907266 ATATAAACTT
*
28907276 ATAAAAAATTATA
1 ATAAAAAATAATA
28907289 ATAAAAAATAATA
1 ATAAAAAATAATA
* *
28907302 AAAACTTATAAAT-ATT
1 ATAA---A-AAATAATA
28907318 ATAAAAATATAATAA
1 ATAAAAA-ATAAT-A
* *
28907333 ATATAAAA-AATT
1 ATAAAAAATAATA
28907345 ATAAAAAATAAT-
1 ATAAAAAATAATA
28907357 ATAAA
1 ATAAA
28907362 CGTATAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
12 14 0.25
13 24 0.42
14 3 0.05
15 6 0.11
16 6 0.11
17 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAAATAATA
Found at i:28907351 original size:56 final size:58
Alignment explanation
Indices: 28907275--28907390 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 58
28907265 AATATAAACT
* * *
28907275 TATAAAAAATTATAATAAAAAATAATAAAAACTTATAAATATTATAAAAATATAATAAA
1 TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAA-ATAAAAAA
*
28907334 TATAAAAAA-T-T-ATAAAAAATAATATAAACGTATAAAAATTATAAAAAATAAAAAA
1 TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAAATAAAAAA
28907389 TA
1 TA
28907391 AACTTGAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
55 9 0.17
56 33 0.62
57 1 0.02
58 1 0.02
59 9 0.17
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (58 bp):
TATAAAAAATTATAATAAAAAATAATAAAAACGTATAAAAATTATAAAAAATAAAAAA
Found at i:28908098 original size:31 final size:31
Alignment explanation
Indices: 28908050--28908110 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28908040 TTATAAGTTT
*
28908050 TTTTATAAATTTTTAAATATTTTA-AATATA
1 TTTTATAAATTTATAAATATTTTATAATATA
*
28908080 TTTTATTAACTTTATAAATATTTTATAATAT
1 TTTTA-TAAATTTATAAATATTTTATAATAT
28908111 CTTATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTTATAAATTTATAAATATTTTATAATATA
Found at i:28908115 original size:10 final size:10
Alignment explanation
Indices: 28908050--28908129 Score: 62
Period size: 10 Copynumber: 8.2 Consensus size: 10
28908040 TTATAAGTTT
28908050 TTTTATAA-A
1 TTTTATAATA
28908059 TTTT-TAAATA
1 TTTTAT-AATA
*
28908069 TTTTAAATATA
1 TTTTATA-ATA
*
28908080 TTTTATTA-A
1 TTTTATAATA
*
28908089 CTTTATAAATA
1 TTTTAT-AATA
28908100 TTTTATAATA
1 TTTTATAATA
*
28908110 TCTTAT-AT-
1 TTTTATAATA
28908118 TTTTATAATA
1 TTTTATAATA
28908128 TT
1 TT
28908130 CATAAGTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.11
9 16 0.29
10 19 0.35
11 14 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATAATA
Found at i:28908141 original size:19 final size:18
Alignment explanation
Indices: 28908100--28908142 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
28908090 TTTATAAATA
*
28908100 TTTTATAATATCTTATAT
1 TTTTATAATATCATATAT
28908118 TTTTATAATATTCATA-AGT
1 TTTTATAATA-TCATATA-T
28908137 TTTTAT
1 TTTTAT
28908143 TATTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTATAATATCATATAT
Found at i:28908363 original size:20 final size:20
Alignment explanation
Indices: 28908340--28908378 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28908330 AGATTTTTTA
28908340 TATTTTTATAAATTTTATAT
1 TATTTTTATAAATTTTATAT
*
28908360 TATTTTTATAATTTTTATA
1 TATTTTTATAAATTTTATA
28908379 AGTTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTTATAAATTTTATAT
Found at i:28908987 original size:18 final size:18
Alignment explanation
Indices: 28908940--28908994 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
28908930 TATATGTCAC
*
28908940 ATTAATAAATA-ATTAAAA
1 ATTAA-AAATATATTTAAA
*
28908958 ATTATAAA-ATATTTAAA
1 ATTAAAAATATATTTAAA
*
28908975 ATTAAAAATATATATAAA
1 ATTAAAAATATATTTAAA
28908993 AT
1 AT
28908995 GTTGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 16 0.52
18 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAATATATTTAAA
Found at i:28911397 original size:18 final size:18
Alignment explanation
Indices: 28911374--28911408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28911364 ATAACAGTAA
* *
28911374 ATTTTAGAATTTTTTTAT
1 ATTTTAAAATATTTTTAT
28911392 ATTTTAAAATATTTTTA
1 ATTTTAAAATATTTTTA
28911409 AAAGAATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTAAAATATTTTTAT
Found at i:28914456 original size:74 final size:74
Alignment explanation
Indices: 28914368--28914518 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
28914358 AGTTAATTAA
28914368 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
1 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
*
28914433 TCCATGTTG
66 TCCATCTTG
28914442 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
1 AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
28914507 TCCATCTTG
66 TCCATCTTG
28914516 AGA
1 AGA
28914519 AAAAAAAGAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (74 bp):
AGATTAAGCATAATATATATCAACTTAGTGGAAGGAAAGATGATAATCTTCATCTTCCTCCACCA
TCCATCTTG
Found at i:28915202 original size:97 final size:97
Alignment explanation
Indices: 28915029--28915246 Score: 312
Period size: 97 Copynumber: 2.2 Consensus size: 97
28915019 ATAATGTTTA
** * **
28915029 GAAACCATCGCTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTATTCATTGTTGTTA
1 GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
* *
28915094 GGTATTCCGGGATGACAGTGTAATCAGATAGT
66 AGTATTCCGGGATGACAGAGTAATCAGATAGT
*
28915126 GAAACCATCATTGTCGGGTAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
1 GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
*
28915191 AGTA-TCTCGGGATGACAGAGTAATTAGATAGT
66 AGTATTC-CGGGATGACAGAGTAATCAGATAGT
* *
28915223 GAAAATCATCATTATCGGGCAACC
1 G-AAACCATCATTGTCGGGCAACC
28915247 AAAGATGGTA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
96 2 0.02
97 86 0.80
98 19 0.18
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (97 bp):
GAAACCATCATTGTCGGGCAACCCGAGGTGGTAGAATGTACATATTTTAGTAGTCATCATTGTTA
AGTATTCCGGGATGACAGAGTAATCAGATAGT
Found at i:28916727 original size:16 final size:16
Alignment explanation
Indices: 28916697--28916731 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28916687 TAAAAAGTAA
28916697 AAACACTAAGTTAAAT
1 AAACACTAAGTTAAAT
*
28916713 AAACTACTAAGTAAAAT
1 AAAC-ACTAAGTTAAAT
28916730 AA
1 AA
28916732 CCAAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (16 bp):
AAACACTAAGTTAAAT
Found at i:28917963 original size:6 final size:6
Alignment explanation
Indices: 28917952--28917981 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28917942 ATGGTACAAG
28917952 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTGAA
28917982 CTGCTGCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TTTGAA
Found at i:28930735 original size:23 final size:23
Alignment explanation
Indices: 28930709--28930784 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
28930699 ATAAGTGCCA
28930709 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28930732 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28930755 CACTGATATGTAGACGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28930778 CACTGAT
1 CACTGAT
28930785 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28931259 original size:30 final size:30
Alignment explanation
Indices: 28931225--28931283 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
28931215 TCCTTGACTC
28931225 AAACTTTAGCAAAATTACAATTTTGCCCCT
1 AAACTTTAGCAAAATTACAATTTTGCCCCT
* * * *
28931255 AAACTTTTGCATATTTACACTTTTGCCCC
1 AAACTTTAGCAAAATTACAATTTTGCCCC
28931284 AAAGCTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AAACTTTAGCAAAATTACAATTTTGCCCCT
Found at i:28933664 original size:47 final size:49
Alignment explanation
Indices: 28933547--28933670 Score: 164
Period size: 49 Copynumber: 2.6 Consensus size: 49
28933537 TCATTTTCAC
* *
28933547 ATGCCATAGTCCA-ACTATGGTCTTACATGTAATCACATATCACATACCG
1 ATGCCATAGTCCAGA-TATGGTCTTACACGGAATCACATATCACATACCG
* * *
28933596 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACA-A-TG
1 ATGCCATAGTCCAGATATGGTCTTACACGGAATCACATATCACATACCG
*
28933643 ATGCCATATTCCAGATATGGTCTTACAC
1 ATGCCATAGTCCAGATATGGTCTTACAC
28933671 AGAGATTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 26 0.39
48 1 0.02
49 39 0.59
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (49 bp):
ATGCCATAGTCCAGATATGGTCTTACACGGAATCACATATCACATACCG
Found at i:28935867 original size:23 final size:23
Alignment explanation
Indices: 28935841--28935916 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
28935831 ATAAGTGCCA
28935841 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28935864 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28935887 CACTGATATGTAGACGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28935910 CACTGAT
1 CACTGAT
28935917 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28936391 original size:30 final size:30
Alignment explanation
Indices: 28936357--28936415 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
28936347 TCCTTGACTC
28936357 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
28936387 AAACTTTTGCATATTTACACTTTTGCCCC
1 AAACTTTGGCAAAATTACAATTTTGCCCC
28936416 AAAGCTCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:28940659 original size:42 final size:42
Alignment explanation
Indices: 28940600--28940704 Score: 174
Period size: 42 Copynumber: 2.5 Consensus size: 42
28940590 CACGGCCAAG
28940600 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
1 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
28940642 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
1 CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
* * * *
28940684 TCACATGCCCGTCTGCCAGGC
1 CCACACGCCCGTGTGCTAGGC
28940705 TGTCTACCAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.18, C:0.39, G:0.24, T:0.19
Consensus pattern (42 bp):
CCACACGCCCGTGTGCTAGGCCGTGTACCCTTCGAAATAGCC
Found at i:28941172 original size:20 final size:20
Alignment explanation
Indices: 28941147--28941185 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28941137 AACATTCAAA
28941147 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
28941167 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
28941186 ACCATACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:28942350 original size:24 final size:25
Alignment explanation
Indices: 28942273--28942394 Score: 156
Period size: 25 Copynumber: 4.9 Consensus size: 25
28942263 TCCTGTACAT
* * *
28942273 GTATGCTTAGACGAGTTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATTG
28942298 GTATGCTCACACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATTG
* * *
28942323 GTATGATCTCACGAGCTG-AAATTA
1 GTATGCTCACACGAGCTGTAAATTG
* * *
28942347 GTATGCTCACACGAGCTATATATCG
1 GTATGCTCACACGAGCTGTAAATTG
28942372 GTATGCTCACACGAGCTGTAAAT
1 GTATGCTCACACGAGCTGTAAAT
28942395 CAGCATGCTC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
24 20 0.24
25 62 0.76
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATTG
Found at i:28942351 original size:49 final size:50
Alignment explanation
Indices: 28942283--28942411 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 50
28942273 GTATGCTTAG
* * * * *
28942283 ACGAGTTGTAAATTGGTATGCTCACACGAGCTGTAAATTGGTATGATCTC
1 ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
* *
28942333 ACGAGCTG-AAATTAGTATGCTCACACGAGCTATATATCGGTATGCTCAC
1 ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
* * *
28942382 ACGAGCTGTAAATCAGCATGCTCATACGAG
1 ACGAGCTGTAAATTAGTATGCTCACACGAG
28942412 TTGTGGGTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 43 0.63
50 25 0.37
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (50 bp):
ACGAGCTGTAAATTAGTATGCTCACACGAGCTATAAATCGGTATGATCAC
Found at i:28942402 original size:25 final size:25
Alignment explanation
Indices: 28942273--28942411 Score: 136
Period size: 25 Copynumber: 5.6 Consensus size: 25
28942263 TCCTGTACAT
* * * **
28942273 GTATGCTTAGACGAGTTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATCA
**
28942298 GTATGCTCACACGAGCTGTAAATTG
1 GTATGCTCACACGAGCTGTAAATCA
* * *
28942323 GTATGATCTCACGAGCTG-AAATTA
1 GTATGCTCACACGAGCTGTAAATCA
* * *
28942347 GTATGCTCACACGAGCTATATATCG
1 GTATGCTCACACGAGCTGTAAATCA
28942372 GTATGCTCACACGAGCTGTAAATCA
1 GTATGCTCACACGAGCTGTAAATCA
* *
28942397 GCATGCTCATACGAG
1 GTATGCTCACACGAG
28942412 TTGTGGGTCG
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 20 0.21
25 76 0.79
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCA
Found at i:28957138 original size:27 final size:29
Alignment explanation
Indices: 28957090--28957143 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
28957080 TGAATTGTGA
* *
28957090 AAATTAATCAATTTT-TATTTTGTTTTAG
1 AAATTAATCAATTTTCAATTTGGTTTTAG
28957118 AAATTAA-CAATTTTCAATTTGGTTTT
1 AAATTAATCAATTTTCAATTTGGTTTT
28957144 TGGTTTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (29 bp):
AAATTAATCAATTTTCAATTTGGTTTTAG
Found at i:28958242 original size:14 final size:14
Alignment explanation
Indices: 28958223--28958251 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28958213 ATCAAGTTCG
28958223 AATATAACTACGAA
1 AATATAACTACGAA
28958237 AATATAACTACGAA
1 AATATAACTACGAA
28958251 A
1 A
28958252 CTGGACTTAA
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:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AATATAACTACGAA
Found at i:28959919 original size:33 final size:34
Alignment explanation
Indices: 28959848--28959927 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
28959838 TTATTGAAAG
* *
28959848 TGTTGAAGACACCAACGAAGTAATAAGAGTACTG
1 TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
* *
28959882 TGTTGAAGACACTAATGAAGT-ATTAGAGTACTC
1 TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
28959915 TGTTGAAGACACT
1 TGTTGAAGACACT
28959928 TTCAACTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 23 0.55
34 19 0.45
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (34 bp):
TGTTGAAGACACTAACGAAGTAATAAGAGTACTC
Found at i:28960671 original size:18 final size:18
Alignment explanation
Indices: 28960648--28960682 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28960638 AGGCGCTCTC
* *
28960648 CACCAAGTTATTCTCGAT
1 CACCAAGATATGCTCGAT
28960666 CACCAAGATATGCTCGA
1 CACCAAGATATGCTCGA
28960683 AGTTACTCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (18 bp):
CACCAAGATATGCTCGAT
Found at i:28967251 original size:23 final size:23
Alignment explanation
Indices: 28967225--28967316 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 23
28967215 GGACTCAGCA
*
28967225 CAGCTTGTATGAGCTTACTGTTT
1 CAGCTTGTATGAGCTTACCGTTT
* *
28967248 CAGC-TCTACGGAGCTTACCGTTT
1 CAGCTTGTA-TGAGCTTACCGTTT
*
28967271 CAGCTCG-ATAGAGCTTACCGTTTAT
1 CAGCTTGTAT-GAGCTTACCG-TT-T
* *
28967296 CAGCTCGAAATGAGCTTACCG
1 CAGCTTG-TATGAGCTTACCG
28967317 ATCATGGCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.05
23 31 0.55
24 2 0.04
25 8 0.14
26 10 0.18
27 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
CAGCTTGTATGAGCTTACCGTTT
Found at i:28967316 original size:26 final size:23
Alignment explanation
Indices: 28967235--28967316 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
28967225 CAGCTTGTAT
* * **
28967235 GAGCTTACTGTTTCAGCTCTACG
1 GAGCTTACCGTTTCAGCTCGAAA
*
28967258 GAGCTTACCGTTTCAGCTCGATA
1 GAGCTTACCGTTTCAGCTCGAAA
28967281 GAGCTTACCGTTTATCAGCTCGAAA
1 GAGCTTACCG-TT-TCAGCTCGAAA
28967306 TGAGCTTACCG
1 -GAGCTTACCG
28967317 ATCATGGCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
23 29 0.57
24 2 0.04
25 10 0.20
26 10 0.20
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGAAA
Found at i:28975766 original size:29 final size:29
Alignment explanation
Indices: 28975725--28975841 Score: 146
Period size: 29 Copynumber: 4.1 Consensus size: 29
28975715 GAAACATAAA
* *
28975725 TATGAAAATTAATTATGGTGAATTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* *
28975754 CATTTAAACTAATTATGGTGAATTTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
*
28975783 TATGTAAACTAATTATGGT-AAATTATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
* * * *
28975811 TATGTAAATTAATTATGATAAATATATAT
1 TATGTAAACTAATTATGGTGAATTTATAT
28975840 TA
1 TA
28975842 ACTAATTATG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
28 25 0.33
29 51 0.67
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (29 bp):
TATGTAAACTAATTATGGTGAATTTATAT
Found at i:28975817 original size:14 final size:14
Alignment explanation
Indices: 28975777--28975841 Score: 80
Period size: 14 Copynumber: 4.6 Consensus size: 14
28975767 TATGGTGAAT
28975777 TTATATTATGTAAA
1 TTATATTATGTAAA
*
28975791 CTA-ATTATGGTAAA
1 TTATATTAT-GTAAA
28975805 TTATATTATGTAAA
1 TTATATTATGTAAA
28975819 TTA-ATTATGATAAA
1 TTATATTATG-TAAA
28975833 TATATATTA
1 T-TATATTA
28975842 ACTAATTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.25
14 22 0.50
15 7 0.16
16 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.46
Consensus pattern (14 bp):
TTATATTATGTAAA
Found at i:28975826 original size:57 final size:58
Alignment explanation
Indices: 28975725--28975841 Score: 146
Period size: 57 Copynumber: 2.0 Consensus size: 58
28975715 GAAACATAAA
* * * * * *
28975725 TATGAAAATTAATTATGGTGAATTTATATCATTTAAACTAATTATGGTGAATTTATAT
1 TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
* * *
28975783 TATGTAAACTAATTATGGT-AAATTATATTATGTAAATTAATTATGATAAATATATAT
1 TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
28975840 TA
1 TA
28975842 ACTAATTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 33 0.66
58 17 0.34
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (58 bp):
TATGAAAACTAATTATGGTGAAATTATATCATGTAAACTAATTATGATAAATATATAT
Found at i:28984458 original size:20 final size:21
Alignment explanation
Indices: 28984433--28984474 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28984423 AAATAAAAGA
* *
28984433 TGGAAACGAGCT-CATTGAGC
1 TGGAAACAAGCTGAATTGAGC
28984453 TGGAAACAAGCTGAATTGAGC
1 TGGAAACAAGCTGAATTGAGC
28984474 T
1 T
28984475 CAACAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (21 bp):
TGGAAACAAGCTGAATTGAGC
Found at i:28986494 original size:20 final size:20
Alignment explanation
Indices: 28986456--28986492 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
28986446 TTTTTGGAGG
*
28986456 TATCGATATTTTAGTAAATT
1 TATCGATATCTTAGTAAATT
28986476 TATCGATA-CTTAGTAAA
1 TATCGATATCTTAGTAAA
28986493 ATACCGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (20 bp):
TATCGATATCTTAGTAAATT
Found at i:28989465 original size:18 final size:18
Alignment explanation
Indices: 28989442--28989478 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28989432 ATTAAGACTA
28989442 ATATGTAGTTGATTGATG
1 ATATGTAGTTGATTGATG
28989460 ATATGTAGTTGATTGATG
1 ATATGTAGTTGATTGATG
28989478 A
1 A
28989479 CAAAGTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (18 bp):
ATATGTAGTTGATTGATG
Found at i:28989488 original size:18 final size:18
Alignment explanation
Indices: 28989446--28989488 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28989436 AGACTAATAT
* *
28989446 GTAGTTGATTGATGATAT
1 GTAGTTGATTGATGAAAA
28989464 GTAGTTGATTGATGACAAA
1 GTAGTTGATTGATGA-AAA
28989483 GT-GTTG
1 GTAGTTG
28989489 TCATTGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.28, C:0.02, G:0.30, T:0.40
Consensus pattern (18 bp):
GTAGTTGATTGATGAAAA
Found at i:29002266 original size:40 final size:40
Alignment explanation
Indices: 29002222--29002483 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
29002212 GCTCCTCGTT
* *
29002222 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAGT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA-TCTCGCA
* * *
29002262 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29002302 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29002341 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29002380 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29002419 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29002460 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29002484 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 127 0.62
40 65 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29010350 original size:39 final size:39
Alignment explanation
Indices: 29010233--29010439 Score: 312
Period size: 39 Copynumber: 5.3 Consensus size: 39
29010223 GCTCCTCGTT
* *
29010233 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAGT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTA-TCTCGCA
* * *
29010273 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
29010313 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
29010352 CAAATGCCTTC-GGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
29010390 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
29010429 CAAATGCCTTC
1 CAAATGCCTTC
29010440 AGATCTTAGT
Statistics
Matches: 158, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
38 38 0.24
39 71 0.45
40 47 0.30
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:29010402 original size:77 final size:79
Alignment explanation
Indices: 29010233--29010439 Score: 314
Period size: 77 Copynumber: 2.6 Consensus size: 79
29010223 GCTCCTCGTT
* *
29010233 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAGT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTA-TCTCGCACAAATGCCTTCGGGACTTAACCC
*
29010296 GGATTTAGTAACTCGCA
63 GGAATTAGTAACTCGCA
*
29010313 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGA
*
29010376 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
29010390 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC
29010440 AGATCTTAGT
Statistics
Matches: 120, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
77 72 0.60
78 3 0.03
79 30 0.25
80 15 0.12
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:29014372 original size:28 final size:27
Alignment explanation
Indices: 29014350--29014456 Score: 151
Period size: 27 Copynumber: 3.8 Consensus size: 27
29014340 TTTTACATAC
29014350 TTTTTTAATTTTTTTTAATTTTAAAATA
1 TTTTTTAA-TTTTTTTAATTTTAAAATA
29014378 TTTTTTTAATTTTTTTAATTTTAAAATA
1 -TTTTTTAATTTTTTTAATTTTAAAATA
*
29014406 TTTTTTTATTTTTTTAATTTTAAAATA
1 TTTTTTAATTTTTTTAATTTTAAAATA
*
29014433 TTTTTAAAATACTTTTTTAATTTT
1 TTTTT-TAAT--TTTTTTAATTTT
29014457 TTAAAATTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
27 31 0.43
28 21 0.29
29 8 0.11
30 12 0.17
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTTAATTTTTTTAATTTTAAAATA
Found at i:29014372 original size:40 final size:38
Alignment explanation
Indices: 29014319--29014399 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 38
29014309 AATATATTTA
29014319 TTTTTTTAATTTTAAAATA-TTTTTTACATACTTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTTTTA-AT--TTTTTTAAT
29014359 TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
1 TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
29014397 TTT
1 TTT
29014400 AAAATATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
38 12 0.30
40 21 0.52
41 7 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (38 bp):
TTTTTTTAATTTTAAAATATTTTTTTAATTTTTTTAAT
Found at i:29014390 original size:8 final size:9
Alignment explanation
Indices: 29014318--29014426 Score: 69
Period size: 9 Copynumber: 11.6 Consensus size: 9
29014308 AAATATATTT
29014318 ATTTTTTTA
1 ATTTTTTTA
**
29014327 A-TTTTAAA
1 ATTTTTTTA
29014335 ATATTTTTTA
1 AT-TTTTTTA
29014345 CATACTTTTTTA
1 -AT--TTTTTTA
29014357 ATTTTTTTTA
1 A-TTTTTTTA
***
29014367 ATTTTAAAA
1 ATTTTTTTA
29014376 TATTTTTTTA
1 -ATTTTTTTA
29014386 ATTTTTTTA
1 ATTTTTTTA
**
29014395 A-TTTTAAA
1 ATTTTTTTA
*
29014403 ATATTTTTTT
1 AT-TTTTTTA
29014413 ATTTTTTTA
1 ATTTTTTTA
29014422 ATTTT
1 ATTTT
29014427 AAAATATTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
8 12 0.16
9 27 0.36
10 25 0.33
11 3 0.04
12 8 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:29014390 original size:27 final size:28
Alignment explanation
Indices: 29014350--29014456 Score: 162
Period size: 28 Copynumber: 3.8 Consensus size: 28
29014340 TTTTACATAC
29014350 TTTTTTAATTTTTTTTAATTTTAAAATAT
1 TTTTTTAA-TTTTTTTAATTTTAAAATAT
29014379 TTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTTTAATTTTTTTAATTTTAAAATAT
29014407 TTTTTT-ATTTTTTTAATTTTAAAATAT
1 TTTTTTAATTTTTTTAATTTTAAAATAT
**
29014434 TTTTAAAATACTTTTTTAATTTT
1 TTTTTTAAT--TTTTTTAATTTT
29014457 TTAAAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
27 25 0.34
28 28 0.38
29 8 0.11
30 12 0.16
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:29014411 original size:19 final size:19
Alignment explanation
Indices: 29014317--29014390 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
29014307 TAAATATATT
29014317 TATTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
* **
29014336 TATTTTTTACATACTTTTTTAA
1 TATTTTTT---TAATTTTAAAA
29014358 T-TTTTTTTAATTTTAAAA
1 TATTTTTTTAATTTTAAAA
29014376 TATTTTTTTAATTTT
1 TATTTTTTTAATTTT
29014391 TTTAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.20
19 21 0.47
21 6 0.13
22 9 0.20
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTTTAATTTTAAAA
Found at i:29014437 original size:11 final size:11
Alignment explanation
Indices: 29014423--29014473 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
29014413 ATTTTTTTAA
29014423 TTTTAAAATAT
1 TTTTAAAATAT
29014434 TTTTAAAATACT
1 TTTTAAAATA-T
*
29014446 TTTT-TAAT-T
1 TTTTAAAATAT
29014455 TTTT-AAA-AT
1 TTTTAAAATAT
29014464 TTTTAAAATA
1 TTTTAAAATA
29014474 AAAATGGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 12 0.35
10 3 0.09
11 14 0.41
12 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29014466 original size:30 final size:30
Alignment explanation
Indices: 29014360--29014473 Score: 132
Period size: 27 Copynumber: 4.0 Consensus size: 30
29014350 TTTTTTAATT
**
29014360 TTTTTTAATTTTAAAATATTTTTTTAAT--
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
* *
29014388 TTTTTTAATTTTAAAATATTTTT---TTAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
29014415 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
*
29014445 TTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 TTTTTTAA-TTTTAAAATATTTTTAAAATA
29014474 AAAATGGGCC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
25 1 0.01
27 23 0.30
28 23 0.30
30 22 0.29
31 7 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:29018519 original size:45 final size:45
Alignment explanation
Indices: 29018452--29018626 Score: 237
Period size: 45 Copynumber: 3.9 Consensus size: 45
29018442 GTGTACTGAG
* **
29018452 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTAGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* * *
29018497 TACCATTGATTATAAAAGTGGTTGCTATGTGCTGACTCCACCAAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* **
29018542 AATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
* *
29018587 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACC
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACC
29018627 GTGTAACGGT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
43 6 0.05
44 13 0.12
45 94 0.83
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCAAA
Found at i:29026540 original size:27 final size:27
Alignment explanation
Indices: 29026510--29026605 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 27
29026500 AAATATATAA
*
29026510 ACTAAATAAATTAGTATATTGAAATAT
1 ACTAAATAAATTAGTATATTAAAATAT
* * * ** *
29026537 ACTAAACAAA-TATTTATGTTTAATTTAA
1 ACTAAATAAATTA-GTAT-ATTAAAATAT
*
29026565 ACTATAATAAATTAGTAAATTAAAATAT
1 ACTA-AATAAATTAGTATATTAAAATAT
* *
29026593 ATTAAAAAAATTA
1 ACTAAATAAATTA
29026606 TTAGAGAAGT
Statistics
Matches: 49, Mismatches: 16, Indels: 8
0.67 0.22 0.11
Matches are distributed among these distances:
26 2 0.04
27 20 0.41
28 18 0.37
29 7 0.14
30 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (27 bp):
ACTAAATAAATTAGTATATTAAAATAT
Found at i:29029684 original size:23 final size:23
Alignment explanation
Indices: 29029652--29029703 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
29029642 GAGTTGACAT
* **
29029652 TAATGATTAAACCGTTAATCTTC
1 TAATGCTTAAACAATTAATCTTC
*
29029675 TAATGCTTAAACAATTAATTTTC
1 TAATGCTTAAACAATTAATCTTC
29029698 TAATGC
1 TAATGC
29029704 AGTGAAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (23 bp):
TAATGCTTAAACAATTAATCTTC
Found at i:29033413 original size:20 final size:20
Alignment explanation
Indices: 29033285--29033444 Score: 92
Period size: 20 Copynumber: 7.8 Consensus size: 20
29033275 ATTTTGTATA
* *
29033285 TTACCAAAATTTATAAGGAAA
1 TTACCAAAATTTCTAA-GAAT
* * *
29033306 TT-CCAAATTTTTTAAGGAT
1 TTACCAAAATTTCTAAGAAT
* * * *
29033325 TTACAAAAAGTTCTAAGTAG
1 TTACCAAAATTTCTAAGAAT
* *
29033345 TTACCAAAATTTCTAATAAA
1 TTACCAAAATTTCTAAGAAT
*** *
29033365 TTATTGAAATTTCT-A-AAG
1 TTACCAAAATTTCTAAGAAT
*
29033383 TTACACAAAAATTTCTAAGACT
1 TTAC-C-AAAATTTCTAAGAAT
29033405 TTACCAAAATTAGTATCTAAGAAT
1 TTACCAAAA-T--T-TCTAAGAAT
29033429 TTACCAAAATTTCTAA
1 TTACCAAAATTTCTAA
29033445 TATGCCATAT
Statistics
Matches: 105, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 65 0.62
21 6 0.06
22 5 0.05
23 2 0.02
24 17 0.16
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (20 bp):
TTACCAAAATTTCTAAGAAT
Found at i:29037077 original size:17 final size:19
Alignment explanation
Indices: 29037045--29037079 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29037035 TTATATATTT
29037045 AAGAATAGATTAAGTGAAG
1 AAGAATAGATTAAGTGAAG
29037064 AAGAATA-A-TAAGTGAA
1 AAGAATAGATTAAGTGAA
29037080 TTAGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (19 bp):
AAGAATAGATTAAGTGAAG
Found at i:29039833 original size:22 final size:22
Alignment explanation
Indices: 29039803--29039845 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29039793 CAGAATGATT
29039803 TGTTAATTATTAAAATATATTA
1 TGTTAATTATTAAAATATATTA
* **
29039825 TGTTGATTATTATGATATATT
1 TGTTAATTATTAAAATATATT
29039846 CAGGAATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
TGTTAATTATTAAAATATATTA
Found at i:29040029 original size:24 final size:24
Alignment explanation
Indices: 29039999--29040045 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29039989 TTCAGGTTGA
29039999 GATTTCAATGCATCTCATCTCATT
1 GATTTCAATGCATCTCATCTCATT
29040023 GATTTCAATGCATCTCATCTCAT
1 GATTTCAATGCATCTCATCTCAT
29040046 CACATCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (24 bp):
GATTTCAATGCATCTCATCTCATT
Found at i:29048093 original size:9 final size:9
Alignment explanation
Indices: 29048079--29048109 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29048069 GATAAAGGAA
29048079 AATTAAATT
1 AATTAAATT
29048088 AATTAAATT
1 AATTAAATT
29048097 AATTAAAATT
1 AATT-AAATT
29048107 AAT
1 AAT
29048110 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:29048572 original size:37 final size:37
Alignment explanation
Indices: 29048526--29048596 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
29048516 AAAAATAGTA
*
29048526 TTATTTTAATAGT-TTAATATTAAATTTAAT-TTAATAC
1 TTATCTTAATAGTATT-ATATT-AATTTAATATTAATAC
*
29048563 TTATCTTAATAGTATTTTATTAATTTAATATTAA
1 TTATCTTAATAGTATTATATTAATTTAATATTAA
29048597 AATTATTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 8 0.27
37 20 0.67
38 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (37 bp):
TTATCTTAATAGTATTATATTAATTTAATATTAATAC
Found at i:29053871 original size:6 final size:6
Alignment explanation
Indices: 29053814--29053889 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
29053804 TAAACAAATT
* * * * * *
29053814 AAATTA AAATAA AAATTAA ATACAA AAACAA AGATAA AGATAA AAATGAA
1 AAATAA AAATAA AAA-TAA AAATAA AAATAA AAATAA AAATAA AAAT-AA
* * *
29053864 AAATAA AACTAA AACTTA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
29053890 TTTTTAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 46 0.81
7 11 0.19
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:29065828 original size:12 final size:12
Alignment explanation
Indices: 29065811--29065835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29065801 ACATATGAAG
29065811 ACCAATAATTAA
1 ACCAATAATTAA
29065823 ACCAATAATTAA
1 ACCAATAATTAA
29065835 A
1 A
29065836 ATGACTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ACCAATAATTAA
Found at i:29067941 original size:6 final size:6
Alignment explanation
Indices: 29067897--29067923 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29067887 CAATTTGGTT
29067897 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
29067924 AATTAATTTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:29067955 original size:21 final size:22
Alignment explanation
Indices: 29067909--29067949 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29067899 TTTATTTTTA
*
29067909 TTTTTATTTTTATTTAATTAAT
1 TTTTTATTTTTATATAATTAAT
*
29067931 TTTTTATTTTT-TATGATTA
1 TTTTTATTTTTATATAATTA
29067950 TCTTTTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTATTTTTATATAATTAAT
Found at i:29076809 original size:26 final size:25
Alignment explanation
Indices: 29076778--29076841 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
29076768 TATTTTCTCG
29076778 AAATTTTATTAAGGGCAAAATCATC
1 AAATTTTATTAAGGGCAAAATCATC
* **
29076803 AAAATTTTACT-AGAGGCAAAATTGTC
1 -AAATTTTATTAAG-GGCAAAATCATC
29076829 -AATTTTATTAAGG
1 AAATTTTATTAAGG
29076842 ATAAAATTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 9 0.28
25 4 0.12
26 19 0.59
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (25 bp):
AAATTTTATTAAGGGCAAAATCATC
Found at i:29080786 original size:23 final size:23
Alignment explanation
Indices: 29080733--29080782 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29080723 AATCACAACT
**
29080733 TGAAACATTTTTCAGTTATGTTG
1 TGAAACATTTTTCAGTTATGAAG
29080756 TGAAACATTTTTCAGTTAT-AAG
1 TGAAACATTTTTCAGTTATGAAG
29080778 TGAAA
1 TGAAA
29080783 ACATGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (23 bp):
TGAAACATTTTTCAGTTATGAAG
Found at i:29083101 original size:5 final size:5
Alignment explanation
Indices: 29083091--29083144 Score: 81
Period size: 5 Copynumber: 10.6 Consensus size: 5
29083081 AATCAAAGCT
**
29083091 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTCC TTGCC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC
29083142 TTT
1 TTT
29083145 GGGTTTTGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
5 41 0.93
6 3 0.07
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:29093990 original size:40 final size:40
Alignment explanation
Indices: 29093953--29094138 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
29093943 GCTACTCGTT
* *
29093953 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
29093993 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
29094033 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
29094073 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
29094114 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
29094139 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29098781 original size:40 final size:40
Alignment explanation
Indices: 29098744--29098929 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
29098734 GCTACTCGTT
* *
29098744 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
29098784 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
29098824 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
29098864 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
29098905 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
29098930 CATCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29118719 original size:18 final size:18
Alignment explanation
Indices: 29118696--29118733 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29118686 TGAAAGGTTG
29118696 TTGATAGATAAACAACTT
1 TTGATAGATAAACAACTT
29118714 TTGATAGATAAACAACTT
1 TTGATAGATAAACAACTT
29118732 TT
1 TT
29118734 ATGAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGATAGATAAACAACTT
Found at i:29142540 original size:10 final size:10
Alignment explanation
Indices: 29142525--29142614 Score: 62
Period size: 10 Copynumber: 9.0 Consensus size: 10
29142515 TTCAAATAAT
*
29142525 TATAAAAAAA
1 TATAAAAATA
29142535 TATAAAAATA
1 TATAAAAATA
*
29142545 TTTAAAAATA
1 TATAAAAATA
29142555 TATATAAAGA-A
1 TATA-AAA-ATA
* *
29142566 TTATAAGAATT
1 -TATAAAAATA
*
29142577 TATAAAATTA
1 TATAAAAATA
*
29142587 T-TAAAATTA
1 TATAAAAATA
29142596 T-TAAAAAT-
1 TATAAAAATA
29142604 TCATAAAAATA
1 T-ATAAAAATA
29142615 AAAATAGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 15 0.23
10 37 0.58
11 6 0.09
12 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
TATAAAAATA
Found at i:29142543 original size:22 final size:22
Alignment explanation
Indices: 29142518--29142571 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
29142508 ATGATTTTTC
29142518 AAATAATTATAAAAAAATATAA
1 AAATAATTATAAAAAAATATAA
* *
29142540 AAAT-ATT-TAAAAATATATAT
1 AAATAATTATAAAAAAATATAA
*
29142560 AAAGAATTATAA
1 AAATAATTATAA
29142572 GAATTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 6 0.22
22 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATAATTATAAAAAAATATAA
Found at i:29147166 original size:17 final size:16
Alignment explanation
Indices: 29147144--29147178 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
29147134 TTTATGTATT
29147144 AAGTTGATTGTTTCGAA
1 AAGTTGATTGTTTC-AA
29147161 AAGTTGATTGTTTCAA
1 AAGTTGATTGTTTCAA
29147177 AA
1 AA
29147179 TTCTCTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (16 bp):
AAGTTGATTGTTTCAA
Found at i:29156457 original size:17 final size:15
Alignment explanation
Indices: 29156435--29156476 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 15
29156425 ATTCCCTAAT
29156435 TTATTTTTATAATTAA
1 TTATTTTTATAA-TAA
29156451 TTAATTTTT-TAAT-A
1 TT-ATTTTTATAATAA
29156465 TTATTTTTATAA
1 TTATTTTTATAA
29156477 AAAAACCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 1 0.04
16 5 0.21
17 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTTTATAATAA
Found at i:29157417 original size:61 final size:61
Alignment explanation
Indices: 29157359--29157479 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
29157349 ATATAAAATA
** *
29157359 TTCAACAAATTTAG-CACTCAATGTTTACAAAACTTGTCATTTTAGTT-TGAATTCTAAAAAG
1 TTCAACAAATTTAGTC-CTCAAAATTTACAAAACTTGTCAATTTAGTTCT-AATTCTAAAAAG
* *
29157420 TTCAATAAATTTAGTCCTCAAAATTTACAAAATTTGTCAATTTAGTTCTAATTCTAAAAA
1 TTCAACAAATTTAGTCCTCAAAATTTACAAAACTTGTCAATTTAGTTCTAATTCTAAAAA
29157480 ATTAATAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
61 51 0.96
62 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (61 bp):
TTCAACAAATTTAGTCCTCAAAATTTACAAAACTTGTCAATTTAGTTCTAATTCTAAAAAG
Found at i:29160668 original size:189 final size:189
Alignment explanation
Indices: 29160337--29160704 Score: 619
Period size: 189 Copynumber: 1.9 Consensus size: 189
29160327 TCGAGCTACC
* *
29160337 GGAGAGAAGGTTTCTTTGAAATCAACACCATATTGTTATGCATAACCTTTCGCCACAAGACAAGC
1 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
* *
29160402 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTTTCTTGAACACCCACTTCAAACCAATTG
66 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
* * *
29160467 CATTTTTGTCTTTCGACAAGTCGACCATGTCCCAAGTTCCATTCTTTTCAATAGAAACA
131 CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTCAATAGAAACA
*
29160526 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACGAGC
1 GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
**
29160591 TTTGTGCTTTTGGATGCTTCCATCTGTACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
66 TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
* * *
29160656 TAATTCTGTCTTTCGGCAAGTCGACCATCTCCCAATTTCCATTCTTTTC
131 CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTC
29160705 GATGGATTTC
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
189 166 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (189 bp):
GGAGAGAAGGTTTCTTCGAAATCAACACCATATTGCTATGCATAACCTTTCGCCACAAGACAAGC
TTTGTGCTTTTGGATGCTTCCATCTACACCAAATTTTGTCTTAAACACCCACTTCAAACCAATTG
CAATTCTGTCTTTCGACAAGTCGACCATCTCCCAAGTTCCATTCTTTTCAATAGAAACA
Found at i:29162106 original size:17 final size:17
Alignment explanation
Indices: 29162065--29162098 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29162055 TTAAATCAGG
29162065 AACAAATTGAACATTGT
1 AACAAATTGAACATTGT
29162082 AACAAATTGAACATTGT
1 AACAAATTGAACATTGT
29162099 CCAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
AACAAATTGAACATTGT
Found at i:29173091 original size:20 final size:20
Alignment explanation
Indices: 29173052--29173091 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29173042 TCTGACGAGA
*
29173052 AAATTCATTTTTAGTGTATT
1 AAATTCATTTTTAGTCTATT
* *
29173072 AAATTTATTTTTGGTCTATT
1 AAATTCATTTTTAGTCTATT
29173092 GGGAAGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (20 bp):
AAATTCATTTTTAGTCTATT
Found at i:29176652 original size:93 final size:90
Alignment explanation
Indices: 29176539--29176707 Score: 284
Period size: 90 Copynumber: 1.8 Consensus size: 90
29176529 GGATGGTTGA
* *
29176539 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC---TGGATGCGAACGCCCGAACTCGTTGAGT
29176604 TGAGTCCGAGTTCGTGAGATGTAACTAG
63 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
29176632 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGGATGCGAACGCCCGAGCTCGTTGAGTTGA
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGGATGCGAACGCCCGAACTCGTTGAGTTGA
29176697 GTCCGAGTTCG
66 GTCCGAGTTCG
29176708 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
90 39 0.53
93 34 0.47
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (90 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGGATGCGAACGCCCGAACTCGTTGAGTTGA
GTCCGAGTTCGTGAGATGTAACTAG
Found at i:29176657 original size:47 final size:46
Alignment explanation
Indices: 29176542--29176706 Score: 200
Period size: 47 Copynumber: 3.6 Consensus size: 46
29176532 TGGTTGAGCA
*
29176542 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TG-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA--GATGCGAACTGC
* *
29176588 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATG-TAACTAGGC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGATGCGAACT--GC
29176634 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTG-GATGCGAAC-GC
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGATGCGAACTGC
*
29176679 -CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
29176707 GCTTATGGGC
Statistics
Matches: 106, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
42 2 0.02
43 32 0.30
45 5 0.05
46 29 0.27
47 33 0.31
48 5 0.05
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGATGCGAACTGC
Found at i:29189779 original size:16 final size:18
Alignment explanation
Indices: 29189743--29189780 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
29189733 ATTTAGTTTT
29189743 TTAACTTATATACTATAA
1 TTAACTTATATACTATAA
*
29189761 TTAACTTA-ATA-TTTAA
1 TTAACTTATATACTATAA
29189777 TTAA
1 TTAA
29189781 AAATAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAACTTATATACTATAA
Found at i:29192375 original size:50 final size:50
Alignment explanation
Indices: 29192250--29192495 Score: 249
Period size: 50 Copynumber: 4.8 Consensus size: 50
29192240 ATTTGGGTAA
* *
29192250 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* * *
29192306 TGAGGTCCCATGTAAGACCATGTCTGGGAGATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** ** *
29192356 AGAGGTCCTATGTAAGACCACATCTGGGACATGGTGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
29192406 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGTACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
29192456 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
29192496 TAGTACATAA
Statistics
Matches: 159, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
50 117 0.74
53 3 0.02
55 1 0.01
56 38 0.24
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:29200085 original size:50 final size:51
Alignment explanation
Indices: 29199968--29200208 Score: 227
Period size: 50 Copynumber: 4.7 Consensus size: 51
29199958 TAAAGAGATG
* * * *
29199968 CCATGTAAGACCATGTTTGGGACATGGCATTAGCATCATTGAGATTATGTGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC--TGAG---ATGAGAGGTC
* * *
29200024 CTATGTAAGACCATGTTTGGGAGATTGCGTTGGCA-CTGAGATGAGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
29200074 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC-GAGATGAGAGGTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
** * * * * * **
29200124 CCCCGTAAGACCATGTTTGGGACATGACATGGGCA-CCGATATGAGAACTC
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
* * * * *
29200174 TCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCA
29200209 ATACAGAAAA
Statistics
Matches: 158, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 121 0.77
51 1 0.01
53 4 0.03
55 1 0.01
56 30 0.19
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (51 bp):
CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGCTGAGATGAGAGGTC
Found at i:29200159 original size:100 final size:102
Alignment explanation
Indices: 29199968--29200208 Score: 254
Period size: 100 Copynumber: 2.3 Consensus size: 102
29199958 TAAAGAGATG
* * * * *
29199968 CCATGTAAGACCATGTTTGGGACATGGCATTAGCATCATTGAGATTATGTGAGGTCCTATGTAAG
1 CCATGTAAGACCATGTTTGGGACATGGCATTGGCAGC--TGAG--TATGAGAGGTCCCACGTAAG
* * * * **
29200033 ACCATGTTTGGGAGATTGCGTTGGCACTGAGATGAGAGGTC
62 ACCATGTTTGGGACATTGCATGGGCACCGAGATGAGAACTC
* *
29200074 CCATGTAAGACCATGTTTGGGACATGGCGTTGGCAGC-GAG-ATGAGAGGTCCCCCGTAAGACCA
1 CCATGTAAGACCATGTTTGGGACATGGCATTGGCAGCTGAGTATGAGAGGTCCCACGTAAGACCA
*
29200137 TGTTTGGGACA-TGACATGGGCACCGATATGAGAACTC
66 TGTTTGGGACATTG-CATGGGCACCGAGATGAGAACTC
* * * *
29200174 TCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CCATGTAAGACCATGTTTGGGACATGGCATTGGCA
29200209 ATACAGAAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
99 2 0.02
100 76 0.66
103 3 0.03
106 34 0.30
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (102 bp):
CCATGTAAGACCATGTTTGGGACATGGCATTGGCAGCTGAGTATGAGAGGTCCCACGTAAGACCA
TGTTTGGGACATTGCATGGGCACCGAGATGAGAACTC
Found at i:29200474 original size:12 final size:12
Alignment explanation
Indices: 29200457--29200488 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29200447 ATGAGTTATT
*
29200457 TAAGTAAGCAAG
1 TAAGTAAACAAG
29200469 TAAGTAAACAAG
1 TAAGTAAACAAG
29200481 TAAGTAAA
1 TAAGTAAA
29200489 AAACGAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:29203373 original size:9 final size:9
Alignment explanation
Indices: 29203359--29203386 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29203349 TTTTGTTACA
29203359 ACAATTAAT
1 ACAATTAAT
29203368 ACAATTAAT
1 ACAATTAAT
29203377 ACAATTAAT
1 ACAATTAAT
29203386 A
1 A
29203387 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:29203408 original size:68 final size:68
Alignment explanation
Indices: 29203333--29203529 Score: 290
Period size: 59 Copynumber: 3.1 Consensus size: 68
29203323 GTTTGTTTTG
*
29203333 CTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
1 CTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
29203398 TTA
66 TTA
29203401 CTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGATAAAT
1 CTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
29203457 TTA
66 TTA
* *
29203460 CTAATCAAATGTTAGATTTTATTACAATAATTAATACAATT-A-ACAATTAATAATTTGATAATT
1 CTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
29203523 TTA
66 TTA
29203526 CTAA
1 CTAA
29203530 CAATTAATTT
Statistics
Matches: 117, Mismatches: 3, Indels: 20
0.84 0.02 0.14
Matches are distributed among these distances:
59 56 0.48
60 1 0.01
62 1 0.01
65 2 0.02
66 27 0.23
67 2 0.02
68 28 0.24
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
CTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
TTA
Found at i:29203539 original size:16 final size:16
Alignment explanation
Indices: 29203518--29203559 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
29203508 AATAATTTGA
*
29203518 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
29203534 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
29203550 TAGTTTTAAT
1 TAATTTTAAT
29203560 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:29203543 original size:22 final size:22
Alignment explanation
Indices: 29203533--29203593 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
29203523 TTACTAACAA
* * *
29203533 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
29203555 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
29203577 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
29203594 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:29203551 original size:59 final size:63
Alignment explanation
Indices: 29203333--29203551 Score: 222
Period size: 59 Copynumber: 3.5 Consensus size: 63
29203323 GTTTGTTTTG
* *
29203333 CTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGATAAAT
1 CTAATCAAA-GTTAGA-TTT-TAATAACAATTAATACAATT-A-ACAATTAATAATTTGATAAAT
29203398 TTA
61 TTA
* * *
29203401 CTAATCAAATGTTAGATTTT-ATTACAA-CAAT-TAA-T-ACAATTAATAATTTGATAAATTTA
1 CTAATCAAA-GTTAGATTTTAATAACAATTAATACAATTAACAATTAATAATTTGATAAATTTA
* * *
29203460 CTAATCAAATGTTAGATTTTATTACAATAATTAATACAATTAACAATTAATAATTTGATAATTTT
1 CTAATCAAA-GTTAGATTTTA--ATAACAATTAATACAATTAACAATTAATAATTTGATAAATTT
29203525 A
63 A
29203526 CTAA-C-AA-TTA-ATTTTAATAACAATTA
1 CTAATCAAAGTTAGATTTTAATAACAATTA
29203552 GTTTTAATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
59 52 0.39
61 6 0.05
62 8 0.06
63 5 0.04
64 7 0.05
65 7 0.05
66 28 0.21
67 3 0.02
68 16 0.12
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (63 bp):
CTAATCAAAGTTAGATTTTAATAACAATTAATACAATTAACAATTAATAATTTGATAAATTTA
Found at i:29204761 original size:20 final size:21
Alignment explanation
Indices: 29204738--29204785 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
29204728 AATCAAGTAA
29204738 AATTAACATAA-TTAAACATT
1 AATTAACATAATTTAAACATT
**
29204758 AATTAATTTAATTTAAACA-T
1 AATTAACATAATTTAAACATT
*
29204778 GATTAACA
1 AATTAACA
29204786 AGGTGAACGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (21 bp):
AATTAACATAATTTAAACATT
Found at i:29211047 original size:45 final size:45
Alignment explanation
Indices: 29210983--29211074 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
29210973 TACAATTGAA
29210983 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
1 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
29211028 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
1 TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
29211073 TT
1 TT
29211075 GAGCTCCGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (45 bp):
TTATGCTAATCAAATTAGCACACAACCTCTACGAGATTAACATTC
Found at i:29219767 original size:25 final size:26
Alignment explanation
Indices: 29219736--29219791 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
29219726 AAATTAAAAG
29219736 AAAAGAAAAAG-AACGAAGAAGA-AGA
1 AAAAG-AAAAGTAACGAAGAAGAGAGA
*
29219761 AAAAGAAGAGTAACGAAGAAGATGAGA
1 AAAAGAAAAGTAACGAAGAAGA-GAGA
29219788 AAAA
1 AAAA
29219792 CTAAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
27 7 0.26
ACGTcount: A:0.68, C:0.04, G:0.25, T:0.04
Consensus pattern (26 bp):
AAAAGAAAAGTAACGAAGAAGAGAGA
Found at i:29232846 original size:25 final size:25
Alignment explanation
Indices: 29232808--29232885 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
29232798 TATTAGTTTT
* * * *
29232808 AGCTCTTATAAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGTTATTC
**
29232833 AGCTCGTATGAGCTTATTGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
29232858 AGCTCGGAGGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
29232883 AGC
1 AGC
29232886 CCCGGAGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:29232895 original size:25 final size:25
Alignment explanation
Indices: 29232818--29232899 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
29232808 AGCTCTTATA
* * * * *
29232818 AGCTTACCGATACTCAGCTCGTATG
1 AGCTTACCGTTATTCAGCCCGGAGG
** *
29232843 AGCTTATTGTTATTCAGCTCGGAGG
1 AGCTTACCGTTATTCAGCCCGGAGG
29232868 AGCTTACCGTTATTCAGCCCCGGA-G
1 AGCTTACCGTTATTCAG-CCCGGAGG
29232893 AGCTTAC
1 AGCTTAC
29232900 TATTTATAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 42 0.89
26 5 0.11
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (25 bp):
AGCTTACCGTTATTCAGCCCGGAGG
Found at i:29237761 original size:20 final size:20
Alignment explanation
Indices: 29237718--29237766 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
29237708 GTGACCCCTG
*
29237718 TTTTCAAAATTTTTAGATTC
1 TTTTCAAAAATTTTAGATTC
*
29237738 TTTTCTAAAAATTTTA-ATTTT
1 TTTTC-AAAAATTTTAGA-TTC
29237759 TTTTCAAA
1 TTTTCAAA
29237767 TTAGTCCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTCAAAAATTTTAGATTC
Found at i:29245857 original size:21 final size:20
Alignment explanation
Indices: 29245829--29245867 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29245819 TGACCCATGC
*
29245829 TTTCAAAATTTTCAATTTTT
1 TTTCAAAACTTTCAATTTTT
*
29245849 TTTCTAAAACTTTCTATTT
1 TTTC-AAAACTTTCAATTT
29245868 ATTTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTCAAAACTTTCAATTTTT
Found at i:29253002 original size:16 final size:17
Alignment explanation
Indices: 29252969--29253020 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
29252959 TTTAAAATTT
* *
29252969 ATATATGAATTGTAAAA
1 ATATATAAATTATAAAA
29252986 ATATATAAATT-TAAAA
1 ATATATAAATTATAAAA
*
29253002 A-ATCTAAAATTATAAAA
1 ATATAT-AAATTATAAAA
29253019 AT
1 AT
29253021 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 16 0.53
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATATATAAATTATAAAA
Done.