Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 119 of 187
Found at i:35292266 original size:82 final size:81
Alignment explanation
Indices: 35292153--35292308 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35292143 AAATTGTACA
* *
35292153 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35292217 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35292234 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35292299 TGCGAGTTGA
65 TGCGAATTGA
35292309 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35292320 original size:82 final size:81
Alignment explanation
Indices: 35292149--35292329 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
35292139 GATTAAATTG
* *
35292149 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35292214 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35292230 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35292294 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35292312 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35292330 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35300373 original size:27 final size:27
Alignment explanation
Indices: 35300342--35300519 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35300332 TAAATTGTAC
35300342 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35300369 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35300395 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35300423 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35300451 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35300478 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35300505 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35300520 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35300456 original size:82 final size:81
Alignment explanation
Indices: 35300343--35300498 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35300333 AAATTGTACA
* *
35300343 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
35300407 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
35300424 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
35300489 TGCGAGTTGA
65 TGCGAATTGA
35300499 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:35300510 original size:82 final size:81
Alignment explanation
Indices: 35300339--35300519 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
35300329 GATTAAATTG
* *
35300339 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
35300404 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
35300420 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
35300484 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
35300502 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
35300520 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35303309 original size:14 final size:14
Alignment explanation
Indices: 35303290--35303341 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
35303280 TAATAGACAC
*
35303290 AATTTTAACAAATA
1 AATTTTAACAATTA
35303304 AATTTTAACAATGTTA
1 AATTTTAACAA--TTA
*
35303320 AATATTAACAATTA
1 AATTTTAACAATTA
35303334 AATTTTAA
1 AATTTTAA
35303342 TTTTTAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (14 bp):
AATTTTAACAATTA
Found at i:35303883 original size:11 final size:11
Alignment explanation
Indices: 35303866--35303903 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
35303856 TTTTTAATCA
35303866 AATATATATTT
1 AATATATATTT
* *
35303877 TATATATATTA
1 AATATATATTT
35303888 AATATATATTT
1 AATATATATTT
35303899 AATAT
1 AATAT
35303904 GGGCCGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:35308563 original size:43 final size:41
Alignment explanation
Indices: 35308455--35308563 Score: 132
Period size: 40 Copynumber: 2.6 Consensus size: 41
35308445 TTCTTCTATT
*
35308455 TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTGATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTAATC
* * *
35308496 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTATGATTTAATCC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTAT-ATGTAAT-C
*
35308539 T-CTCCACTGTAACTTCAGGGAGATA
1 TGCTCCACTGCAACTTCAGGGAGATA
35308564 GGATTTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 22 0.39
41 8 0.14
42 7 0.12
43 20 0.35
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTATATGTAATC
Found at i:35309028 original size:88 final size:88
Alignment explanation
Indices: 35308879--35309315 Score: 700
Period size: 88 Copynumber: 5.0 Consensus size: 88
35308869 AAGACTGATG
** * *
35308879 TCTTCGATCTGCTT-TGCTACCAGTACAGGAAGGCAAGATCTG-TCATTTTCGACCTACTCCACT
1 TCTTCGATCTGCTTCT-CTGTCAGTACAGGAAGGCAAGATCTGCT-ATTTTCAACCTGCTCCACT
*
35308942 GCTGCCCAGGGAGACAAGGCTGGTA
64 ACTGCCCAGGGAGACAAGGCTGGTA
*
35308967 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
35309032 TGCCCAGGGAGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
*
35309055 TCTTCGA-CTTGCTTCTCTGTCAGTACAGGAAGGAAAGATCTGCTATTTTCAACCTGCTCCACTA
1 TCTTCGATC-TGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTA
*
35309119 CTGCCCAGGGGGACAAGGCTGGTA
65 CTGCCCAGGGAGACAAGGCTGGTA
* *
35309143 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTGAAGCTGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
*
35309208 TGCCCAGGGGGACAAGGCTGGTA
66 TGCCCAGGGAGACAAGGCTGGTA
*
35309231 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
* *
35309296 CGCCTAGGGAGACAAGGCTG
66 TGCCCAGGGAGACAAGGCTG
35309316 AAGTTTTACC
Statistics
Matches: 327, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
87 1 0.00
88 323 0.99
89 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTAC
TGCCCAGGGAGACAAGGCTGGTA
Found at i:35317704 original size:9 final size:9
Alignment explanation
Indices: 35317692--35317758 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
35317682 TTTTGTTAAA
35317692 AATTAACCG
1 AATTAACCG
35317701 AATTAACCG
1 AATTAACCG
35317710 AATT-ACCTG
1 AATTAACC-G
*
35317719 AATTAATCG
1 AATTAACCG
*
35317728 AATTACCCG
1 AATTAACCG
*
35317737 AATTAATCG
1 AATTAACCG
35317746 AATTAACCG
1 AATTAACCG
35317755 AATT
1 AATT
35317759 GAATCACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 3 0.06
9 45 0.90
10 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:35317884 original size:18 final size:18
Alignment explanation
Indices: 35317861--35317904 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35317851 AATTTTTATG
*
35317861 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGAATA
35317879 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
35317897 CTTGGGTT
1 ATTGGGTT
35317905 TGGATTGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:35318493 original size:24 final size:24
Alignment explanation
Indices: 35318460--35318507 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
35318450 AATTTAACAT
*
35318460 CATATAAACATTATCATATATCTA
1 CATATAAACATTACCATATATCTA
*
35318484 CATATGAACATTACCATATATCTA
1 CATATAAACATTACCATATATCTA
35318508 TGCCTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (24 bp):
CATATAAACATTACCATATATCTA
Found at i:35322278 original size:50 final size:49
Alignment explanation
Indices: 35322152--35322392 Score: 225
Period size: 50 Copynumber: 4.9 Consensus size: 49
35322142 TGAATATAAC
* * * * ** *
35322152 ATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGATGTTTC-T-TG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTG
* * **
35322199 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATACTG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTG
* * ** *
35322251 ATGCCCATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTG
* * *
35322300 AGTGCCAATGCCATGTCCCAAACATGGTCATACATGGGACCTCTTATCTCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-G
* * *
35322351 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
35322393 ATTCCCTTAA
Statistics
Matches: 156, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 115 0.74
51 1 0.01
52 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (49 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTG
Found at i:35330104 original size:26 final size:25
Alignment explanation
Indices: 35330074--35330160 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
35330064 AATTCATATT
35330074 CAGGAATGCTCATCTGAG-CATATAAA
1 CAGGAA-GCTCATCTGAGCCATAT-AA
*
35330100 CAGGAAGCTCTCTCTCGAGCCATATAA
1 CAGGAAGCTC-ATCT-GAGCCATATAA
* **
35330127 CAGGAAGCTCATCTGAACTGTATAA
1 CAGGAAGCTCATCTGAGCCATATAA
*
35330152 CGGGAAGCT
1 CAGGAAGCT
35330161 TATTCAAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
25 20 0.38
26 12 0.23
27 15 0.29
28 5 0.10
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (25 bp):
CAGGAAGCTCATCTGAGCCATATAA
Found at i:35330157 original size:25 final size:25
Alignment explanation
Indices: 35330122--35330188 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
35330112 TCTCGAGCCA
*
35330122 TATAACAGGAAGCTCATCTGAA-CTG
1 TATAACAGGAAGCTCAT-TCAAGCTG
* *
35330147 TATAACGGGAAGCTTATTCAAGCTG
1 TATAACAGGAAGCTCATTCAAGCTG
*
35330172 TATACCAGGAAGCTCAT
1 TATAACAGGAAGCTCAT
35330189 GCGAGCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 3 0.09
25 32 0.91
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (25 bp):
TATAACAGGAAGCTCATTCAAGCTG
Found at i:35333517 original size:174 final size:174
Alignment explanation
Indices: 35333226--35333553 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
35333216 AACTCAAGGT
*
35333226 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTTGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35333291 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
35333356 ACTTTAGACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
35333400 ACTTACCTTTTCCGCTGTCCAAAATTGACTTGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35333465 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
*
35333530 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
35333554 TGTACAATTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:35333545 original size:29 final size:30
Alignment explanation
Indices: 35333506--35333584 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
35333496 CTTAATAATC
35333506 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
35333536 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
35333565 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35333585 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:35341004 original size:29 final size:29
Alignment explanation
Indices: 35340941--35341008 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35340931 TAATCAACCG
35340941 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35340970 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35340999 CGCACACTTA
1 CGCACACTTA
35341009 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35341120 original size:174 final size:174
Alignment explanation
Indices: 35340830--35341157 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
35340820 AACTCAAGGT
* *
35340830 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
35340895 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
35340960 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
35341004 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
35341069 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
35341134 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
35341158 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:35341149 original size:29 final size:30
Alignment explanation
Indices: 35341110--35341188 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
35341100 CTTAATAATC
35341110 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
35341140 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
35341169 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35341189 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:35354382 original size:13 final size:13
Alignment explanation
Indices: 35354364--35354389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35354354 AATTAAAAAT
35354364 TATTGAAGATAAA
1 TATTGAAGATAAA
35354377 TATTGAAGATAAA
1 TATTGAAGATAAA
35354390 AAAAATAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
TATTGAAGATAAA
Found at i:35363762 original size:23 final size:23
Alignment explanation
Indices: 35363736--35363857 Score: 156
Period size: 23 Copynumber: 5.3 Consensus size: 23
35363726 ATAAGTGACA
35363736 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
35363759 CACTGATACGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
35363782 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35363805 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* * * *
35363828 TATTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35363851 CACTGAT
1 CACTGAT
35363858 CAATAACACT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:35363803 original size:46 final size:46
Alignment explanation
Indices: 35363736--35363857 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
35363726 ATAAGTGACA
* * *
35363736 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGTCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
*
35363782 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
* * *
35363828 TATTGAAATGTAACCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
35363858 CAATAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
Found at i:35379346 original size:108 final size:108
Alignment explanation
Indices: 35379157--35379375 Score: 402
Period size: 108 Copynumber: 2.0 Consensus size: 108
35379147 ATACAACATA
*
35379157 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAATGAACCTTGTCGCA
1 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCGCA
35379222 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
66 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
35379265 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCGCA
1 CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCGCA
* * *
35379330 TAAGTAAATTTTCAAATAGGATTACTGGAGCAACTATTGTTCC
66 TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
35379373 CTT
1 CTT
35379376 TCAGAAATTC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (108 bp):
CTTGTAAAATAAAATATGTTATGTTTTATTCTTTAGTCGATTGTTAAAAAACGAACCTTGTCGCA
TAAGTAAAATTTCAAATAAGATTACTGGAACAACTATTGTTCC
Found at i:35381234 original size:28 final size:28
Alignment explanation
Indices: 35381194--35381249 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
35381184 GTATACTCTG
35381194 ACAATATTTATATATAAATTCATGAGTA
1 ACAATATTTATATATAAATTCATGAGTA
35381222 ACAATATTTATATATAAATTCATGAGTA
1 ACAATATTTATATATAAATTCATGAGTA
35381250 TGAGGAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
ACAATATTTATATATAAATTCATGAGTA
Found at i:35387829 original size:23 final size:22
Alignment explanation
Indices: 35387799--35387845 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
35387789 TTTTAGCGTT
35387799 TGAAGAAGAACCACTTGTAGGTC
1 TGAAGAAGAACCACTTGTA-GTC
*
35387822 TGAAGAAGAACCTCTTGTAGTC
1 TGAAGAAGAACCACTTGTAGTC
35387844 TG
1 TG
35387846 TGTTATACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
TGAAGAAGAACCACTTGTAGTC
Found at i:35388636 original size:17 final size:17
Alignment explanation
Indices: 35388609--35388654 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
35388599 AAAGTTTAGG
35388609 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
35388627 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
35388642 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
35388655 TAGGGGGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:35389024 original size:9 final size:9
Alignment explanation
Indices: 35389006--35389042 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35388996 TATAGTTTGA
*
35389006 TATTCAAAT
1 TATTCGAAT
35389015 TATTCGAAT
1 TATTCGAAT
*
35389024 TATTCGAGT
1 TATTCGAAT
35389033 TATTCGAAT
1 TATTCGAAT
35389042 T
1 T
35389043 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:35389111 original size:9 final size:9
Alignment explanation
Indices: 35389094--35389133 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
35389084 TCGAGTTGAT
35389094 TCGAATAAC
1 TCGAATAAC
*
35389103 TCGATTAAC
1 TCGAATAAC
35389112 TCGAATAAC
1 TCGAATAAC
35389121 TCGAATAAC
1 TCGAATAAC
35389130 TCGA
1 TCGA
35389134 TTCGTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:35389261 original size:74 final size:71
Alignment explanation
Indices: 35389135--35389282 Score: 242
Period size: 74 Copynumber: 2.0 Consensus size: 71
35389125 ATAACTCGAT
35389135 TCGTTTAACTCGAAATACGATTTTTTTTTATTTTTCCGAGTCGAATCAAGTTTTGCTCACTCCTA
1 TCGTTTAACTCGAAATACGATTTTTTTTTATTTTTCCGAGTCGAATCAAGTTTTGCTCACTCCTA
35389200 GCTACA
66 GCTACA
* *
35389206 TCGTTTAACTCGAAATACGAATTTTTTTTTTGATTTTTTCGAGTCGAATCGAGTTTTGCTCACTC
1 TCGTTTAACTCGAAATACG-A-TTTTTTTTT-ATTTTTCCGAGTCGAATCAAGTTTTGCTCACTC
*
35389271 CTAGTTACA
63 CTAGCTACA
35389280 TCG
1 TCG
35389283 CCTTCAAGTC
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 19 0.27
72 1 0.01
73 9 0.13
74 42 0.59
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (71 bp):
TCGTTTAACTCGAAATACGATTTTTTTTTATTTTTCCGAGTCGAATCAAGTTTTGCTCACTCCTA
GCTACA
Found at i:35392839 original size:22 final size:23
Alignment explanation
Indices: 35392814--35392856 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
35392804 CTTATGGTAT
*
35392814 AATAATCTTGA-AATTTTTTTAA
1 AATAATCTTCACAATTTTTTTAA
*
35392836 AATATTCTTCACAATTTTTTT
1 AATAATCTTCACAATTTTTTT
35392857 TTAATATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (23 bp):
AATAATCTTCACAATTTTTTTAA
Found at i:35400800 original size:31 final size:31
Alignment explanation
Indices: 35400765--35400826 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
35400755 TTCATATTTT
35400765 CTTTCCCTAAACTAGAACTATCATACTCCTG
1 CTTTCCCTAAACTAGAACTATCATACTCCTG
*
35400796 CTTTCCCTAAATTAGAACTATCATACTCCTG
1 CTTTCCCTAAACTAGAACTATCATACTCCTG
35400827 GAAAGTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (31 bp):
CTTTCCCTAAACTAGAACTATCATACTCCTG
Found at i:35404053 original size:26 final size:26
Alignment explanation
Indices: 35404024--35404095 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
35404014 GAGCCATGAT
35404024 CGGTAAGCTCATTCTGAGCTGA-AGAA
1 CGGTAAGCTCATTC-GAGCTGATAGAA
** * *
35404050 CGGTAAGCTCATAAGAGCTGATATAT
1 CGGTAAGCTCATTCGAGCTGATAGAA
*
35404076 CGGTAAGCTCATACGAGCTG
1 CGGTAAGCTCATTCGAGCTG
35404096 TGGTGAGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.17
26 33 0.82
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (26 bp):
CGGTAAGCTCATTCGAGCTGATAGAA
Found at i:35404883 original size:43 final size:42
Alignment explanation
Indices: 35404714--35404883 Score: 182
Period size: 43 Copynumber: 4.0 Consensus size: 42
35404704 CATAATAGCT
* * * *
35404714 CATACAATGCC-ATATCCCAGATATGGTCTTACATGTTATCA
1 CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* * * * *
35404755 CATATCGATGCCACTG-CCCAGACAGGGTCTTATACGAAATCA
1 CATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* *
35404797 TATGACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
1 CAT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* *
35404840 CAATACAATGCCAATGTCCCAGACATGGTCTTACATGTTATCA
1 C-ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
35404883 C
1 C
35404884 CTCTCAGTAA
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
41 4 0.04
42 38 0.36
43 62 0.58
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
Found at i:35408772 original size:24 final size:23
Alignment explanation
Indices: 35408689--35408770 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
35408679 TTATTATTGG
* *
35408689 TTTTATAAAATTTTAAATGTATA
1 TTTTTTAAAATTTTAAATATATA
*
35408712 --TTTTAAATGTTTTATAATAT-TA
1 TTTTTTAAA-ATTTTA-AATATATA
35408734 TTTTTTAAAATTTTAAATATATA
1 TTTTTTAAAATTTTAAATATATA
35408757 TTTTTTAAAATTTT
1 TTTTTTAAAATTTT
35408771 TATTTTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
21 6 0.12
22 12 0.24
23 25 0.50
24 7 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTTTAAAATTTTAAATATATA
Found at i:35408783 original size:15 final size:15
Alignment explanation
Indices: 35408744--35408783 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
35408734 TTTTTTAAAA
*
35408744 TTTTAAATATATATT
1 TTTTAAATTTATATT
*
35408759 TTTTAAAATTTTTATT
1 TTTT-AAATTTATATT
35408775 TTTTAAATT
1 TTTTAAATT
35408784 CTAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTAAATTTATATT
Found at i:35408817 original size:21 final size:22
Alignment explanation
Indices: 35408723--35408816 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
35408713 TTTAAATGTT
*
35408723 TTAT-AATATTATTTTTTAAAA
1 TTATAAATATTATTTTTTTAAA
*
35408744 TTTTAAATA-TATATTTTTTAAA
1 TTATAAATATTAT-TTTTTTAAA
*
35408766 --AT---TTTTA-TTTTTTAAA
1 TTATAAATATTATTTTTTTAAA
*
35408782 TTCTAAATATTATTTTTTTAATA
1 TTATAAATATTATTTTTTTAA-A
35408805 TTATAAAATATT
1 TTAT-AAATATT
35408817 TAAATATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
16 9 0.16
17 1 0.02
18 3 0.05
20 1 0.02
21 10 0.18
22 20 0.36
23 4 0.07
24 7 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATAAATATTATTTTTTTAAA
Found at i:35408897 original size:22 final size:22
Alignment explanation
Indices: 35408863--35408929 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
35408853 TTATTATTTG
* *
35408863 TTTTATAATATTTTAAATGTATA
1 TTTTA-AAAATTTTAAATATATA
35408886 TTTTAAAAATTTTAAATATATA
1 TTTTAAAAATTTTAAATATATA
35408908 TTTT---AATTTTAAATATA-A
1 TTTTAAAAATTTTAAATATATA
35408926 TTTT
1 TTTT
35408930 TTAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 5 0.12
19 13 0.31
22 19 0.45
23 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
TTTTAAAAATTTTAAATATATA
Found at i:35414712 original size:30 final size:30
Alignment explanation
Indices: 35414676--35414777 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
35414666 CATAGAGCAA
* *
35414676 TTCATATCATCTGGATATGGGCGATTTGAG
1 TTCATATCACCCGGATATGGGCGATTTGAG
* * * * *
35414706 TTCATATCACCCGAACATGGGTGGTTCGAG
1 TTCATATCACCCGGATATGGGCGATTTGAG
* *
35414736 TTCATATCAGCCGGATATGGGC-AGCTTGAG
1 TTCATATCACCCGGATATGGGCGA-TTTGAG
35414766 TTCATATCACCC
1 TTCATATCACCC
35414778 AGAGCAACCA
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (30 bp):
TTCATATCACCCGGATATGGGCGATTTGAG
Found at i:35417112 original size:23 final size:24
Alignment explanation
Indices: 35417084--35417143 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
35417074 TGAAGTTGGA
*
35417084 TTTGGTACGAAATGGTATGG-GGT
1 TTTGGTACGAAATGGTATGGAAGT
*
35417107 TTTGGTACGAAATGGTATGGAATT
1 TTTGGTACGAAATGGTATGGAAGT
35417131 TTTGGTACGAAAT
1 TTTGGTACGAAAT
35417144 AAACCAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.37
Consensus pattern (24 bp):
TTTGGTACGAAATGGTATGGAAGT
Found at i:35417573 original size:25 final size:24
Alignment explanation
Indices: 35417544--35417597 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35417534 CCAATTAATT
**
35417544 GAGCTAATAAAATTTTGCTGAATGA
1 GAGCT-ATAAAATTCAGCTGAATGA
* *
35417569 GAGCTCTAAAATTCAGCTGAATGG
1 GAGCTATAAAATTCAGCTGAATGA
35417593 GAGCT
1 GAGCT
35417598 CCAATGGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (24 bp):
GAGCTATAAAATTCAGCTGAATGA
Found at i:35417579 original size:24 final size:24
Alignment explanation
Indices: 35417551--35417598 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35417541 ATTGAGCTAA
**
35417551 TAAAATTTTGCTGAATGAGAGCTC
1 TAAAATTCAGCTGAATGAGAGCTC
*
35417575 TAAAATTCAGCTGAATGGGAGCTC
1 TAAAATTCAGCTGAATGAGAGCTC
35417599 CAATGGACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (24 bp):
TAAAATTCAGCTGAATGAGAGCTC
Found at i:35421354 original size:20 final size:20
Alignment explanation
Indices: 35421319--35421373 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
35421309 TTTCTCACTT
*
35421319 TTTTTCACTCTCTTTTT-TCGA
1 TTTTT-ACTTTCTTTTTCTC-A
35421340 TTTTT-CTTTCTTTTTCTCA
1 TTTTTACTTTCTTTTTCTCA
*
35421359 TTTTTATTTTCTTTT
1 TTTTTACTTTCTTTT
35421374 GTAGTTTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 15 0.50
20 10 0.33
21 5 0.17
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTACTTTCTTTTTCTCA
Found at i:35423138 original size:13 final size:13
Alignment explanation
Indices: 35423120--35423144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35423110 TGAAAAATGA
35423120 AAAACCTCACAAC
1 AAAACCTCACAAC
35423133 AAAACCTCACAA
1 AAAACCTCACAA
35423145 ATCTCTCAAA
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:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCTCACAAC
Found at i:35423926 original size:24 final size:24
Alignment explanation
Indices: 35423870--35423930 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
35423860 ATAGAGTTGG
*
35423870 TTTTGGTACGAAATGGTATGGGGA
1 TTTTGGTACGAAATGGTATGGGAA
35423894 -TTTGGTACGAAATGGTAT-GGAA
1 TTTTGGTACGAAATGGTATGGGAA
35423916 TTTTTGGTACGAAAT
1 -TTTTGGTACGAAAT
35423931 AAACCAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 3 0.09
23 18 0.53
24 13 0.38
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (24 bp):
TTTTGGTACGAAATGGTATGGGAA
Found at i:35426696 original size:14 final size:15
Alignment explanation
Indices: 35426663--35426711 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
35426653 TTTGAATATC
35426663 TTTAAAAATA--AT-
1 TTTAAAAATATTATA
*
35426675 TTTAAAAA-ATCATAA
1 TTTAAAAATATTAT-A
35426690 TTTAAAAATATTATA
1 TTTAAAAATATTATA
35426705 TTTAAAA
1 TTTAAAA
35426712 TTTAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 1 0.03
12 8 0.26
13 2 0.06
15 16 0.52
16 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAAATATTATA
Found at i:35426716 original size:22 final size:21
Alignment explanation
Indices: 35426688--35426782 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 21
35426678 AAAAAATCAT
35426688 AATTTAAAAATATTATATTTAA
1 AATTTAAAAATA-TATATTTAA
*
35426710 AATTT---AATA-ATAATTAA
1 AATTTAAAAATATATATTTAA
*
35426727 AATTAAAAATATATATATTTAAA
1 AATTTAAAA-ATATATATTT-AA
* *
35426750 AATTTTAAAATATACATTTAA
1 AATTTAAAAATATATATTTAA
35426771 AATATTATAAAA
1 AAT-TTA-AAAA
35426783 CAAATAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
17 11 0.19
19 4 0.07
20 1 0.02
21 8 0.14
22 21 0.36
23 13 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTAAAAATATATATTTAA
Found at i:35426751 original size:23 final size:22
Alignment explanation
Indices: 35426725--35426782 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
35426715 AATAATAATT
*
35426725 AAAATTAAAAATATATATATTTA
1 AAAATTAAAAA-ATATACATTTA
**
35426748 AAAATTTTAAAATATACATTTA
1 AAAATTAAAAAATATACATTTA
*
35426770 AAATATTATAAAA
1 AAA-ATTAAAAAA
35426783 CAAATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTAAAAAATATACATTTA
Found at i:35426771 original size:38 final size:35
Alignment explanation
Indices: 35426680--35426779 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 35
35426670 ATAATTTTAA
*
35426680 AAAATCATAATTTAAAAATATTATATTTAAAATTT
1 AAAATAATAATTTAAAAATATTATATTTAAAATTT
*
35426715 AATAATAATTAAAATTAAAAATATATATATTTAAAAATTTT
1 AA-AATAA-T-AATTTAAAAATAT-TATATTT-AAAA-TTT
35426756 AAAAT-ATACATTT-AAAATATTATA
1 AAAATAATA-ATTTAAAAATATTATA
35426780 AAACAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
35 2 0.04
36 8 0.15
37 9 0.16
38 16 0.29
39 8 0.15
40 7 0.13
41 5 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAATAATAATTTAAAAATATTATATTTAAAATTT
Found at i:35426855 original size:12 final size:12
Alignment explanation
Indices: 35426838--35426863 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35426828 TTAATATTTT
35426838 ATAATATTTAAA
1 ATAATATTTAAA
35426850 ATAATATTTAAA
1 ATAATATTTAAA
35426862 AT
1 AT
35426864 TTTAAAAATA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATTTAAA
Found at i:35426869 original size:20 final size:20
Alignment explanation
Indices: 35426829--35426902 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
35426819 AATATATTTT
*
35426829 TAATATTTTATAATATTTAAAA
1 TAATA-TTTAAAAT-TTTAAAA
35426851 TAATATTTAAAATTTTAAAAA
1 TAATATTTAAAATTTT-AAAA
*
35426872 TAACATTT-AAATTTTAAAA
1 TAATATTTAAAATTTTAAAA
35426891 -AATAATTTAAAA
1 TAAT-ATTTAAAA
35426903 AAATACATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.04
19 8 0.17
20 13 0.28
21 18 0.39
22 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATTTAAAATTTTAAAA
Found at i:35426870 original size:54 final size:55
Alignment explanation
Indices: 35426810--35426932 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 55
35426800 AGCTCATATC
* *
35426810 TTTAAAAATAATATATTTTTAATATTTT-ATAAT-ATTTAAAATAAT-ATTTAAAA-T
1 TTTAAAAATAATATA--TTTAA-ATTTTAAAAATAATTTAAAAAAATAATTTAAAATT
*
35426864 TTTAAAAAT-A-ACATTTAAATTTTAAAAAATAATTTAAAAAAATACATTTAAAATT
1 TTTAAAAATAATATATTTAAATTTT-AAAAATAATTTAAAAAAATA-ATTTAAAATT
35426919 TTTAAAAATAATAT
1 TTTAAAAATAATAT
35426933 TATAAAACAT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
49 5 0.09
50 5 0.09
51 4 0.07
52 13 0.23
53 1 0.02
54 17 0.30
55 10 0.18
56 1 0.02
57 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (55 bp):
TTTAAAAATAATATATTTAAATTTTAAAAATAATTTAAAAAAATAATTTAAAATT
Found at i:35426912 original size:14 final size:13
Alignment explanation
Indices: 35426881--35426916 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
35426871 ATAACATTTA
*
35426881 AATTTTAAAAAAT
1 AATTTAAAAAAAT
35426894 AATTTAAAAAAAT
1 AATTTAAAAAAAT
35426907 ACATTTAAAA
1 A-ATTTAAAA
35426917 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTTAAAAAAAT
Found at i:35426918 original size:34 final size:35
Alignment explanation
Indices: 35426867--35426939 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 35
35426857 TTAAAATTTT
35426867 AAAAATAACATTTAAATTTTAAAAAATAAT-TTAA
1 AAAAATAACATTTAAATTTTAAAAAATAATATTAA
* *
35426901 AAAAAT-ACATTTAAAATTTTTAAAAATAATATTAT
1 AAAAATAACATTT-AAATTTTAAAAAATAATATTAA
35426936 AAAA
1 AAAA
35426940 CATTTCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 6 0.17
34 22 0.63
35 7 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (35 bp):
AAAAATAACATTTAAATTTTAAAAAATAATATTAA
Found at i:35426938 original size:23 final size:22
Alignment explanation
Indices: 35426896--35426939 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
35426886 TAAAAAATAA
35426896 TTTAAAAAAATACATTTAAAATT
1 TTTAAAAAAATA-ATTTAAAATT
35426919 TTTAAAAATAAT-ATTATAAAA
1 TTTAAAAA-AATAATT-TAAAA
35426940 CATTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.16
23 13 0.68
24 3 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAAAAATAATTTAAAATT
Found at i:35427058 original size:24 final size:23
Alignment explanation
Indices: 35426992--35427058 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
35426982 ACAAATAAAT
* *
35426992 AAAAGACAAATAAAAAAAACTTA
1 AAAAGAAAAAAAAAAAAAACTTA
* *
35427015 AAAAGTAAATAAATAAAAAACTTA
1 AAAAG-AAAAAAAAAAAAAACTTA
35427039 AAAAGAAAAAAAAAAGAAAA
1 AAAAGAAAAAAAAAA-AAAA
35427059 ACAACATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 13 0.36
24 23 0.64
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAGAAAAAAAAAAAAAACTTA
Found at i:35429435 original size:9 final size:9
Alignment explanation
Indices: 35429421--35429487 Score: 116
Period size: 9 Copynumber: 7.4 Consensus size: 9
35429411 TTTGGTTAAA
35429421 AATTAACCG
1 AATTAACCG
35429430 AATTAACCG
1 AATTAACCG
*
35429439 AATTAACCA
1 AATTAACCG
35429448 AATTAACCG
1 AATTAACCG
*
35429457 AATTACCCG
1 AATTAACCG
35429466 AATTAACCG
1 AATTAACCG
35429475 AATTAACCG
1 AATTAACCG
35429484 AATT
1 AATT
35429488 GAATCACTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:35429630 original size:18 final size:18
Alignment explanation
Indices: 35429590--35429633 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35429580 AATTTTTATG
**
35429590 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
35429608 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
35429626 CTTGGGTT
1 ATTGGGTT
35429634 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:35434083 original size:18 final size:17
Alignment explanation
Indices: 35434057--35434092 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35434047 TTTGGTTATA
35434057 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
35434075 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
35434092 T
1 T
35434093 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:35434229 original size:56 final size:49
Alignment explanation
Indices: 35434183--35434276 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 49
35434173 TTTGGTCTTC
*
35434183 AAACAGTATTTTATATTACTTATATTGTTTGATTAAAAATTATAA--TT
1 AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATTTT
*
35434230 AAACAATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
1 AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
35434277 AACACTACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (49 bp):
AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATTTT
Found at i:35438766 original size:16 final size:16
Alignment explanation
Indices: 35438745--35438778 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35438735 CAACTCATTC
35438745 TTGATCCTCTTTATTG
1 TTGATCCTCTTTATTG
35438761 TTGATCCTCTTTATTG
1 TTGATCCTCTTTATTG
35438777 TT
1 TT
35438779 CGTGATCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.59
Consensus pattern (16 bp):
TTGATCCTCTTTATTG
Found at i:35443463 original size:21 final size:21
Alignment explanation
Indices: 35443422--35443464 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35443412 AATAAAGTAG
*
35443422 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
35443443 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
35443464 A
1 A
35443465 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:35443517 original size:20 final size:22
Alignment explanation
Indices: 35443480--35443529 Score: 86
Period size: 20 Copynumber: 2.4 Consensus size: 22
35443470 ATATAATAAT
35443480 AATTATATCAAGAATTTTATTA
1 AATTATATCAAGAATTTTATTA
35443502 AATTATAT-AA-AATTTTATTA
1 AATTATATCAAGAATTTTATTA
35443522 AATTATAT
1 AATTATAT
35443530 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 2 0.07
22 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTATATCAAGAATTTTATTA
Found at i:35443530 original size:10 final size:10
Alignment explanation
Indices: 35443492--35443530 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
35443482 TTATATCAAG
*
35443492 AATTTTATTA
1 AATTATATTA
*
35443502 AATTATATAA
1 AATTATATTA
*
35443512 AATTTTATTA
1 AATTATATTA
35443522 AATTATATT
1 AATTATATT
35443531 TAATAATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTATATTA
Found at i:35443790 original size:46 final size:44
Alignment explanation
Indices: 35443701--35443807 Score: 117
Period size: 46 Copynumber: 2.4 Consensus size: 44
35443691 ATTATAACAT
* *
35443701 CATTCTATTCAACCAAACAAAAGAATGCTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACAAAAGAATACTATTACAGCTCTATTC
* ** *
35443745 GATTCCATTCAACCAAACAATTGAATTACTGATTACTGCTCTATTC
1 CATTCCATTCAACCAAACAAAAGAA-TACT-ATTACAGCTCTATTC
*
35443791 CATTACAGTT-AACCAAA
1 CATTCCA-TTCAACCAAA
35443808 TGTACCCTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
44 21 0.40
45 3 0.06
46 26 0.50
47 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (44 bp):
CATTCCATTCAACCAAACAAAAGAATACTATTACAGCTCTATTC
Found at i:35444825 original size:28 final size:28
Alignment explanation
Indices: 35444794--35444859 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
35444784 ATAAAAAATA
*
35444794 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
35444822 ACCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
35444850 ACCAAAATAT
1 ACCAAAATAT
35444860 ACAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTTTTATTT
Found at i:35444874 original size:19 final size:19
Alignment explanation
Indices: 35444852--35444888 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35444842 TTTTATTTAC
*
35444852 CAAAATATACAAAAAAAAA
1 CAAAAAATACAAAAAAAAA
*
35444871 CAAAAAATAGAAAAAAAA
1 CAAAAAATACAAAAAAAA
35444889 CCTGACACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08
Consensus pattern (19 bp):
CAAAAAATACAAAAAAAAA
Found at i:35444947 original size:27 final size:27
Alignment explanation
Indices: 35444917--35444993 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
35444907 GGCCAATCAC
* * *
35444917 ATTGGCAGCACTAAAGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
*
35444944 ATTGGTGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
35444971 ATTGGCGGCACCAATGGTGCCAA
1 ATTGGCGGCACCAATGGTGCCAA
35444994 AGGACTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATGTG
Found at i:35445595 original size:18 final size:18
Alignment explanation
Indices: 35445574--35445657 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
35445564 AGTAATAACT
35445574 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
** * **
35445592 CTATCCTCATTTAA-ACT
1 CTATTTTAATTTAATAAA
*
35445609 CTATTGTAATTTAATAAA
1 CTATTTTAATTTAATAAA
*
35445627 CTATTCTT-ATTTAATAACT
1 CTATT-TTAATTTAATAA-A
*
35445646 CTATTTTCATTT
1 CTATTTTAATTT
35445658 GAAATATAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
17 12 0.24
18 28 0.56
19 10 0.20
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.50
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:35445619 original size:35 final size:37
Alignment explanation
Indices: 35445566--35445650 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 37
35445556 TCTAATTAAG
*
35445566 TAATAACTCTATTTTAATTTAATAAACTATCCTCATT
1 TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
* *
35445603 T-A-AACTCTATTGTAATTTAATAAACTATTCTTATT
1 TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
35445638 TAATAACTCTATT
1 TAATAACTCTATT
35445651 TTCATTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 31 0.72
36 2 0.05
37 10 0.23
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (37 bp):
TAATAACTCTATTGTAATTTAATAAACTATCCTCATT
Found at i:35445822 original size:82 final size:82
Alignment explanation
Indices: 35445728--35445892 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
35445718 TTAATTAAAA
*
35445728 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAACTTATAAATAGATAAAATAG
*
35445793 TTTATGTTTCCATTATT
66 TTTATGTTTCCACTATT
35445810 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAACTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAACTTATAAATAGATAAAATAG
35445875 TTTATGTTTCCACTATT
66 TTTATGTTTCCACTATT
35445892 T
1 T
35445893 TTTTCCTTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (82 bp):
TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAACTTATAAATAGATAAAATAG
TTTATGTTTCCACTATT
Found at i:35445995 original size:19 final size:19
Alignment explanation
Indices: 35445973--35446038 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
35445963 TTTAATTTTT
35445973 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
35445992 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
35446010 TTACATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
35446029 TTAAATTAAA
1 TTAAATTAAA
35446039 CTATTTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:35446460 original size:27 final size:27
Alignment explanation
Indices: 35446430--35446493 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
35446420 TTTTTTTGGT
35446430 ATATTTTGATAAATAAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAATTATA
* *
35446457 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGATAAATAAAAAAAATTATA
35446484 ATATTTTGAT
1 ATATTTTGAT
35446494 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.41
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAAATTATA
Found at i:35452196 original size:3 final size:3
Alignment explanation
Indices: 35452188--35452215 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35452178 AAAACAGGAG
35452188 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
35452216 ACTATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:35458252 original size:14 final size:13
Alignment explanation
Indices: 35458235--35458281 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 13
35458225 AGTAGACTCG
35458235 TGAAAACAAAATTT
1 TGAAAA-AAAATTT
*
35458249 TGAAAAAAAA-AT
1 TGAAAAAAAATTT
35458261 TGAAAAAAAA--T
1 TGAAAAAAAATTT
35458272 TGAAAAAAAA
1 TGAAAAAAAA
35458282 GAAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 11 0.34
12 11 0.34
13 4 0.12
14 6 0.19
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAATTT
Found at i:35458263 original size:12 final size:12
Alignment explanation
Indices: 35458248--35458281 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
35458238 AAACAAAATT
35458248 TTGAAAAAAAAA
1 TTGAAAAAAAAA
35458260 TTG-AAAAAAAA
1 TTGAAAAAAAAA
35458271 TTGAAAAAAAA
1 TTGAAAAAAAA
35458282 GAAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:35458266 original size:11 final size:11
Alignment explanation
Indices: 35458252--35458289 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
35458242 AAAATTTTGA
35458252 AAAAAAAATTG
1 AAAAAAAATTG
35458263 AAAAAAAATTG
1 AAAAAAAATTG
35458274 AAAAAAAA--G
1 AAAAAAAATTG
35458283 AAAAAAA
1 AAAAAAA
35458290 TTGTATACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.30
11 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:35467073 original size:12 final size:13
Alignment explanation
Indices: 35467058--35467086 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35467048 ATTTATTTTT
35467058 ATATAAAAAA-TA
1 ATATAAAAAATTA
35467070 ATATAAAAAATTA
1 ATATAAAAAATTA
35467083 ATAT
1 ATAT
35467087 GGGTGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:35477457 original size:6 final size:6
Alignment explanation
Indices: 35477448--35477481 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35477438 AAAGAAGAAA
* *
35477448 AAAATC AAAATC AAAATC AAAGTC AAAAGC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
35477482 AGAGAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:35477936 original size:13 final size:13
Alignment explanation
Indices: 35477903--35477928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35477893 AAAAAAGATG
35477903 ATGAAAAATGAAA
1 ATGAAAAATGAAA
35477916 ATGAAAAATGAAA
1 ATGAAAAATGAAA
35477929 GAGTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:35479392 original size:87 final size:87
Alignment explanation
Indices: 35479157--35479837 Score: 1069
Period size: 87 Copynumber: 7.8 Consensus size: 87
35479147 AGATCAGTGA
*
35479157 AGATCAAAAACCAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCAAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
*
35479222 CCTTCCTACGTTAGCAGCGAAGC
65 CCTTCCTACGTTAACAGCGAAGC
* *
35479245 AGATCAAAAACCAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAACAGATCTTG
1 AGATCAAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
* * *
35479310 CCTTCCTGCGTTAATAGTGAAGC
65 CCTTCCTACGTTAACAGCGAAGC
* * * * *
35479333 AGATCGAAAACAAAACATTGCCTCAATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
35479398 CTTCCTACGTTAGCAGCGAAGC
66 CTTCCTACGTTAACAGCGAAGC
*
35479420 AGATCAAAAACAAAGCCTTGCCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
**
35479485 CTTCCTGTGTTAACAGCGAAGC
66 CTTCCTACGTTAACAGCGAAGC
* *
35479507 AGATCAAAAACAAAGCCTTGCTTCCATCGGTTGCAGTGGAGATGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
35479572 CTTCCTACATTAACAGCGAAGC
66 CTTCCTACGTTAACAGCGAAGC
*
35479594 ATATCAAAAACAAAGCC-T-CCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
35479657 CTTCCTACGTTAACAGCGAAGC
66 CTTCCTACGTTAACAGCGAAGC
* * *
35479679 AGACCAAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGATTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* * * *
35479744 CTTCCTGCGTTAATAGCAAAGT
66 CTTCCTACGTTAACAGCGAAGC
* *
35479766 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
35479831 CTTCCTA
66 CTTCCTA
35479838 AGCACTAGCG
Statistics
Matches: 542, Mismatches: 49, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
85 79 0.15
86 2 0.00
87 369 0.68
88 92 0.17
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (87 bp):
AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTACGTTAACAGCGAAGC
Found at i:35479694 original size:259 final size:261
Alignment explanation
Indices: 35479161--35479837 Score: 1070
Period size: 259 Copynumber: 2.6 Consensus size: 261
35479151 CAGTGAAGAT
*
35479161 CAAAAACCAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTT
1 CAAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTT
* * *
35479226 CCTACGTTAGCAGCGAAGCAGATCAAAAACCAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGG
65 CCTGCGTTAACAGCGAAGCAGATCAAAAA-CAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* * * * * * *
35479291 TTAAAGATAACAGATCTTGCCTTCCTGCGTTAATAGTGAAGCAGATCGAAAACAAAACATTGCCT
129 TTAAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAACACTGCCT
*
35479356 CAATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAGCAGCGAAGCA
194 CAATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCA
*
35479421 GAT
259 GAC
*
35479424 CAAAAACAAAGCCTTGCCTCCATCTGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTC
1 CAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTC
* * *
35479489 CTGTGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCTTCCATCGGTTGCAGTGGAGATGGTT
66 CTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTT
* * *
35479554 AAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCATATCAAAAACAAAGC-CT-CCTCC
131 AAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAACACTGCCTCA
*
35479617 ATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
196 ATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
35479682 C
261 C
* *
35479683 CAAAAACAAAGCCTTGCCTCTATCGGTTGCAGTGGAGCTGATTAAAGATAGCAGATCTTGCCTTC
1 CAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTC
* * * * *
35479748 CTGCGTTAATAGCAAAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTT
66 CTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTT
35479813 AAAGATAGCAGATCTTGCCTTCCTA
131 AAAGATAGCAGATCTTGCCTTCCTA
35479838 AGCACTAGCG
Statistics
Matches: 382, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
259 211 0.55
260 1 0.00
261 82 0.21
262 82 0.21
263 6 0.02
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (261 bp):
CAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTC
CTGCGTTAACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTT
AAAGATAGCAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCAAAAACAAAACACTGCCTCA
ATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGA
C
Found at i:35480072 original size:44 final size:42
Alignment explanation
Indices: 35480002--35480203 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 42
35479992 AAATCAATCC
* * *
35480002 TATCTTCCTGAATTTACAGT-GAAGCAGATTAAAACCATAGATCT
1 TATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAACC--AGATCT
* * *** * *
35480046 TATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCC-CATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAGATCT
* * ** *
35480087 TATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAG--ATTA-AAACCAGATCT
* * * *
35480131 TATTTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAA-C-CAGATCT
*
35480175 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGAT
35480204 CGCATCCCAT
Statistics
Matches: 118, Mismatches: 32, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
41 30 0.25
42 3 0.03
43 3 0.03
44 81 0.69
45 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAGATCT
Found at i:35480098 original size:41 final size:41
Alignment explanation
Indices: 35480042--35480231 Score: 139
Period size: 44 Copynumber: 4.5 Consensus size: 41
35480032 AAAACCATAG
* * * *
35480042 ATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCC
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACCC
* * *
35480083 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGA-CAAAAGAAACCA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC----GAAACCC
* * * * * **
35480127 ATCCTATTTCCCTGAAGTTACAGTGGAGCGGATTAAAACCAC
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACC-C
* * *
35480169 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCC
1 --ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACCC
* *
35480212 ATCTTATCTCCTTAAAGTTG
1 ATCTTATCTCCCTGAAGTTG
35480232 TAGTGGAACA
Statistics
Matches: 113, Mismatches: 28, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
40 1 0.01
41 50 0.44
43 1 0.01
44 61 0.54
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (41 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCGAAACCC
Found at i:35480116 original size:129 final size:128
Alignment explanation
Indices: 35479956--35480238 Score: 433
Period size: 129 Copynumber: 2.2 Consensus size: 128
35479946 AAATTACAAG
** * * * *
35479956 TCTTATCTCCCTAAGCAGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTT-CCTGAATTTACA
1 TCTTATCTCCCTAAGTTGTAGTGGAGCAGACAAAAGAAACCAATCCTAT-TTCCCTGAAGTTACA
*
35480020 GTGAAGCAGATTAAAACCATAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCCA
65 GTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCCA
35480084 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAGAAACCAATCCTATTTCCCTGAAGTTACA
1 TCTTATCTCCCT-AAGTTGTAGTGGAGCAGACAAAAGAAACCAATCCTATTTCCCTGAAGTTACA
* * *
35480149 GTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCCA
65 GTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCCA
*
35480213 TCTTATCTCCTTAAAGTTGTAGTGGA
1 TCTTATCTCCCT-AAGTTGTAGTGGA
35480239 ACAGGCTGTA
Statistics
Matches: 141, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 14 0.10
129 127 0.90
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTAAGTTGTAGTGGAGCAGACAAAAGAAACCAATCCTATTTCCCTGAAGTTACAG
TGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCCA
Found at i:35487771 original size:17 final size:17
Alignment explanation
Indices: 35487751--35487784 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35487741 AAATAAATTC
35487751 TTTTAAAAATTTCAAAA
1 TTTTAAAAATTTCAAAA
**
35487768 TTTTAAAGCTTTCAAAA
1 TTTTAAAAATTTCAAAA
35487785 GAAGCTACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTTAAAAATTTCAAAA
Found at i:35491690 original size:98 final size:98
Alignment explanation
Indices: 35491580--35491762 Score: 305
Period size: 98 Copynumber: 1.9 Consensus size: 98
35491570 TCGATACTTG
*
35491580 TGAATCTTAACTTGATTTTTTGAAACATCGAAGCTAAAGATGGTATGGTACTTGACCTAGGTA-T
1 TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
*
35491644 CGATACCTATGCTTACACTTTTTGAAATGGTATT
66 -AATACCTATGCTTACACTTTTTGAAATGGTATT
* * *
35491678 TGAATTTTAACTTGATTTTTTGAAATATCAAAGCTAAATATGGTATGGTACTTGACCTAGGTACT
1 TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
35491743 AATACCTATGCTTACACTTT
66 AATACCTATGCTTACACTTT
35491763 GAAAAGTTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 78 0.99
99 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (98 bp):
TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
AATACCTATGCTTACACTTTTTGAAATGGTATT
Found at i:35494409 original size:14 final size:14
Alignment explanation
Indices: 35494392--35494424 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
35494382 TACCATTTGA
*
35494392 CATATATTTCATAG
1 CATATATGTCATAG
35494406 CATATATGTCATAG
1 CATATATGTCATAG
35494420 CATAT
1 CATAT
35494425 TCCCAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (14 bp):
CATATATGTCATAG
Found at i:35496535 original size:21 final size:22
Alignment explanation
Indices: 35496495--35496538 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
35496485 ATAGTAAAGT
*
35496495 AAAATAAAAAAAGGAAAGAAAC
1 AAAATAAAAAAAGAAAAGAAAC
*
35496517 AAAAT-AAAGAAGAAAAGAAAC
1 AAAATAAAAAAAGAAAAGAAAC
35496538 A
1 A
35496539 GAGAGCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (22 bp):
AAAATAAAAAAAGAAAAGAAAC
Found at i:35497828 original size:21 final size:21
Alignment explanation
Indices: 35497799--35497843 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35497789 TATGTGTAGA
* *
35497799 CACCTCGTGTGTCGTATCAGG
1 CACCACGTGTGTCATATCAGG
*
35497820 CACCACGTGTGTCATTTCAGG
1 CACCACGTGTGTCATATCAGG
35497841 CAC
1 CAC
35497844 TTATGTGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (21 bp):
CACCACGTGTGTCATATCAGG
Found at i:35498185 original size:35 final size:35
Alignment explanation
Indices: 35498146--35498216 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
35498136 AAGGTGAAAA
*
35498146 TAAAGTGATTTGAAATAGTGAAATAATACTTGAAT
1 TAAAGTGATTTGAAATAGTAAAATAATACTTGAAT
*
35498181 TAAAGTGATTTGAAATAGTAAAATAATATTTGAAT
1 TAAAGTGATTTGAAATAGTAAAATAATACTTGAAT
35498216 T
1 T
35498217 TTAATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.37
Consensus pattern (35 bp):
TAAAGTGATTTGAAATAGTAAAATAATACTTGAAT
Found at i:35500429 original size:17 final size:17
Alignment explanation
Indices: 35500407--35500439 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35500397 TCATCTTTTA
35500407 CCCTCTTTTATTTCAAG
1 CCCTCTTTTATTTCAAG
35500424 CCCTCTTTTATTTCAA
1 CCCTCTTTTATTTCAA
35500440 CAAAAGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.48
Consensus pattern (17 bp):
CCCTCTTTTATTTCAAG
Found at i:35504241 original size:20 final size:19
Alignment explanation
Indices: 35504194--35504242 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
35504184 GATTTGAAAT
*
35504194 TAATTTTTGTTATTTGCTTA
1 TAATTTTT-TTATTTGCTAA
* *
35504214 GAAATTTTTTATTGTGCTAA
1 TAATTTTTTTATT-TGCTAA
35504234 TAATTTTTT
1 TAATTTTTT
35504243 ATAGGAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.61
Consensus pattern (19 bp):
TAATTTTTTTATTTGCTAA
Found at i:35504784 original size:41 final size:40
Alignment explanation
Indices: 35504724--35504979 Score: 277
Period size: 41 Copynumber: 6.2 Consensus size: 40
35504714 TTTACATAAT
** * * *
35504724 CGCCGCTAATGCTGTGGTCTTTCGCGACGTTTTCTA-AATTG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTACAA--G
*
35504765 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAAAAAAG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTT--ACAAG
35504807 CGCCGCTAATGCT-ACGGTCTTTAGCGGCGTTTTTTACAAAG
1 CGCCGCTAATGCTCA-GGTCTTTAGCGGCGTTTTTTAC-AAG
* *
35504848 CGCCGCTAATGCT-ACGGTCTTTGGCGGCGTTTTTTACTAAC
1 CGCCGCTAATGCTCA-GGTCTTTAGCGGCGTTTTTTAC-AAG
*
35504889 CGCCGCTAATGCTACA-GTCTGTAGCGGCGTTTTTTACTAAG
1 CGCCGCTAATGCT-CAGGTCTTTAGCGGCGTTTTTTAC-AAG
* * *
35504930 CACCGCTAATGCTCAGGTCTTTAGCGGCGTTTCTTCAAAAG
1 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTT-TTTACAAG
35504971 CGCCGCTAA
1 CGCCGCTAA
35504980 AAACCGCAGC
Statistics
Matches: 189, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
40 3 0.02
41 145 0.77
42 37 0.20
43 2 0.01
44 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (40 bp):
CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTACAAG
Found at i:35504852 original size:83 final size:82
Alignment explanation
Indices: 35504724--35504979 Score: 327
Period size: 82 Copynumber: 3.1 Consensus size: 82
35504714 TTTACATAAT
** * * * *
35504724 CGCCGCTAATGCTGTGGTCTTTCGCGACGTTTTCTA-AATTGCGCCGCTAATGCTCAGGTCTTTA
1 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAA-AGCGCCGCTAATGCTCAGGTCTTTA
35504788 GCGGCGTTTTTTAAAAAAG
65 GCGGCGTTTTTT-AAAAAG
*
35504807 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCT-ACGGTCTTTG
1 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTCA-GGTCTTTA
** *
35504871 GCGGCGTTTTTTACTAAC
65 GCGGCGTTTTTTAAAAAG
* * * *
35504889 CGCCGCTAATGCTACAGTCTGTAGCGGCGTTTTTTACTAAGCACCGCTAATGCTCAGGTCTTTAG
1 CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTCAGGTCTTTAG
* *
35504954 CGGCGTTTCTTCAAAAG
66 CGGCGTTTTTTAAAAAG
35504971 CGCCGCTAA
1 CGCCGCTAA
35504980 AAACCGCAGC
Statistics
Matches: 150, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
82 83 0.55
83 65 0.43
84 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (82 bp):
CGCCGCTAATGCTACGGTCTTTAGCGGCGTTTTTTACAAAGCGCCGCTAATGCTCAGGTCTTTAG
CGGCGTTTTTTAAAAAG
Found at i:35505016 original size:123 final size:124
Alignment explanation
Indices: 35504765--35505020 Score: 270
Period size: 123 Copynumber: 2.1 Consensus size: 124
35504755 TTCTAAATTG
* *
35504765 CGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAAAAAAGCGCCGCTAATGCTACGGTCTTTA
1 CGCCGCTAATGCTCAGGTCTGTAGCGGCGTTTTTTAAAAAAGCACCGCTAATGCTACGGTCTTTA
* ** * * * * * ** * * *
35504830 GCGGCGTTTTTTACAAAGCGCCGCTAATGCTACGGTCTTTGGCGGCGTTTTTTACTAAC
66 GCGGCGTTTTTCACAAAGCGCCGCTAAAACCACAGTCATTAGCGACGCATATTACAAAA
**
35504889 CGCCGCTAATGCTACA-GTCTGTAGCGGCGTTTTTT-ACTAAGCACCGCTAATGCT-CAGGTCTT
1 CGCCGCTAATGCT-CAGGTCTGTAGCGGCGTTTTTTAAAAAAGCACCGCTAATGCTAC-GGTCTT
* *
35504951 TAGCGGCGTTTCTTCA-AAAGCGCCGCTAAAAACCGCAG-CATTAGCGACGCATATTAGAAAA
64 TAGCGGCGTTT-TTCACAAAGCGCCGCT-AAAACCACAGTCATTAGCGACGCATATTACAAAA
35505012 CGCCGCTAA
1 CGCCGCTAA
35505021 AGATCGGAGC
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
122 1 0.01
123 67 0.61
124 39 0.36
125 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (124 bp):
CGCCGCTAATGCTCAGGTCTGTAGCGGCGTTTTTTAAAAAAGCACCGCTAATGCTACGGTCTTTA
GCGGCGTTTTTCACAAAGCGCCGCTAAAACCACAGTCATTAGCGACGCATATTACAAAA
Found at i:35506292 original size:74 final size:73
Alignment explanation
Indices: 35506125--35506373 Score: 417
Period size: 74 Copynumber: 3.4 Consensus size: 73
35506115 GCACCAATTT
* * *
35506125 GCGGCGTTTATTGTAAAAACGCCGCAAAAGTTTAACCAAAATGACTTCGTTTTTATACTGTTTAT
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
35506190 TGGTATTA
66 TGGTATTA
*
35506198 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGTCTTCGTTTTGTATACTGTTTA
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTT-TATACTGTTTA
35506263 TTGGTATTA
65 TTGGTATTA
* *
35506272 GTGGCGTTTCTGGTACAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTTATACTGTTTA
1 GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCG-TTTTTATACTGTTTA
35506337 TTGGTATTA
65 TTGGTATTA
*
35506346 GCGGCGTTTCTGGTACAAACGCCGCAAA
1 GCGGCGTTTCTGGTAAAAACGCCGCAAA
35506374 TGATAGTTAT
Statistics
Matches: 166, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
73 49 0.30
74 113 0.68
75 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (73 bp):
GCGGCGTTTCTGGTAAAAACGCCGCAAAAGTTTAACCAAAACGACTTCGTTTTTATACTGTTTAT
TGGTATTA
Found at i:35509246 original size:15 final size:15
Alignment explanation
Indices: 35509226--35509261 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
35509216 ACCACCAATT
*
35509226 TGTTTTCATTTGTAC
1 TGTTTTCATTTCTAC
35509241 TGTTTTCATTTCTAC
1 TGTTTTCATTTCTAC
35509256 T-TTTTC
1 TGTTTTC
35509262 CTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (15 bp):
TGTTTTCATTTCTAC
Found at i:35509928 original size:43 final size:43
Alignment explanation
Indices: 35509874--35510057 Score: 171
Period size: 43 Copynumber: 4.2 Consensus size: 43
35509864 AATACATACA
*
35509874 TTACATAACTTATTAATATATATATTTTAAAATGACACATAAC
1 TTACATAACTTATTAATATATATATTTTAAAATAACACATAAC
* * *
35509917 TTACATAACTTATTAATACATAACATTTTTAATACATAACTTATATAA-
1 TTACATAACTTATTAATATAT-ATA-TTTTAA-A-ATAAC--ACATAAC
*
35509965 -TACGACGTAACTTATTAATATATATATTTTAAAATAATACATAAC
1 TTAC-A--TAACTTATTAATATATATATTTTAAAATAACACATAAC
* * * *
35510010 TTACATAACTTATTAATACATA-A-CTT-ATATAATACATAAC
1 TTACATAACTTATTAATATATATATTTTAAAATAACACATAAC
35510050 TTACATAA
1 TTACATAA
35510058 TACGACATAA
Statistics
Matches: 119, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
40 21 0.18
41 2 0.02
42 1 0.01
43 36 0.30
44 7 0.06
45 7 0.06
46 8 0.07
47 8 0.07
48 7 0.06
49 7 0.06
50 15 0.13
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (43 bp):
TTACATAACTTATTAATATATATATTTTAAAATAACACATAAC
Found at i:35509950 original size:16 final size:15
Alignment explanation
Indices: 35509918--35510052 Score: 111
Period size: 16 Copynumber: 8.7 Consensus size: 15
35509908 ACACATAACT
35509918 TACATAACTTATTAA
1 TACATAACTTATTAA
*
35509933 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
35509949 TACATAACTTATATAA
1 TACATAACTTAT-TAA
35509965 TACGACGTAACTTATTAA
1 TAC-A--TAACTTATTAA
*
35509983 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
*
35509997 -A-ATAA--TACATAA
1 TACATAACTTA-TTAA
35510009 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
35510026 TACATAACTTATATAA
1 TACATAACTTAT-TAA
35510042 TACATAACTTA
1 TACATAACTTA
35510053 CATAATACGA
Statistics
Matches: 100, Mismatches: 5, Indels: 29
0.75 0.04 0.22
Matches are distributed among these distances:
10 1 0.01
11 1 0.01
12 6 0.06
13 1 0.01
14 4 0.04
15 28 0.28
16 39 0.39
17 5 0.05
18 7 0.07
19 8 0.08
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:35509976 original size:93 final size:93
Alignment explanation
Indices: 35509879--35510063 Score: 318
Period size: 93 Copynumber: 2.0 Consensus size: 93
35509869 ATACATTACA
*
35509879 TAACTTATTAATATATATATTTTAAAATGACACATAACTTACATAACTTATTAATACATAACATT
1 TAACTTATTAATATATATATTTTAAAATAACACATAACTTACATAACTTATTAATACATAAC-TT
* *
35509944 -TTTAATACATAACTTATATAATACGACG
65 ATATAATACATAACTTACATAATACGACG
*
35509972 TAACTTATTAATATATATATTTTAAAATAATACATAACTTACATAACTTATTAATACATAACTTA
1 TAACTTATTAATATATATATTTTAAAATAACACATAACTTACATAACTTATTAATACATAACTTA
35510037 TATAATACATAACTTACATAATACGAC
66 TATAATACATAACTTACATAATACGAC
35510064 ATAATAACAT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 2 0.02
93 85 0.98
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.38
Consensus pattern (93 bp):
TAACTTATTAATATATATATTTTAAAATAACACATAACTTACATAACTTATTAATACATAACTTA
TATAATACATAACTTACATAATACGACG
Found at i:35510016 original size:9 final size:9
Alignment explanation
Indices: 35510002--35510057 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
35509992 TTTAAAATAA
35510002 TACATAACT
1 TACATAACT
35510011 TACATAACT
1 TACATAACT
*
35510020 TA-TTAA--
1 TACATAACT
35510026 TACATAACT
1 TACATAACT
*
35510035 TATATAA--
1 TACATAACT
35510042 TACATAACT
1 TACATAACT
35510051 TACATAA
1 TACATAA
35510058 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 24 0.63
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:35510046 original size:31 final size:31
Alignment explanation
Indices: 35509918--35510052 Score: 115
Period size: 31 Copynumber: 4.4 Consensus size: 31
35509908 ACACATAACT
*
35509918 TACATAACTTATTAATACATAACATT-TTTAA
1 TACATAACTTATTAATACATAAC-TTATATAA
35509949 TACATAACTTATATAATACGACGTAACTTAT-TAA
1 TACATAACTTAT-TAATAC-A--TAACTTATATAA
* *
35509983 TATATATA-TT-TTAA-A-ATAA--TACATAA
1 TACATA-ACTTATTAATACATAACTTATATAA
35510009 CTTACATAACTTATTAATACATAACTTATATAA
1 --TACATAACTTATTAATACATAACTTATATAA
35510042 TACATAACTTA
1 TACATAACTTA
35510053 CATAATACGA
Statistics
Matches: 85, Mismatches: 4, Indels: 30
0.71 0.03 0.25
Matches are distributed among these distances:
25 2 0.02
26 3 0.04
27 4 0.05
28 7 0.08
29 5 0.06
30 1 0.01
31 28 0.33
32 9 0.11
33 8 0.09
34 12 0.14
35 6 0.07
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (31 bp):
TACATAACTTATTAATACATAACTTATATAA
Found at i:35510080 original size:40 final size:40
Alignment explanation
Indices: 35509994--35510080 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
35509984 ATATATATTT
**
35509994 TAAA-ATAATACATAACTTACATAACTTATTAATACATAAC
1 TAAATATAATACATAACTTACATAAC-TACGAATACATAAC
*
35510034 T-TATATAATACATAACTTACATAA-TACGACATA-ATAAC
1 TAAATATAATACATAACTTACATAACTACGA-ATACATAAC
35510072 ATAAATATA
1 -TAAATATA
35510081 TATCATATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
38 8 0.21
39 5 0.13
40 26 0.67
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (40 bp):
TAAATATAATACATAACTTACATAACTACGAATACATAAC
Found at i:35515767 original size:186 final size:186
Alignment explanation
Indices: 35515453--35515825 Score: 665
Period size: 186 Copynumber: 2.0 Consensus size: 186
35515443 GGATCCAGCT
* *
35515453 CGCAACAATACATGCATTCAGGGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAGAGACTAGATA
1 CGCAACAATACATGCATTCAGGGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATA
* * * * *
35515518 TCTCAGATGCAAGCGGCAACGAGTGAGCAAATTACATAACTTAAAGAGGAGGCAACATCGAGAGA
66 GCTCAAATGCAAGCGACAACAAGTGAGCAAATTACACAACTTAAAGAGGAGGCAACATCGAGAGA
35515583 AGCTAAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAATCAGATGCGG
131 AGCTAAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAATCAGATGCGG
35515639 CGCAACAATACATGCATTCAGGGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATA
1 CGCAACAATACATGCATTCAGGGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATA
* *
35515704 GCTCAAATGCAAGCGACAACAAGTGAGCAAATTACACAACTTGAAGCGGAGGCAACATCGAGAGA
66 GCTCAAATGCAAGCGACAACAAGTGAGCAAATTACACAACTTAAAGAGGAGGCAACATCGAGAGA
35515769 AGCTAAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAATCAGATGCGG
131 AGCTAAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAATCAGATGCGG
35515825 C
1 C
35515826 AGCGAGAGAA
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 178 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (186 bp):
CGCAACAATACATGCATTCAGGGAGTCAGGCTCAAGCTGAAGTTCAGAGGTTAAAAGACCAGATA
GCTCAAATGCAAGCGACAACAAGTGAGCAAATTACACAACTTAAAGAGGAGGCAACATCGAGAGA
AGCTAAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAATCAGATGCGG
Found at i:35515845 original size:66 final size:66
Alignment explanation
Indices: 35515762--35515908 Score: 208
Period size: 66 Copynumber: 2.2 Consensus size: 66
35515752 GAGGCAACAT
* * *
35515762 CGAGAGAAGCTAAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTTAAATCAGATGCGG
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTTAAAGCAAATGCGG
35515825 CAG
64 CAG
* *
35515828 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAAATGCGGCA
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTTAAAGCAAATGCGGCA
35515893 G
66 G
*
35515894 CGAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
35515909 CTACAGCGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 68 0.93
67 4 0.05
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTTAAAGCAAATGCGGCA
G
Found at i:35515904 original size:21 final size:21
Alignment explanation
Indices: 35515890--35515948 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
35515880 AGCAAATGCG
35515890 GCAGCGAGAGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
35515911 ACAGCGAGAGAAGTAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
*
35515932 GCAGCGAGGGAAGCAGA
1 GCAGCGAGAGAAGCAGA
35515949 ACAGCTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.42, T:0.05
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:35516335 original size:43 final size:43
Alignment explanation
Indices: 35516308--35516728 Score: 583
Period size: 43 Copynumber: 9.8 Consensus size: 43
35516298 TGTGGTGAAG
* * *
35516308 GCGCCGCTAAATACCATGGTCTATAGCGGCGTTT-TTCACGATAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTT--GGGTAA
* ** * * * * *
35516352 GCGCTGCTAAAGGTCATTGTCTTTCGCGGTGTTTATTGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
*
35516395 GCGCCGCTAAAGACGATGGTCTATAGCGGCGTTTGTTGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* **
35516438 GCGCCGCTAAAGACCATGGTCTATAACGGCGTTTGTTGGACAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* *
35516481 GCGCCGCTATAGACCATGGTCTATAGTGGCGTTTGTTGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* *
35516524 GCGCCGCGAAAGACCATGGTCTATAGCGGCATTTGTTGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* *
35516567 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTGGTAT
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* * *
35516610 GCGCCGCTAAAGACCATGGTCTATAGTGTCGTTTGATGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
* *
35516653 GCGCAGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGTAA
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
35516696 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTT
1 GCGCCGCTAAAGACCATGGTCTATAGCGGCGTT
35516729 GTAAAGAAAA
Statistics
Matches: 331, Mismatches: 45, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
43 303 0.92
44 26 0.08
45 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (43 bp):
GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGTAA
Found at i:35518699 original size:23 final size:22
Alignment explanation
Indices: 35518666--35518732 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
35518656 CACTTTCTGT
*
35518666 TTACTCACTTCGGTGGTGTCCA
1 TTACCCACTTCGGTGGTGTCCA
** ** *
35518688 GTTACCTGCTTCGGCAGTGTTCTA
1 -TTACCCACTTCGGTGGTG-TCCA
35518712 TTACCCACTTCGGTGGTGTCC
1 TTACCCACTTCGGTGGTGTCC
35518733 CGTTTAAGTC
Statistics
Matches: 32, Mismatches: 11, Indels: 3
0.70 0.24 0.07
Matches are distributed among these distances:
22 2 0.06
23 27 0.84
24 3 0.09
ACGTcount: A:0.12, C:0.28, G:0.24, T:0.36
Consensus pattern (22 bp):
TTACCCACTTCGGTGGTGTCCA
Found at i:35522803 original size:29 final size:29
Alignment explanation
Indices: 35522748--35522804 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
35522738 TAATTTGTAC
**
35522748 AGGATGGATTCTGAGAAATTATTTTTGAG
1 AGGATGGATTCTGAGAAATTAGGTTTGAG
*
35522777 AGGATGGGTTCTGAAGAAA-TAGGTTTGA
1 AGGATGGATTCTG-AGAAATTAGGTTTGA
35522805 TGAGATAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (29 bp):
AGGATGGATTCTGAGAAATTAGGTTTGAG
Found at i:35526639 original size:41 final size:41
Alignment explanation
Indices: 35526581--35526663 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
35526571 ATTAAAATGC
35526581 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
1 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
*
35526622 CATAGTCTAGCTGTGGTCTTACATTTAAACATTGCCATGGT
1 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
35526663 C
1 C
35526664 TAACCATGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (41 bp):
CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
Found at i:35526665 original size:35 final size:35
Alignment explanation
Indices: 35526578--35526677 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 35
35526568 TTCATTAAAA
*
35526578 TGCCATAGTCTAGCTATGGTCTTACATTTAAACAT
1 TGCCATGGTCTAGCTATGGTCTTACATTTAAACAT
35526613 TGCCATGGTCATAGTCTAGCTGTGGTCTTACATTTAAACAT
1 TGCCATGGTC-TAG-CTA----TGGTCTTACATTTAAACAT
* *
35526654 TGCCATGGTCTAACCATGGTCTTA
1 TGCCATGGTCTAGCTATGGTCTTA
35526678 TCCTTCAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
35 17 0.30
36 3 0.05
37 3 0.05
39 2 0.04
40 2 0.04
41 29 0.52
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (35 bp):
TGCCATGGTCTAGCTATGGTCTTACATTTAAACAT
Found at i:35534275 original size:33 final size:33
Alignment explanation
Indices: 35534091--35534302 Score: 95
Period size: 33 Copynumber: 6.2 Consensus size: 33
35534081 CATTTCCATA
** * **
35534091 GTCTTACATTTGTAATGCCATAACCCAGTTATG
1 GTCTTACATTTAAAATGCCATAGCCCAACTATG
* *
35534124 GTCTTATCA-TCAGAATGCCATAGCCCAACTATG
1 GTCTTA-CATTTAAAATGCCATAGCCCAACTATG
* * * * *
35534157 GTCTTACACATGTATCTATACTGCCATGGTCCAACCATG
1 GTCTT--ACA--T-T-TAAAATGCCATAGCCCAACTATG
** * ** * **
35534196 GTCTTATGTTCAAGGTGCCATAACCCAGTTATG
1 GTCTTACATTTAAAATGCCATAGCCCAACTATG
* *
35534229 GTCTTTTCA-TTAAAATGCCATAGCCCAGCTATG
1 GTC-TTACATTTAAAATGCCATAGCCCAACTATG
* * *
35534262 GTCTTACATTTAAACATTGCCATGGTCCAACCATG
1 GTCTTACATTTAAA-A-TGCCATAGCCCAACTATG
35534297 GTCTTA
1 GTCTTA
35534303 TCCATCAATT
Statistics
Matches: 130, Mismatches: 37, Indels: 22
0.69 0.20 0.12
Matches are distributed among these distances:
32 4 0.03
33 72 0.55
34 8 0.06
35 22 0.17
37 1 0.01
38 1 0.01
39 22 0.17
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (33 bp):
GTCTTACATTTAAAATGCCATAGCCCAACTATG
Found at i:35535536 original size:29 final size:28
Alignment explanation
Indices: 35535488--35535545 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
35535478 CCTAATAAAT
*
35535488 TCTTTTAAAACACAAATTAATTCAAAAA
1 TCTTTTAAAACACAAATTAACTCAAAAA
* *
35535516 TCTTTCTAAAATCAC-ACTTAACTCATAAA
1 TCTTT-TAAAA-CACAAATTAACTCAAAAA
35535545 T
1 T
35535546 AATAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 5 0.20
29 17 0.68
30 3 0.12
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (28 bp):
TCTTTTAAAACACAAATTAACTCAAAAA
Found at i:35538846 original size:8 final size:8
Alignment explanation
Indices: 35538835--35538868 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
35538825 TATAAAATAA
35538835 AAAAATTT
1 AAAAATTT
35538843 AAAAATTT
1 AAAAATTT
35538851 AAAAATTAT
1 AAAAATT-T
*
35538860 TAAAATTT
1 AAAAATTT
35538868 A
1 A
35538869 TTCTTACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAAATTT
Found at i:35538864 original size:17 final size:16
Alignment explanation
Indices: 35538835--35538868 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
35538825 TATAAAATAA
35538835 AAAAATTTAAAAATTT
1 AAAAATTTAAAAATTT
*
35538851 AAAAATTATTAAAATTT
1 AAAAATT-TAAAAATTT
35538868 A
1 A
35538869 TTCTTACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATTTAAAAATTT
Found at i:35541058 original size:42 final size:43
Alignment explanation
Indices: 35540990--35541096 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 43
35540980 CTAAATACCA
* * * **
35540990 GCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCTCAAAAAC
1 GCCGCTAAAGAACACAACCTTTAGCGGCGCTTCTAGCAAAAAC
*
35541033 GCCGCTAAAGAACA-AACCTTTAGCGGTGCTTCTAGCAAAAAC
1 GCCGCTAAAGAACACAACCTTTAGCGGCGCTTCTAGCAAAAAC
* * *
35541075 ACCGCTAAA-AACATAATCTTTA
1 GCCGCTAAAGAACACAACCTTTA
35541097 AAAAAATTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.07
42 38 0.69
43 13 0.24
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (43 bp):
GCCGCTAAAGAACACAACCTTTAGCGGCGCTTCTAGCAAAAAC
Found at i:35544916 original size:24 final size:24
Alignment explanation
Indices: 35544889--35544936 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
35544879 AACGACGCCG
*
35544889 TTTTGCTATGCTAAAATTT-TTTTA
1 TTTTG-TATGCCAAAATTTATTTTA
*
35544913 TTTTGTTTGCCAAAATTTATTTTA
1 TTTTGTATGCCAAAATTTATTTTA
35544937 AAGTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTTGTATGCCAAAATTTATTTTA
Found at i:35545086 original size:21 final size:23
Alignment explanation
Indices: 35545043--35545095 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 23
35545033 AGCTAAGTGA
*
35545043 TTTTATAAAATATTTATTATTTT
1 TTTTATAAAATATTAATTATTTT
35545066 TTTTAT-AAAT-TTAATT-TTTT
1 TTTTATAAAATATTAATTATTTT
35545086 TTTTA-AAAAT
1 TTTTATAAAAT
35545096 CAAGTACTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 13 0.46
21 5 0.18
22 4 0.14
23 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTATAAAATATTAATTATTTT
Found at i:35545651 original size:21 final size:21
Alignment explanation
Indices: 35545626--35545669 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35545616 ATAAAACATA
*
35545626 AACCC-TAAACCCATAACCCTT
1 AACCCTTAAACCC-CAACCCTT
35545647 AACCCTTAAACCCCAACCCTT
1 AACCCTTAAACCCCAACCCTT
35545668 AA
1 AA
35545670 ACCATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (21 bp):
AACCCTTAAACCCCAACCCTT
Done.