Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 113 of 204
Found at i:35057273 original size:19 final size:19
Alignment explanation
Indices: 35057249--35057302 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
35057239 AATCATATCT
35057249 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
35057268 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
35057287 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
35057303 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:35059565 original size:7 final size:7
Alignment explanation
Indices: 35059553--35059579 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
35059543 CTAATTGGCT
35059553 AAATTAG
1 AAATTAG
35059560 AAATTAG
1 AAATTAG
35059567 AAATTAG
1 AAATTAG
35059574 AAATTA
1 AAATTA
35059580 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (7 bp):
AAATTAG
Found at i:35060329 original size:3 final size:3
Alignment explanation
Indices: 35060315--35060384 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
35060305 TATATGTTAT
* * *
35060315 TAA TAA TTA TAA TAA TAA GTAA AAA GAA -ATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TA-A TAA TAA TAA TAA TAA
35060361 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
35060385 CATTATCATC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 55 0.92
4 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:35061398 original size:20 final size:20
Alignment explanation
Indices: 35061383--35061453 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
35061373 TTGCACATAT
35061383 GTGCCTCTGTTTGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
* * *
35061403 GTGTCTTTGTATGCACTTTG
1 GTGCCTCTGTTTGCACTTTG
*
35061423 GTGCCTCTGTTTGCACTTCG
1 GTGCCTCTGTTTGCACTTTG
*
35061443 GTGTCTCTGTT
1 GTGCCTCTGTT
35061454 GGCATTGCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.06, C:0.23, G:0.25, T:0.46
Consensus pattern (20 bp):
GTGCCTCTGTTTGCACTTTG
Found at i:35070108 original size:20 final size:20
Alignment explanation
Indices: 35070085--35070130 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
35070075 TCCACGCTAC
* *
35070085 CGTGTGAACAGGCACGCAGT
1 CGTGTGAACAGGCACACACT
*
35070105 CGTGTGAATAGGCACACACT
1 CGTGTGAACAGGCACACACT
35070125 CGTGTG
1 CGTGTG
35070131 GCCACCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (20 bp):
CGTGTGAACAGGCACACACT
Found at i:35070944 original size:24 final size:24
Alignment explanation
Indices: 35070912--35070973 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
35070902 TCAAAGAAGT
* **
35070912 TGATAGTAATAGTGTGAGTTATAA
1 TGATAGTAATAGTGTAAACTATAA
*
35070936 TGATAGTAATAGTGTAAACTATGA
1 TGATAGTAATAGTGTAAACTATAA
*
35070960 TGATAGTGATAGTG
1 TGATAGTAATAGTG
35070974 AACTTTGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (24 bp):
TGATAGTAATAGTGTAAACTATAA
Found at i:35074070 original size:22 final size:22
Alignment explanation
Indices: 35074045--35074089 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
35074035 TCTATTACTT
*
35074045 AAACATAGTATCCAATTATACC
1 AAACATAATATCCAATTATACC
*
35074067 AAACATAATATCCATTTATACC
1 AAACATAATATCCAATTATACC
35074089 A
1 A
35074090 GCTCAATCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (22 bp):
AAACATAATATCCAATTATACC
Found at i:35075176 original size:18 final size:19
Alignment explanation
Indices: 35075148--35075190 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
35075138 GCTGTGTTGC
* *
35075148 GACACAGGGCTGAATGTGG
1 GACACAGGGCTAAACGTGG
*
35075167 GACACA-GGCTAAACGTGT
1 GACACAGGGCTAAACGTGG
35075185 GACACA
1 GACACA
35075191 AGTATCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.33, C:0.21, G:0.33, T:0.14
Consensus pattern (19 bp):
GACACAGGGCTAAACGTGG
Found at i:35076376 original size:13 final size:13
Alignment explanation
Indices: 35076358--35076434 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
35076348 AGTTCTTCAT
*
35076358 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
*
35076371 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
*
35076384 TGCTTTTCAAAAG
1 TGCTTTTCAGAAG
*
35076397 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
35076410 TGCTTTTCAGAAG
1 TGCTTTTCAGAAG
35076423 TGCTTTTCAGAA
1 TGCTTTTCAGAA
35076435 ATTTGAGTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (13 bp):
TGCTTTTCAGAAG
Found at i:35084315 original size:58 final size:55
Alignment explanation
Indices: 35084245--35084399 Score: 163
Period size: 57 Copynumber: 2.7 Consensus size: 55
35084235 TAGAGAGTTC
* *
35084245 AACTA-TAATTAAACTTAATCATTTTAA-TATTAAATTAATATAATACTTATCAAGAT
1 AACTATTAATTAAACTTAAT-A-TTAAACTATTAAATTAATAAAATA-TTATCAAGAT
*
35084301 AACTATTAGATTAAATTTAATATTAAATCTATTAAATTAATAAAATATTATCAAGAT
1 AACTATTA-ATTAAACTTAATATTAAA-CTATTAAATTAATAAAATATTATCAAGAT
* * *
35084358 AAGTATTTAA-TATAATTTAATATTAAATCTATTAAAATAATA
1 AACTA-TTAATTA-AACTTAATATTAAA-CTATTAAATTAATA
35084400 TTATTTTTGG
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
56 11 0.12
57 46 0.52
58 31 0.35
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (55 bp):
AACTATTAATTAAACTTAATATTAAACTATTAAATTAATAAAATATTATCAAGAT
Found at i:35084376 original size:57 final size:58
Alignment explanation
Indices: 35084272--35084399 Score: 190
Period size: 57 Copynumber: 2.2 Consensus size: 58
35084262 ATCATTTTAA
*
35084272 TATTAAATTAATATAATACTTATCAAGATAACTATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAAAATACTTATCAAGATAACTATTAGATTAAATTTAATATTAAATC
*
35084330 TATTAAATTAATAAAATA-TTATCAAGATAAGTATTTA-A-TATAATTTAATATTAAATC
1 TATTAAATTAATAAAATACTTATCAAGATAACTA-TTAGATTA-AATTTAATATTAAATC
*
35084387 TATTAAAATAATA
1 TATTAAATTAATA
35084400 TTATTTTTGG
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
56 2 0.03
57 43 0.66
58 20 0.31
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTATCAAGATAACTATTAGATTAAATTTAATATTAAATC
Found at i:35087065 original size:27 final size:27
Alignment explanation
Indices: 35087024--35087079 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
35087014 CTAGTTGACG
35087024 TAAGTTCGTGCTACATATAATATGTTA
1 TAAGTTCGTGCTACATATAATATGTTA
*
35087051 TAAGTTCGTGTTACATATAATATGTTA
1 TAAGTTCGTGCTACATATAATATGTTA
35087078 TA
1 TA
35087080 TTAAATTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (27 bp):
TAAGTTCGTGCTACATATAATATGTTA
Found at i:35088657 original size:40 final size:40
Alignment explanation
Indices: 35088612--35088818 Score: 261
Period size: 40 Copynumber: 5.2 Consensus size: 40
35088602 AACAATTGAA
**
35088612 TGAATGCACATAAGTGCGTCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
35088652 TGAATGCACATACGTGCTCCTATTTGTACTTTGGTACCCT
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
35088692 TGAATGCATATAAGTGCCCCTGTTTCTACCTCGATACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* *
35088732 TTAATGCACATAAGTGCCGCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
35088772 TGAAAGCACATCAGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
*
35088812 TAAATGC
1 TGAATGC
35088819 CTTTACGTGC
Statistics
Matches: 139, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (40 bp):
TGAATGCACATAAGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:35088829 original size:120 final size:119
Alignment explanation
Indices: 35088614--35088835 Score: 331
Period size: 120 Copynumber: 1.9 Consensus size: 119
35088604 CAATTGAATG
* *
35088614 AATGCACATAAGTGCGTCTGTTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCTATTTGT
1 AATGCACATAAGTGCGTCTGTTTGTACTTCGGTACCCCTGAAAGCACATACGTGCCCCTATTTGT
* * *
35088679 ACTTTGGTACCCTTGAATGCATATAAGTGCCCCTGTTTCTACCTCGATACCCCTT
66 ACTTCGGTACCCCTAAATGCATATAAGTG-CCCTGTTTCTACCTCGATACCCCTT
35088734 AATGCACATAAGTGCCG-CTGTTTGTACTTCGGTACCCCTGAAAGCACAT-CAGTGCCCCTATTT
1 AATGCACATAAGTG-CGTCTGTTTGTACTTCGGTACCCCTGAAAGCACATAC-GTGCCCCTATTT
* * *
35088797 GTACTTCGGTACCCCTAAATGCCTTTACGTGCCCTGTTT
64 GTACTTCGGTACCCCTAAATGCATATAAGTGCCCTGTTT
35088836 ATACTCTGGT
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
119 9 0.10
120 81 0.88
121 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (119 bp):
AATGCACATAAGTGCGTCTGTTTGTACTTCGGTACCCCTGAAAGCACATACGTGCCCCTATTTGT
ACTTCGGTACCCCTAAATGCATATAAGTGCCCTGTTTCTACCTCGATACCCCTT
Found at i:35095530 original size:40 final size:40
Alignment explanation
Indices: 35095480--35095646 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
35095470 AACAATTGAA
* ** * *
35095480 TGAAAGCACATAAGTGCGTCTGTTTGTTCTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCGGTACCCC
*
35095520 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCGGTACCCC
* * * * *
35095560 TGACTGCACATATGTG-CCATGTTTGTACTTCGGTACCCT
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCGGTACCCC
**
35095599 TGAATGCACATAAGTGCCCCTATTTGTACTTTAGTACCCC
1 TGAATGCACATAAGTGCCCCTATTTGTACTTCGGTACCCC
35095639 TGAATGCA
1 TGAATGCA
35095647 TTTATATGCC
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 34 0.31
40 74 0.69
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (40 bp):
TGAATGCACATAAGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:35095596 original size:39 final size:40
Alignment explanation
Indices: 35095480--35095673 Score: 203
Period size: 40 Copynumber: 4.9 Consensus size: 40
35095470 AACAATTGAA
* * ** *
35095480 TGAAAGCACATAAGTGCGTCTGTTTGTTCTTCGGTACCCC
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
* *
35095520 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
35095560 TGACTGCACATATGTG-CCATGTTTGTACTTCGGTACCCT
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
* * **
35095599 TGAATGCACATAAGTGCCCCTATTTGTACTTTAGTACCCC
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
** * * *
35095639 TGAATGCATTTATATG-CCCTGTTTATACTCCGGTA
1 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTA
35095674 ACTCTAAATT
Statistics
Matches: 126, Mismatches: 27, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 48 0.38
40 78 0.62
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (40 bp):
TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:35095636 original size:79 final size:79
Alignment explanation
Indices: 35095500--35095673 Score: 240
Period size: 79 Copynumber: 2.2 Consensus size: 79
35095490 TAAGTGCGTC
* * * *
35095500 TGTTTGTTCTTCGGTACCCCTGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTGACT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCCTGAAT
*
35095565 GCACATATGTGCCA
66 GCACATATATGCCA
* *
35095579 TGTTTGTACTTCGGTACCCTTGAATGCACATAAGTGCCCCTATTTGTACTTTAGTACCCCTGAAT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCCTGAAT
** *
35095644 GCATTTATATGCCC
66 GCACATATATGCCA
* *
35095658 TGTTTATACTCCGGTA
1 TGTTTGTACTTCGGTA
35095674 ACTCTAAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (79 bp):
TGTTTGTACTTCGGTACCCCTGAATGCACATAAGTGCCCCTATTTGTACTTCAGTACCCCTGAAT
GCACATATATGCCA
Found at i:35099834 original size:6 final size:6
Alignment explanation
Indices: 35099823--35099860 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
35099813 TTGATAATTA
*
35099823 CCTCTT CCTCTT CCTCTT CTTCTT CCTC-T CGCTCTT CC
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT C-CTCTT CC
35099861 ACGATTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 2 0.07
6 24 0.86
7 2 0.07
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (6 bp):
CCTCTT
Found at i:35101202 original size:22 final size:20
Alignment explanation
Indices: 35101151--35101203 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
35101141 TACAATGACT
*
35101151 AAAATTTTAAAATTTAATAA
1 AAAATTTTAAAATTAAATAA
*
35101171 AATAA-ATTAATAATTAAAATAA
1 AA-AATTTTAA-AATT-AAATAA
35101193 AAAATTTTAAA
1 AAAATTTTAAA
35101204 CTTGAATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAAATTAAATAA
Found at i:35104534 original size:235 final size:233
Alignment explanation
Indices: 35104187--35104662 Score: 588
Period size: 237 Copynumber: 2.0 Consensus size: 233
35104177 AATCACATTT
* * * *
35104187 AAATATTGATTTAAAATTTACGAAAATTTGTGTAATAATATTTGGTACAGTGAAATTTTTAAACT
1 AAATAATGATTTAAAATTTACGAAAATATGTGTAATAATATTTAGTACAATGAAATTTTTAAACT
* ** * * *
35104252 CCATAAGTAGATTTAAGGAGTTTCGAGTATCTTATAAAAGTATAGTAAATTATTAAATATATATA
66 CCATAAATAGATTTAAAAAGTTAC-AGTATCTTATAAAAGTATAGTAAATAATTAAAAATATATA
**
35104317 TTTAAAAAAGAAATACATCAATTTTTTAAAATTGCTTATGTA-CCAAATACTC-ACCTATTAATT
130 TTT---AAA-AAAT--ATCAATTTTTTAAAAGGGCTT-TGTAGCCAAATACTCTACCTATT-ATT
*
35104380 ATTATAATATTACTTT-A-AATGTAATATTTAGATTTCTATAACAAA
187 ATAATAATATTACTTTAATAATGTAATATTTAGATTTCTATAACAAA
* * * *
35104425 AAATAATGATTTAAAA-TTATGAAAATATG-GATAGTGATATTTAGTACAATGAATTTTTTAAAC
1 AAATAATGATTTAAAATTTACGAAAATATGTG-TAATAATATTTAGTACAATGAAATTTTTAAAC
* **
35104488 TCTATAAATAGATTTAAAAAGTTAC-GTATCTTATAAGGGTATAGTAAATAATTAAAAATATATA
65 TCCATAAATAGATTTAAAAAGTTACAGTATCTTATAAAAGTATAGTAAATAATTAAAAATATATA
* **
35104552 TTTAAAAAATATCAATTTTTTAAGAGGGCTTTGTATGCCAAATACTCTTTCTATTATTATAATAA
130 TTTAAAAAATATCAATTTTTTAAAAGGGCTTTGTA-GCCAAATACTCTACCTATTATTATAATAA
35104617 TATTACTTTAAATAATGTAATATTTAGATTTCTATAACAAA
194 TATTACTTT-AATAATGTAATATTTAGATTTCTATAACAAA
35104658 AAATA
1 AAATA
35104663 GAATGTGAAG
Statistics
Matches: 208, Mismatches: 23, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
228 4 0.02
229 18 0.09
230 28 0.13
231 9 0.04
232 4 0.02
233 33 0.16
235 38 0.18
236 1 0.00
237 58 0.28
238 15 0.07
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (233 bp):
AAATAATGATTTAAAATTTACGAAAATATGTGTAATAATATTTAGTACAATGAAATTTTTAAACT
CCATAAATAGATTTAAAAAGTTACAGTATCTTATAAAAGTATAGTAAATAATTAAAAATATATAT
TTAAAAAATATCAATTTTTTAAAAGGGCTTTGTAGCCAAATACTCTACCTATTATTATAATAATA
TTACTTTAATAATGTAATATTTAGATTTCTATAACAAA
Found at i:35106182 original size:2 final size:2
Alignment explanation
Indices: 35106175--35106206 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35106165 AATAAGGCCT
35106175 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35106207 ATGTTGGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35108232 original size:14 final size:13
Alignment explanation
Indices: 35108209--35108255 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
35108199 AAATAATAAA
35108209 AATAAATTTTTTT
1 AATAAATTTTTTT
35108222 AATAAATTTTTTT
1 AATAAATTTTTTT
*
35108235 -ATATA-TTTTTT
1 AATAAATTTTTTT
35108246 AAT-AATTTTT
1 AATAAATTTTT
35108256 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 7 0.23
12 10 0.33
13 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATAAATTTTTTT
Found at i:35108233 original size:12 final size:12
Alignment explanation
Indices: 35108209--35108255 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
35108199 AAATAATAAA
35108209 AATAAATTTTTTT
1 AATAAA-TTTTTT
35108222 AATAAATTTTTT
1 AATAAATTTTTT
* *
35108234 TATATATTTTTT
1 AATAAATTTTTT
35108246 AAT-AATTTTT
1 AATAAATTTTT
35108256 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 6 0.20
12 18 0.60
13 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATAAATTTTTT
Found at i:35109903 original size:40 final size:41
Alignment explanation
Indices: 35109852--35110111 Score: 148
Period size: 40 Copynumber: 6.1 Consensus size: 41
35109842 TTTGGATTAG
* *
35109852 AATTTTGTATGAATATTTTAATTTTTTTGTATGAATATTGT
1 AATTTTTTATGAATATTGTAATTTTTTTGTATGAATATTGT
* * *
35109893 -ATTTTTTATGAATATTGTAATTATTTTATAATTAA-ATT-T
1 AATTTTTTATGAATATTGTAATTTTTTTGT-ATGAATATTGT
* * * * *
35109932 -A-TATTTAT-AGTTTTG-GATTAGTATTTTGTATGGATATTGT
1 AATTTTTTATGAATATTGTAATT--T-TTTTGTATGAATATTGT
35109972 AATTTTTTGTATGAATATTGTAA---TTTTGTATGAATATTGT
1 AA-TTTTT-TATGAATATTGTAATTTTTTTGTATGAATATTGT
35110012 AATTTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGT
1 AA--TTTTT-TATGAATATTGTAA--TT-T--TTTTGTATGAATATTGT
35110061 AATGTCGGGATATATTAT-AATATTGTAA-TTTTTTGTATGAATATTGT
1 AAT-T-----T-T-TTATGAATATTGTAATTTTTTTGTATGAATATTGT
35110108 AATT
1 AATT
35110112 ATTGTATAAT
Statistics
Matches: 172, Mismatches: 18, Indels: 53
0.71 0.07 0.22
Matches are distributed among these distances:
36 3 0.02
37 5 0.03
38 9 0.05
39 10 0.06
40 47 0.27
41 26 0.15
43 3 0.02
44 3 0.02
45 5 0.03
46 2 0.01
47 21 0.12
48 1 0.01
49 20 0.12
50 1 0.01
53 11 0.06
54 4 0.02
55 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (41 bp):
AATTTTTTATGAATATTGTAATTTTTTTGTATGAATATTGT
Found at i:35109960 original size:101 final size:100
Alignment explanation
Indices: 35109835--35110020 Score: 302
Period size: 101 Copynumber: 1.9 Consensus size: 100
35109825 ATATTTAGTG
* *
35109835 TTTATAGTTTGGATTAGAATTTTGTATGAATATTTTAATTTTTTTGTATGAATATTGT-ATTTTT
1 TTTATAGTTTGGATTAGAATTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGTAATTTTG
35109899 TATGAATATTGTAATTATTTTATAATTAAATTTATA
65 TATGAATATTGTAATTATTTTATAATTAAATTTATA
* *
35109935 TTTATAGTTTTGGATTAGTATTTTGTATGGATATTGTAATTTTTTGTATGAATATTGTAATTTTG
1 TTTATAG-TTTGGATTAGAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTG
*
35110000 TATGAATATTGTAATTTTTTT
65 TATGAATATTGTAATTATTTT
35110021 GTATGAATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
100 26 0.33
101 53 0.67
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (100 bp):
TTTATAGTTTGGATTAGAATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTGT
ATGAATATTGTAATTATTTTATAATTAAATTTATA
Found at i:35110019 original size:41 final size:40
Alignment explanation
Indices: 35109854--35110042 Score: 167
Period size: 41 Copynumber: 4.7 Consensus size: 40
35109844 TGGATTAGAA
*
35109854 TTTTGTATGAATATTTTAATTTTTTTGTATGAATATTGT-A-T
1 TTTTGTATGAATATTGTAA---TTTTGTATGAATATTGTAATT
*
35109895 TTTT-TATGAATATTGTAATTATTTTAT-AATTAAATT-TATATT
1 TTTTGTATGAATATTGTAATT-TTGTATGAA-T--ATTGTA-ATT
* * * * * *
35109937 TATAGTTTTGGAT-TAGT-ATTTTGTATGGATATTGTAATT
1 TTTTG-TATGAATATTGTAATTTTGTATGAATATTGTAATT
35109976 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAA-TT
35110017 TTTTGTATGAATATTGTAATTTTGTA
1 TTTTGTATGAATATTGTAATTTTGTA
35110043 ATTTTGTATG
Statistics
Matches: 119, Mismatches: 15, Indels: 28
0.73 0.09 0.17
Matches are distributed among these distances:
37 4 0.03
38 11 0.09
39 13 0.11
40 37 0.31
41 39 0.33
42 7 0.06
43 3 0.03
44 5 0.04
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
Found at i:35110033 original size:22 final size:22
Alignment explanation
Indices: 35109854--35109919 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
35109844 TGGATTAGAA
*
35109854 TTTTGTATGAATATTTTAATTT
1 TTTTGTATGAATATTGTAATTT
35109876 TTTTGTATGAATATTGT-A--T
1 TTTTGTATGAATATTGTAATTT
*
35109895 TTTT-TATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
35109916 TTTT
1 TTTT
35109920 ATAATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.31
19 6 0.15
21 5 0.13
22 16 0.41
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:35110171 original size:25 final size:24
Alignment explanation
Indices: 35110104--35110188 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 24
35110094 TGTATGAATA
*
35110104 TTGTAATTATTGTATAATTAATTTG
1 TTGTAATTATT-TAAAATTAATTTG
*
35110129 TTAGTAATT-TATATAAATT-ATTGTG
1 TT-GTAATTATTTA-AAATTAATT-TG
*
35110154 TGTGTAATTATTTAAAATTTAATTTA
1 T-TGTAATTATTTAAAA-TTAATTTG
35110180 TTAGTAATT
1 TT-GTAATT
35110189 TAGGATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
24 5 0.10
25 20 0.42
26 20 0.42
27 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (24 bp):
TTGTAATTATTTAAAATTAATTTG
Found at i:35110301 original size:37 final size:37
Alignment explanation
Indices: 35110250--35110330 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
35110240 CATATAAAGT
35110250 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGTTTAA
* * *
35110288 TTATAAAAAATTAAAATTTATTTTATTAATAGTTTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
35110325 TTATAA
1 TTATAA
35110331 CTGACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
Found at i:35110408 original size:15 final size:15
Alignment explanation
Indices: 35110367--35110408 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
35110357 GTTAACTCAT
*
35110367 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
35110382 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
35110398 TTAAATTTTAT
1 TTAAATTTTAT
35110409 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:35114099 original size:47 final size:47
Alignment explanation
Indices: 35113972--35114298 Score: 483
Period size: 47 Copynumber: 6.9 Consensus size: 47
35113962 GATGTACAAG
* * * *
35113972 TGTATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AA-CA
* * * *
35114021 TATATATGCGTGATAAGGTCAAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
35114068 TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
35114115 TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
35114162 TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * *
35114209 TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * *
35114256 TGCATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTG
1 TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
35114299 GAAGTGTATA
Statistics
Matches: 259, Mismatches: 19, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
47 221 0.85
48 2 0.01
49 36 0.14
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (47 bp):
TGTATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
Found at i:35114197 original size:22 final size:22
Alignment explanation
Indices: 35114170--35114291 Score: 63
Period size: 22 Copynumber: 5.3 Consensus size: 22
35114160 CATGTGTATG
35114170 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
35114192 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
35114217 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
35114239 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
35114264 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
35114286 TGTGAT
1 TGTGAT
35114292 GGATGTGGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 28
0.63 0.12 0.25
Matches are distributed among these distances:
22 21 0.29
23 18 0.25
24 18 0.25
25 15 0.21
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:35119916 original size:27 final size:27
Alignment explanation
Indices: 35119856--35119921 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
35119846 AAAATCAGAG
*
35119856 CATTGGCGCCTCTCAGTATGGCACCAA
1 CATTGGCGCCTCCCAGTATGGCACCAA
* * *
35119883 TAATGGCGCCTCCCAG-ATAGGCACCAC
1 CATTGGCGCCTCCCAGTAT-GGCACCAA
35119910 CATTGGCGCCTC
1 CATTGGCGCCTC
35119922 TAATACTATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGTATGGCACCAA
Found at i:35124398 original size:20 final size:18
Alignment explanation
Indices: 35124351--35124399 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
35124341 GTATATAAAC
35124351 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
35124368 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
35124388 ATTAAATTAATA
1 ATTAAATTAATA
35124400 AAATACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:35131380 original size:18 final size:18
Alignment explanation
Indices: 35131357--35131391 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35131347 TAATTTATCA
35131357 TTATTA-TTATTATTAGTG
1 TTATTATTTA-TATTAGTG
35131375 TTATTATTTATATTAGT
1 TTATTATTTATATTAGT
35131392 TCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (18 bp):
TTATTATTTATATTAGTG
Found at i:35131424 original size:16 final size:16
Alignment explanation
Indices: 35131399--35131445 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
35131389 AGTTCATATA
35131399 TTTATCTATATAATT-T
1 TTTAT-TATATAATTAT
*
35131415 TTTATGTATATGCATTAT
1 TTTAT-TATAT-AATTAT
35131433 TTTATTATATAAT
1 TTTATTATATAAT
35131446 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTATTATATAATTAT
Found at i:35131646 original size:16 final size:16
Alignment explanation
Indices: 35131622--35131663 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
35131612 TTCAACTTTA
35131622 ATATATTATTATGTAT
1 ATATATTATTATGTAT
* *
35131638 ATATGTTATTATTTAT
1 ATATATTATTATGTAT
35131654 AT-TATTATTA
1 ATATATTATTA
35131664 AATCTTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
ATATATTATTATGTAT
Found at i:35131658 original size:12 final size:13
Alignment explanation
Indices: 35131622--35131663 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
35131612 TTCAACTTTA
35131622 ATATATTATTATGT
1 ATATATTATTAT-T
35131636 ATATATGTTATTATT
1 ATATA--TTATTATT
35131651 -TATATTATTATT
1 ATATATTATTATT
35131663 A
1 A
35131664 AATCTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
14 9 0.36
15 1 0.04
16 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
ATATATTATTATT
Found at i:35139046 original size:21 final size:21
Alignment explanation
Indices: 35138996--35139051 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
35138986 AATAACTAAC
35138996 TAATCTTAATTAA-C-TAAAT
1 TAATCTTAATTAATCATAAAT
35139015 TAA-CTTTAATTAATCATATAA-
1 TAATC-TTAATTAATCATA-AAT
35139036 TAATCTTAATTAATCA
1 TAATCTTAATTAATCA
35139052 AAGATAGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.34
20 1 0.03
21 16 0.50
22 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATCTTAATTAATCATAAAT
Found at i:35164322 original size:50 final size:50
Alignment explanation
Indices: 35164242--35164534 Score: 460
Period size: 50 Copynumber: 5.8 Consensus size: 50
35164232 ATTTGGGTAA
*
35164242 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
35164292 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
35164342 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
* * *
35164392 AGAAGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
* * * * * *
35164442 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
** *
35164492 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
35164535 TGTTATTATC
Statistics
Matches: 225, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
50 191 0.85
51 34 0.15
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
Found at i:35167583 original size:10 final size:10
Alignment explanation
Indices: 35167568--35167592 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35167558 GTTTCAATCC
35167568 AATTTTCTTT
1 AATTTTCTTT
35167578 AATTTTCTTT
1 AATTTTCTTT
35167588 AATTT
1 AATTT
35167593 ATACCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
AATTTTCTTT
Found at i:35174030 original size:9 final size:9
Alignment explanation
Indices: 35174016--35174045 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35174006 ACCAAAGAAT
35174016 AAAAAATCA
1 AAAAAATCA
35174025 AAAAAATCA
1 AAAAAATCA
*
35174034 AAAAACTCA
1 AAAAAATCA
35174043 AAA
1 AAA
35174046 TCGAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATCA
Found at i:35177532 original size:71 final size:71
Alignment explanation
Indices: 35177446--35177620 Score: 226
Period size: 71 Copynumber: 2.5 Consensus size: 71
35177436 ATCTAGTACG
* * *
35177446 TGTCGCGACACAGGTACCCCTTTATT-TCTACACGCAACTTTGAAGTATTAAAATTTGAAAATAA
1 TGTCGCGACATAGGTACCCCTGTATTGT-GACACGCAACTTTGAAGTATTAAAATTTGAAAATAA
35177510 CAGGCCA
65 CAGGCCA
* * *
35177517 TGTCGTGACATAGGTACCCCTGTGTTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATACC
1 TGTCGCGACATAGGTACCCCTGTATTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATAAC
*
35177582 AGGCCG
66 AGGCCA
* * * * *
35177588 TGTTGCGACATAGGTTCCCTTGTGTTGCGACAC
1 TGTCGCGACATAGGTACCCCTGTATTGTGACAC
35177621 ATTACTTCGA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 90 0.99
72 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (71 bp):
TGTCGCGACATAGGTACCCCTGTATTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATAAC
AGGCCA
Found at i:35184894 original size:12 final size:13
Alignment explanation
Indices: 35184869--35184903 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
35184859 TGATTTACAT
35184869 TTCATCATATCCAA
1 TTCATCA-ATCCAA
35184883 TTCA-CAATCCAA
1 TTCATCAATCCAA
35184895 TTCATCAAT
1 TTCATCAAT
35184904 TTACCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.50
13 6 0.30
14 4 0.20
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (13 bp):
TTCATCAATCCAA
Found at i:35185721 original size:16 final size:17
Alignment explanation
Indices: 35185702--35185746 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
35185692 TTTTAATTAG
35185702 TTTAATTTAATTAATT-
1 TTTAATTTAATTAATTC
35185718 TTTAATCTTAA-TAATTC
1 TTTAAT-TTAATTAATTC
35185735 TTT-A-TTAATTAA
1 TTTAATTTAATTAA
35185747 ACTAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 12 0.46
17 7 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTTAATTAATTC
Found at i:35188065 original size:22 final size:24
Alignment explanation
Indices: 35188022--35188065 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
35188012 TGATAATATG
35188022 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
*
35188046 TTTTGA-ATAA-AATTTAAAGT
1 TTTTGATATAACAAATTAAAGT
35188066 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:35188191 original size:20 final size:20
Alignment explanation
Indices: 35188166--35188207 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
35188156 CAAACTTTAA
35188166 AATCAAGTTAAAA-TTATTTT
1 AATCAAG-TAAAAGTTATTTT
*
35188186 AATCAAGTAAAAGTTCTTTT
1 AATCAAGTAAAAGTTATTTT
35188206 AA
1 AA
35188208 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
AATCAAGTAAAAGTTATTTT
Found at i:35188455 original size:13 final size:13
Alignment explanation
Indices: 35188437--35188500 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
35188427 AGTTCTTCAT
*
35188437 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
35188450 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
35188463 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
35188476 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
35188489 TGCTTTTGAAAA
1 TGCTTTTGAAAA
35188501 TTTTGAGCGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:35203742 original size:11 final size:12
Alignment explanation
Indices: 35203721--35203749 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
35203711 TAAATTATTT
35203721 TAAAAACATAAA
1 TAAAAACATAAA
35203733 TAAAAA-ATAAA
1 TAAAAACATAAA
35203744 TAAAAA
1 TAAAAA
35203750 TTATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAACATAAA
Found at i:35205709 original size:44 final size:44
Alignment explanation
Indices: 35205389--35205717 Score: 141
Period size: 44 Copynumber: 7.5 Consensus size: 44
35205379 TTCTAATCCA
* * * * * *
35205389 CTCCACTACAACTT-TGGGGAGATAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGAGAGATAAGA-TTGCTTACTTAGTCTG
* * * *
35205433 AC-CCGCTGCAATTTCAGG-GGGATAAGACTTGCTTTCTTGAGTCTG
1 -CTCCACTGCAACTTCAGGAGAGATAAGA-TTGCTTACTT-AGTCTG
* ** *
35205478 CTCCACTGCAACTTCAGG-GAGATAAGA--CCCGA-TGT-GATCTA
1 CTCCACTGCAACTTCAGGAGAGATAAGATTGCTTACT-TAG-TCTG
* * * * * * *
35205519 CTCTACAGCAACTTTA-GAGAGATCAGATCTG-TGGATTTAATCTG
1 CTCCACTGCAACTTCAGGAGAGATAAGAT-TGCT-TACTTAGTCTG
* * * *
35205563 CTCCACTGCAACTTCA-GAGAGATAGGATT-ATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGAGAGATAAGATTGCTT-AC-TTAGTCTG
* * *
35205607 CTCCACTACAACTTCAGG-GAAATAAGATTCGC-CACCTTCAGTCTG
1 CTCCACTGCAACTTCAGGAGAGATAAGATT-GCTTA-CTT-AGTCTG
*
35205652 -TCTCACTGTAACTTCAGGAG-GATAAGACTTGCTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGAGAGATAAGA-TTGCTTACTTAGTCTG
35205696 CTCCACTGCAACTTCATGGAGA
1 CTCCACTGCAACTTCA-GGAGA
35205718 TAAAACTAGA
Statistics
Matches: 211, Mismatches: 46, Indels: 53
0.68 0.15 0.17
Matches are distributed among these distances:
40 2 0.01
41 25 0.12
42 2 0.01
43 2 0.01
44 107 0.51
45 69 0.33
46 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGAGAGATAAGATTGCTTACTTAGTCTG
Found at i:35205947 original size:100 final size:100
Alignment explanation
Indices: 35205831--35206127 Score: 416
Period size: 100 Copynumber: 3.0 Consensus size: 100
35205821 TATTTTTAAT
* *
35205831 TGCAATGTTGGTGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTACACCGCCAAGGAA
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAA
* *
35205896 GTAAGATTCACCGATGCGGCTTCAATCTTTTTCAC
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTCAC
* * * **
35205931 TGCAATGTTGGGGAAACAAGACTCACCGTCGTAGCTTCAATCTGTTCCACTATATAGCCAAGGAA
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAA
* * * *
35205996 GTAAGATTCGCTGTTGCGACTTCAATCTTTTTAAT
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTCAC
* * * * *
35206031 TACAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTTCACCACACCGCCAGGGGA
1 TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAA
*
35206096 GTAAGATTCGTCGTTGCGGCTTCAAT-TTTTTC
66 GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTC
35206128 CATTTAATTC
Statistics
Matches: 170, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
99 5 0.03
100 165 0.97
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (100 bp):
TGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAGGAA
GTAAGATTCGCCGTTGCGGCTTCAATCTTTTTCAC
Found at i:35206069 original size:50 final size:50
Alignment explanation
Indices: 35205833--35206080 Score: 155
Period size: 50 Copynumber: 5.0 Consensus size: 50
35205823 TTTTTAATTG
* * * *
35205833 CAATGTTGGTGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTA
1 CAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCACTA
** **** ** * *
35205883 CACCGCCAAGGAAGTAAGATTCACCGATGCG--GCTTCAATCTTTTTCACTG
1 CAATGTTGGGGAAACAAGATTCGCCG-T-CGTAGCTTCAATCTTTTTCACTA
* * * *
35205933 CAATGTTGGGGAAACAAGACTCACCGTCGTAGCTTCAATCTGTTCCACTA
1 CAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCACTA
* **** ** * * *
35205983 -TATAGCCAAGGAAGTAAGATTCGCTGTTGCG-A-CTTCAATCTTTTTAATTA
1 CAAT-GTTGGGGAAACAAGATTCGCCG-T-CGTAGCTTCAATCTTTTTCACTA
*
35206033 CAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTTCAC
1 CAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCAC
35206081 CACACCGCCA
Statistics
Matches: 137, Mismatches: 51, Indels: 20
0.66 0.25 0.10
Matches are distributed among these distances:
48 4 0.03
49 5 0.04
50 119 0.87
51 5 0.04
52 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (50 bp):
CAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTTTTTCACTA
Found at i:35206427 original size:88 final size:88
Alignment explanation
Indices: 35206327--35206488 Score: 279
Period size: 88 Copynumber: 1.8 Consensus size: 88
35206317 ACGAGTGTCA
* * * *
35206327 TCGATCTGCTTCACTGCCAGCACAGGAAGATAAGATCTGTTATTTTCAACCTACTCCACTGCTGC
1 TCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
35206392 TCAGGGAGACAAAGCTGGTATCT
66 TCAGGGAGACAAAGCTGGTATCT
*
35206415 TCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
1 TCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
35206480 TCAGGGAGA
66 TCAGGGAGA
35206489 TAAGTTGAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (88 bp):
TCGATCTACTTCACTGCCAACACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGC
TCAGGGAGACAAAGCTGGTATCT
Found at i:35206475 original size:45 final size:45
Alignment explanation
Indices: 35206338--35206476 Score: 138
Period size: 45 Copynumber: 3.1 Consensus size: 45
35206328 CGATCTGCTT
** * *
35206338 CACTGCCAGCACAGGAAGATAAGATCTGTTATTTTCAACCTACTC
1 CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
*** * * * * * * *
35206383 CACTGCTGCT-CAGGGAGACAA-AGCTGGTATCTTCGATCTACTT
1 CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
35206426 CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
1 CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
35206471 CACTGC
1 CACTGC
35206477 TGCTCAGGGA
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
43 23 0.33
44 19 0.27
45 28 0.40
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (45 bp):
CACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTC
Found at i:35218667 original size:27 final size:27
Alignment explanation
Indices: 35218636--35218714 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
35218626 AAACATAGAT
* * *
35218636 ATATATGTATATATATAAATATAAAAA
1 ATATATATACATATATATATATAAAAA
* * *
35218663 ATATATTTACATGTACATATATAAAAA
1 ATATATATACATATATATATATAAAAA
35218690 ATATATATACATATATATATATAAA
1 ATATATATACATATATATATATAAA
35218715 TTATAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (27 bp):
ATATATATACATATATATATATAAAAA
Found at i:35218719 original size:25 final size:25
Alignment explanation
Indices: 35218638--35218719 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
35218628 ACATAGATAT
* * *
35218638 ATATGTATATATATAAATATAAAAA
1 ATATATATACATATATATATAAAAA
* *
35218663 ATATATTTACATGTACATATATAAAAA
1 ATATATATACA--TATATATATAAAAA
*
35218690 ATATATATACATATATATATATAAA
1 ATATATATACATATATATATAAAAA
*
35218715 TTATA
1 ATATA
35218720 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
25 24 0.52
27 22 0.48
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATACATATATATATAAAAA
Found at i:35220043 original size:15 final size:15
Alignment explanation
Indices: 35220023--35220062 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
35220013 TGACTATTGT
35220023 TTTGGGCCTGGTTAG
1 TTTGGGCCTGGTTAG
*
35220038 TTTGGGCCTCTGTTTAG
1 TTTGGG-C-CTGGTTAG
35220055 TTTGGGCC
1 TTTGGGCC
35220063 ACATAGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 13 0.59
ACGTcount: A:0.05, C:0.17, G:0.35, T:0.42
Consensus pattern (15 bp):
TTTGGGCCTGGTTAG
Found at i:35222719 original size:30 final size:29
Alignment explanation
Indices: 35222658--35222719 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
35222648 AAAATAATAA
** * *
35222658 AATTATTTCCACGAAACTTTCACACATAT
1 AATTATTTCCACGAAACTAACACAAAAAT
*
35222687 AATTATTTCCACATAAACTAACACAAAAAT
1 AATTATTTCCAC-GAAACTAACACAAAAAT
35222717 AAT
1 AAT
35222720 ATTAAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (29 bp):
AATTATTTCCACGAAACTAACACAAAAAT
Found at i:35223173 original size:22 final size:24
Alignment explanation
Indices: 35223130--35223173 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
35223120 TGATAATATG
35223130 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
35223154 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
35223174 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:35223298 original size:20 final size:20
Alignment explanation
Indices: 35223273--35223314 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
35223263 CCAACTTTAA
*
35223273 AATCAAGTTAAAATGATTTT
1 AATCAAGTAAAAATGATTTT
*
35223293 AATCAAGTAAAAATTATTTT
1 AATCAAGTAAAAATGATTTT
35223313 AA
1 AA
35223315 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AATCAAGTAAAAATGATTTT
Found at i:35225327 original size:22 final size:23
Alignment explanation
Indices: 35225297--35225341 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35225287 ATTATTAAAG
35225297 TAGACTCATAT-TGAATTTATTC
1 TAGACTCATATATGAATTTATTC
* * *
35225319 TAGATTCATTTATGGATTTATTC
1 TAGACTCATATATGAATTTATTC
35225342 ACATGTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (23 bp):
TAGACTCATATATGAATTTATTC
Found at i:35231172 original size:18 final size:19
Alignment explanation
Indices: 35231151--35231191 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
35231141 AGTTAACCTT
35231151 TATTATTTAA-AAAATTAA
1 TATTATTTAATAAAATTAA
35231169 TATTATTTAATAAAATTAA
1 TATTATTTAATAAAATTAA
35231188 TATT
1 TATT
35231192 TTGGACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTTAATAAAATTAA
Found at i:35238726 original size:15 final size:15
Alignment explanation
Indices: 35238702--35238738 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
35238692 TGAATTTAGA
35238702 TTAA-TTCAAA-ATT
1 TTAATTTCAAATATT
35238715 TTGAATTTCAAATATT
1 TT-AATTTCAAATATT
35238731 TTAATTTC
1 TTAATTTC
35238739 CAAACAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 2 0.10
15 12 0.57
16 5 0.24
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATTTCAAATATT
Found at i:35243488 original size:50 final size:50
Alignment explanation
Indices: 35243414--35243654 Score: 241
Period size: 50 Copynumber: 4.7 Consensus size: 50
35243404 TCATGTACTA
* * * * *
35243414 CCAATGCCATATCCTAGATATGGTCTTACATGGGAGTC-CTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCACTCATATCGGTG
* * * ** *
35243464 CCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCACTCATATTGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
* * *
35243514 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
*
35243564 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCACTCAT-A--TC--GG-TG
* * * *
35243620 CTAATGACATGTCTCAGACATGGTCTTACATGGGA
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGA
35243655 TCTCTTTACC
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 122 0.76
53 2 0.01
55 2 0.01
56 33 0.21
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
Found at i:35243548 original size:100 final size:104
Alignment explanation
Indices: 35243414--35243659 Score: 277
Period size: 100 Copynumber: 2.4 Consensus size: 104
35243404 TCATGTACTA
* * * * * *
35243414 CCAATGCCATATCCTAGATATGGTCTTACATGGGA-GTCCTCATATCGGTGCCCATGCCATGTCC
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATATCGGTGCCAACGCCATGTCC
*
35243478 CAAACATGGTCTTACGGGGGACCACTCAT-AT-T-GG-TG
65 CAAACATGGTCTTACAGGGGACCACTCATGATCTAGGATG
* * *
35243514 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCAACGCCATGTCCC
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
* * *
35243579 AGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATG
66 AAACATGGTCTTACAGGGGACCACTCATGATCT--AGGATG
* * * *
35243620 CTAATGACATGTCTCAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35243660 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
100 78 0.64
101 3 0.02
102 1 0.01
105 2 0.02
106 37 0.31
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (104 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
AAACATGGTCTTACAGGGGACCACTCATGATCTAGGATG
Found at i:35249454 original size:13 final size:13
Alignment explanation
Indices: 35249436--35249464 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35249426 TTTCAGCAGA
35249436 AATCCACTATTAC
1 AATCCACTATTAC
35249449 AATCCACTATTAC
1 AATCCACTATTAC
35249462 AAT
1 AAT
35249465 GGGGTTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (13 bp):
AATCCACTATTAC
Found at i:35257548 original size:37 final size:35
Alignment explanation
Indices: 35257485--35257587 Score: 86
Period size: 37 Copynumber: 2.9 Consensus size: 35
35257475 ATTTTAAAAA
*
35257485 TAATATTATTTTAATAGTTTAATATTAAATTAAATT
1 TAATATTATCTTAATAGTTTAATATT-AATTAAATT
*
35257521 TAATACTTATCTTAATAGTATT-TTATTAATTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTAA-ATT
* * *
35257558 AAAATGATTATGTTAATA-TTAAAT-TTAATT
1 -TAAT-ATTATCTTAATAGTTTAATATTAATT
35257588 TAATGTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
36 18 0.33
37 21 0.38
38 15 0.27
39 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTAAATT
Found at i:35261248 original size:13 final size:13
Alignment explanation
Indices: 35261211--35261274 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
35261201 TTCTTCATTA
35261211 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
35261224 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
*
35261237 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
35261250 CTTTT-AAGAAGTG
1 CTTTTGAA-AAGTG
35261263 CTTTTGAAAAGT
1 CTTTTGAAAAGT
35261275 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.93
14 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:35271742 original size:4 final size:4
Alignment explanation
Indices: 35271733--35271762 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
35271723 ATAAAGGCAT
35271733 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
35271763 GCCTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:35271853 original size:15 final size:18
Alignment explanation
Indices: 35271815--35271855 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
35271805 AGCAAATACT
35271815 AATAATAAGAACAGTAAC
1 AATAATAAGAACAGTAAC
*
35271833 AGTAATAA-AA-A-TAAC
1 AATAATAAGAACAGTAAC
35271848 AATAATAA
1 AATAATAA
35271856 TACTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 2 0.10
18 7 0.33
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAATAAGAACAGTAAC
Found at i:35271857 original size:39 final size:39
Alignment explanation
Indices: 35271809--35271904 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
35271799 CAACCAAGCA
* *
35271809 AATACTAATAATAAGAA-CAGTAACAG-TAATAAAAATAAC
1 AATAATAATAATAA-AATAAGTAA-AGATAATAAAAATAAC
* *
35271848 AATAATAATACTAAAATAATTAAAGATAATAAAAATAAC
1 AATAATAATAATAAAATAAGTAAAGATAATAAAAATAAC
*
35271887 AGA-AA-AATAAAAAAATAA
1 A-ATAATAATAATAAAATAA
35271905 AGGTAATGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
38 15 0.31
39 32 0.67
40 1 0.02
ACGTcount: A:0.68, C:0.06, G:0.05, T:0.21
Consensus pattern (39 bp):
AATAATAATAATAAAATAAGTAAAGATAATAAAAATAAC
Found at i:35274387 original size:14 final size:14
Alignment explanation
Indices: 35274368--35274397 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35274358 AGTGAGAGAG
*
35274368 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
35274382 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
35274396 GA
1 GA
35274398 ATGAGGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:35277243 original size:29 final size:28
Alignment explanation
Indices: 35277203--35277269 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
35277193 TACCAGAAGC
35277203 AAAAA-AACAAAAA-ATTAGAATATAAAAAT
1 AAAAATAA-AAAAATATTA-AA-ATAAAAAT
* *
35277232 TAAATTAAAAAAATTATTAAAATAAAAAT
1 AAAAATAAAAAAA-TATTAAAATAAAAAT
35277261 AAAAATAAA
1 AAAAATAAA
35277270 TAATGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 23 0.74
30 4 0.13
31 4 0.13
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (28 bp):
AAAAATAAAAAAATATTAAAATAAAAAT
Found at i:35277732 original size:54 final size:54
Alignment explanation
Indices: 35277650--35277758 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
35277640 ATTTCTTCAC
* *
35277650 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCTCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
35277704 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
35277758 T
1 T
35277759 AAGAGCAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (54 bp):
TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
Found at i:35279570 original size:12 final size:12
Alignment explanation
Indices: 35279553--35279597 Score: 53
Period size: 10 Copynumber: 4.1 Consensus size: 12
35279543 TTGCAATTGA
35279553 TTTTTATATAAT
1 TTTTTATATAAT
*
35279565 TTTTTAT-TTA-
1 TTTTTATATAAT
35279575 TTTTTATAT-AT
1 TTTTTATATAAT
35279586 TTTTT-TATAAT
1 TTTTTATATAAT
35279597 T
1 T
35279598 GTTGTTAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:35279577 original size:22 final size:22
Alignment explanation
Indices: 35279552--35279593 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
35279542 ATTGCAATTG
35279552 ATTTTTATATAATTTTTTATTT
1 ATTTTTATATAATTTTTTATTT
*
35279574 ATTTTTATATATTTTTTTAT
1 ATTTTTATATAATTTTTTAT
35279594 AATTGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTATATAATTTTTTATTT
Found at i:35280413 original size:41 final size:41
Alignment explanation
Indices: 35280356--35280675 Score: 281
Period size: 41 Copynumber: 7.8 Consensus size: 41
35280346 ATTTTTAAAC
* *
35280356 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * *
35280397 CTTTAGTGGCGTTTTTACCTTG-GTGCCGCTAATGCTCCGAT
1 CTTTAGCGGCGTTTTTATC-TGAGCGCCGCTAATGCTCGGAT
* * * * *
35280438 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * * *
35280479 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAG
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
35280520 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* *
35280561 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * * *
35280602 CTTTAGTGACGTTTTTTTCTGAGCGCCACTAATTCTCCTG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCT-CGGAT
*
35280643 CTTTAGCGGCGTTTGTT-TCTAAGCGCCGCTAAT
1 CTTTAGCGGCGTTT-TTATCTGAGCGCCGCTAAT
35280676 AGTAACAAAA
Statistics
Matches: 223, Mismatches: 48, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
40 6 0.03
41 208 0.93
42 9 0.04
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:35280493 original size:82 final size:82
Alignment explanation
Indices: 35280356--35280675 Score: 376
Period size: 82 Copynumber: 3.9 Consensus size: 82
35280346 ATTTTTAAAC
* * * * * ** **
35280356 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTC-GGATCTTTAGTGGCGTTTTTACCTTGG
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGG-CCTTTAGCGGCGTTTTTGTCTAAG
* *
35280420 TGCCGCTAATGCTCCGAT
65 CGCCGCTAATGCTCGGAT
* * *
35280438 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
* *
35280503 GCCGCTAAGGCTCGGAG
66 GCCGCTAATGCTCGGAT
* * * *
35280520 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
35280585 GCCGCTAATGCTCGGAT
66 GCCGCTAATGCTCGGAT
* * * *
35280602 CTTTAGTGACGTTTTTTTCTGAGCGCCACTAATTCTCCT-GCCTTTAGCGGCGTTTGTT-TCTAA
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCT-CTGGCCTTTAGCGGCGTTT-TTGTCTAA
35280665 GCGCCGCTAAT
64 GCGCCGCTAAT
35280676 AGTAACAAAA
Statistics
Matches: 206, Mismatches: 29, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
82 200 0.97
83 6 0.03
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
GCCGCTAATGCTCGGAT
Found at i:35281169 original size:15 final size:15
Alignment explanation
Indices: 35281148--35281185 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
35281138 TTTAAGGTTA
35281148 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
35281163 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
35281178 ATTTAGGG
1 ATTTAGGG
35281186 TTTCAATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:35281188 original size:14 final size:14
Alignment explanation
Indices: 35281121--35281188 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
35281111 TACGGGGTAT
*
35281121 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
35281135 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
35281147 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
35281161 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
35281176 AGATTTAGGGTTT
1 AGATTTAGGGTTT
35281189 CAATGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:35285938 original size:21 final size:21
Alignment explanation
Indices: 35285909--35285961 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
35285899 ACATCTTTGA
*
35285909 TATATATATTTATATACAATTT
1 TATATATATTTAT-TAAAATTT
35285931 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
35285951 TATATATATTT
1 TATATATATTT
35285962 GAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.31
21 18 0.62
22 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:35285967 original size:20 final size:19
Alignment explanation
Indices: 35285912--35285970 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
35285902 TCTTTGATAT
35285912 ATATATTTATATACAATTTTA
1 ATATATTTATA-A-AATTTTA
35285933 ATATATTTATTAAAATTTTA
1 ATATATTTA-TAAAATTTTA
35285953 TATATATTTGA-AAAATTT
1 -ATATATTT-ATAAAATTT
35285971 ATCAATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 14 0.40
21 18 0.51
22 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATATTTATAAAATTTTA
Found at i:35286071 original size:16 final size:16
Alignment explanation
Indices: 35286009--35286445 Score: 127
Period size: 16 Copynumber: 25.9 Consensus size: 16
35285999 ACACATAGCC
* *
35286009 TACATGACTTACTTAA
1 TACATAACTTACATAA
* *
35286025 TACACAACTTAAATAA
1 TACATAACTTACATAA
* *
35286041 TTTAAATACCTTACATAA
1 --TACATAACTTACATAA
35286059 TACATAACTTACAT--
1 TACATAACTTACATAA
35286073 T-CATAACTTACATAA
1 TACATAACTTACATAA
35286088 -ACTTATATGTTACCTTACATAA
1 TAC--ATA----A-CTTACATAA
*
35286110 TACATAACTTATATAA
1 TACATAACTTACATAA
** *
35286126 -A-AT-TTTTATATAAA
1 TACATAACTTACAT-AA
35286140 CTTACATAA--TACATAGCA
1 --TACATAACTTACATA--A
35286158 TACATAACTTACATAA
1 TACATAACTTACATAA
*
35286174 TACAAAACTTACATAA
1 TACATAACTTACATAA
* *
35286190 CTTAAATATCTTACA-ACA
1 --TACATAACTTACATA-A
*
35286208 CTTACATAACCTACATAA
1 --TACATAACTTACATAA
35286226 TACATAACTTACATAA
1 TACATAACTTACATAA
35286242 CTTACATAA--TACATAA
1 --TACATAACTTACATAA
*
35286258 TAACTTACAACTTACATAACA
1 T-AC--ATAACTTACAT-A-A
**
35286279 TACATTAA-TTTGATAA
1 TACA-TAACTTACATAA
*
35286295 CTTACATAAGTTACATAA
1 --TACATAACTTACATAA
*
35286313 TACATAACTTACA-ACT
1 TACATAACTTACATA-A
*
35286329 TACATAACATACATTAA
1 TACATAACTTACA-TAA
***
35286346 TTTGGTAACTTACATAA
1 -TACATAACTTACATAA
*
35286363 GTTACACAA--TACATAA
1 --TACATAACTTACATAA
35286379 CTTAC--AACTTACATAACA
1 --TACATAACTTACAT-A-A
* **
35286397 TACATTACTTTGATAA
1 TACATAACTTACATAA
*
35286413 CTTACATAAGTTACATAA
1 --TACATAACTTACATAA
*
35286431 TACACAACTTACATA
1 TACATAACTTACATA
35286446 GCTTACTTAA
Statistics
Matches: 317, Mismatches: 51, Indels: 106
0.67 0.11 0.22
Matches are distributed among these distances:
13 18 0.06
14 8 0.03
15 5 0.02
16 136 0.43
17 22 0.07
18 100 0.32
19 8 0.03
20 3 0.01
21 6 0.02
22 9 0.03
23 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:35286079 original size:13 final size:13
Alignment explanation
Indices: 35286061--35286085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35286051 TTACATAATA
35286061 CATAACTTACATT
1 CATAACTTACATT
35286074 CATAACTTACAT
1 CATAACTTACAT
35286086 AAACTTATAT
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTTACATT
Found at i:35286118 original size:38 final size:38
Alignment explanation
Indices: 35286074--35286245 Score: 113
Period size: 39 Copynumber: 4.5 Consensus size: 38
35286064 AACTTACATT
* * *
35286074 CATAACTTACATAAACTTATATGTTACCTTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
* * *
35286112 CATAACTTATATAAAATTTTTATATAAACTTACATAATA
1 CATAACTTACAT-AAACTTATATATAAACTTACATAATA
* * *
35286151 CATAGCATACAT-AACTTACATAATACAAAACTTACATAACTTA
1 CATAACTTACATAAACTT--AT-ATA-TAAACTTACATAA--TA
* * * * *
35286194 AATATCTTACA-ACAC-T-TACAT-AACCTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
35286228 CATAACTTACAT-AACTTA
1 CATAACTTACATAAACTTA
35286246 CATAATACAT
Statistics
Matches: 101, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
34 13 0.13
35 1 0.01
36 10 0.10
37 4 0.04
38 13 0.13
39 32 0.32
40 3 0.03
41 12 0.12
42 1 0.01
43 12 0.12
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (38 bp):
CATAACTTACATAAACTTATATATAAACTTACATAATA
Found at i:35286170 original size:9 final size:9
Alignment explanation
Indices: 35286138--35286502 Score: 242
Period size: 9 Copynumber: 42.8 Consensus size: 9
35286128 TTTTTATATA
35286138 AACTTACAT
1 AACTTACAT
35286147 AA--TACAT
1 AACTTACAT
* *
35286154 AGCATACAT
1 AACTTACAT
35286163 AACTTACAT
1 AACTTACAT
*
35286172 AA--TACAA
1 AACTTACAT
35286179 AACTTACAT
1 AACTTACAT
*
35286188 AACTTAAAT
1 AACTTACAT
*
35286197 ATCTTACA-
1 AACTTACAT
35286205 ACACTTACAT
1 A-ACTTACAT
*
35286215 AACCTACAT
1 AACTTACAT
35286224 AA--TACAT
1 AACTTACAT
35286231 AACTTACAT
1 AACTTACAT
35286240 AACTTACAT
1 AACTTACAT
*
35286249 AATACATA-AT
1 -A-ACTTACAT
35286259 AACTTAC--
1 AACTTACAT
35286266 AACTTACAT
1 AACTTACAT
*
35286275 AACATACATT
1 AACTTACA-T
**
35286285 AA-TTTGAT
1 AACTTACAT
35286293 AACTTACAT
1 AACTTACAT
*
35286302 AAGTTACAT
1 AACTTACAT
35286311 AA--TACAT
1 AACTTACAT
35286318 AACTTAC--
1 AACTTACAT
35286325 AACTTACAT
1 AACTTACAT
*
35286334 AACATACATT
1 AACTTACA-T
***
35286344 AA-TTTGGT
1 AACTTACAT
35286352 AACTTACAT
1 AACTTACAT
* *
35286361 AAGTTACAC
1 AACTTACAT
35286370 AA--TACAT
1 AACTTACAT
35286377 AACTTAC--
1 AACTTACAT
35286384 AACTTACAT
1 AACTTACAT
*
35286393 AACATACAT
1 AACTTACAT
* **
35286402 TACTTTGAT
1 AACTTACAT
35286411 AACTTACAT
1 AACTTACAT
*
35286420 AAGTTACAT
1 AACTTACAT
*
35286429 AA--TACAC
1 AACTTACAT
35286436 AACTTACAT
1 AACTTACAT
* *
35286445 AGCTTACTT
1 AACTTACAT
35286454 AA--TACAT
1 AACTTACAT
*
35286461 GACTTACAT
1 AACTTACAT
35286470 AACTT--AT
1 AACTTACAT
*
35286477 ACACGTACAT
1 A-ACTTACAT
35286487 AACTTACAT
1 AACTTACAT
*
35286496 AATTTAC
1 AACTTAC
35286503 TTAATACATA
Statistics
Matches: 274, Mismatches: 50, Indels: 64
0.71 0.13 0.16
Matches are distributed among these distances:
7 67 0.24
8 14 0.05
9 176 0.64
10 13 0.05
11 4 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:35286255 original size:25 final size:25
Alignment explanation
Indices: 35286138--35286513 Score: 227
Period size: 25 Copynumber: 14.7 Consensus size: 25
35286128 TTTTTATATA
* *
35286138 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACATAACTTACAT
*
35286163 AACTTACATAATACAAAACTTACAT
1 AACTTACATAATACATAACTTACAT
* *
35286188 AACTTAAATATCTTACA-ACACTTACAT
1 AACTTACATA--ATACATA-ACTTACAT
*
35286215 AACCTACATAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
35286240 AACTTACATAATACATAATAACTTAC--
1 AACTTACATAATAC---ATAACTTACAT
**
35286266 AACTTACATAACATACATTAA-TTTGAT
1 AACTTACAT-A-ATACA-TAACTTACAT
35286293 AACTTACATAAGTTACATAA--TACAT
1 AACTTACATAA--TACATAACTTACAT
* *
35286318 AACTTACA-ACTTACATAACATACATT
1 AACTTACATA-ATACATAACTTACA-T
*** * *
35286344 AA-TTTGGTAACTTACATAAGTTACAC
1 AACTTACATAA--TACATAACTTACAT
35286370 AA--TACATAACTTAC--AACTTACAT
1 AACTTACATAA--TACATAACTTACAT
* * **
35286393 AACATACATTACTTTGATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
* *
35286420 AAGTTACATAATACACAACTTACAT
1 AACTTACATAATACATAACTTACAT
* * *
35286445 AGCTTACTTAATACATGACTTACAT
1 AACTTACATAATACATAACTTACAT
* * *
35286470 AACTTATACACGTACATAACTTACAT
1 AACTTACATA-ATACATAACTTACAT
* *
35286496 AATTTACTTAATACATAA
1 AACTTACATAATACATAA
35286514 ATTATGTAAC
Statistics
Matches: 272, Mismatches: 51, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
23 16 0.06
24 1 0.00
25 135 0.50
26 47 0.17
27 60 0.22
28 13 0.05
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:35286473 original size:118 final size:119
Alignment explanation
Indices: 35286207--35286475 Score: 368
Period size: 118 Copynumber: 2.3 Consensus size: 119
35286197 ATCTTACAAC
* *
35286207 ACTTACATAACCTACAT-AA-TACATAACTTACATAACTTACATAATACATAATAACTTACAACT
1 ACTTACATAACATACATGAATTACATAACTTACATAACTTACACAATAC--AATAACTTACAACT
*
35286270 TACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
64 TACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACAACTTACA
* *** *
35286326 ACTTACATAACATACATTAATTTGGTAACTTACATAAGTTACACAATAC-ATAACTTACAACTTA
1 ACTTACATAACATACATGAATTACATAACTTACATAACTTACACAATACAATAACTTACAACTTA
*
35286390 CATAACATACATTACTTTGATAACTTACATAAGTTACATAATACACAACTTACA
66 CATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACAACTTACA
* *
35286444 TAGCTTAC-TTA-ATACATGACTTACATAACTTA
1 -A-CTTACATAACATACATGAATTACATAACTTA
35286476 TACACGTACA
Statistics
Matches: 132, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
118 83 0.63
119 19 0.14
120 7 0.05
121 23 0.17
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (119 bp):
ACTTACATAACATACATGAATTACATAACTTACATAACTTACACAATACAATAACTTACAACTTA
CATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACAACTTACA
Found at i:35286475 original size:59 final size:59
Alignment explanation
Indices: 35286207--35286443 Score: 361
Period size: 59 Copynumber: 4.0 Consensus size: 59
35286197 ATCTTACAAC
* ** *
35286207 ACTTACATAACCTACA-TAA-TACATAACTTACATAACTTACATAATACATAATAACTTACA
1 ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATAC---ATAACTTACA
35286267 ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
1 ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
* *
35286326 ACTTACATAACATACATTAATTTGGTAACTTACATAAGTTACACAATACATAACTTACA
1 ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
* *
35286385 ACTTACATAACATACATTACTTTGATAACTTACATAAGTTACATAATACACAACTTACA
1 ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
35286444 TAGCTTACTT
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
59 122 0.74
60 15 0.09
61 3 0.02
62 25 0.15
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (59 bp):
ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATAACTTACA
Found at i:35294933 original size:18 final size:19
Alignment explanation
Indices: 35294909--35294958 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
35294899 AGCAACCGAT
35294909 AGAGGAACATGCTCGA-GA
1 AGAGGAACATGCTCGAGGA
* *
35294927 GGAGGAACATGCT-TAGGA
1 AGAGGAACATGCTCGAGGA
35294945 AGAGGAACATGCTC
1 AGAGGAACATGCTC
35294959 TGGTGTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.36, C:0.16, G:0.34, T:0.14
Consensus pattern (19 bp):
AGAGGAACATGCTCGAGGA
Found at i:35295866 original size:29 final size:31
Alignment explanation
Indices: 35295809--35295875 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
35295799 GATATCAGTC
* *
35295809 ATGCAGTGAACAGTATGTAATATCATTAATCG
1 ATGCAGTGAACAGTA-GTAAAATCATTAATCA
35295841 ATGCAGT-AACAGTA-TAAAATCATTAATCA
1 ATGCAGTGAACAGTAGTAAAATCATTAATCA
35295870 ATGCAG
1 ATGCAG
35295876 ATATGCAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 7 0.21
32 7 0.21
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGTAAAATCATTAATCA
Found at i:35296288 original size:27 final size:27
Alignment explanation
Indices: 35296258--35296452 Score: 212
Period size: 27 Copynumber: 7.2 Consensus size: 27
35296248 TCATCTCCTA
**
35296258 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35296285 GGGGTATTTCAATCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
35296312 GGGCTATTTCGGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
35296339 GGGGTATTTCAGTCATTTTACTTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
35296366 GAGGTATTT-TGTTCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
35296393 GGGGTATTTCGGTCATTCTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
35296420 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
35296447 GAGGTA
1 GGGGTA
35296453 GTTTGGTCAT
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 136 0.99
28 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:35296382 original size:81 final size:81
Alignment explanation
Indices: 35296256--35296462 Score: 270
Period size: 81 Copynumber: 2.6 Consensus size: 81
35296246 TTTCATCTCC
** * ** * *
35296256 TAGGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCTTATGGGGCTATTT
1 TAGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
*
35296321 CGGTCATTTTACCCTA
66 CGGTCATTCTACCCTA
** * *
35296337 TAGGGGTATTTCAGTCATTTTACTTTATGGAGGTATTTTGTTCATTTTACCCTATGGGGGTATTT
1 TAGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
35296402 CGGTCATTCTACCCTA
66 CGGTCATTCTACCCTA
** * *
35296418 TAGGGGTATTTTGGTCATTTTACCCTATGGAGGTAGTTTGGTCAT
1 TAGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTTGATCAT
35296463 AATAGTGTAA
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 108 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (81 bp):
TAGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
CGGTCATTCTACCCTA
Found at i:35296462 original size:54 final size:53
Alignment explanation
Indices: 35296269--35296452 Score: 251
Period size: 54 Copynumber: 3.4 Consensus size: 53
35296259 GGGTATAACA
* * *
35296269 GTCATTTTACCCTATGGGGGTATTTCAATCATTTTATCTTATGGGGCTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTATGGGG-TATTTTG
* *
35296323 GTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACTTTATGGAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTATGG-GGTATTTTG
* * * *
35296377 TTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTAT-GGGGTATTTTG
*
35296431 GTCATTTTACCCTATGGAGGTA
1 GTCATTTTACCCTATGGGGGTA
35296453 GTTTGGTCAT
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
54 111 0.97
55 4 0.03
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCTTATGGGGTATTTTG
Found at i:35305124 original size:20 final size:19
Alignment explanation
Indices: 35305061--35305125 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
35305051 AACCCAATAA
* * *
35305061 GTATCGATATTTTTAAGAGG
1 GTATCAATAATTTTAA-AAG
*
35305081 GTATCAATAATTTTATAAAA
1 GTATCAATAATTTTA-AAAG
35305101 GTATCAATAATTTTAAAATG
1 GTATCAATAATTTTAAAA-G
35305121 GTATC
1 GTATC
35305126 GATACCAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 3 0.08
20 34 0.89
21 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (19 bp):
GTATCAATAATTTTAAAAG
Found at i:35305368 original size:19 final size:19
Alignment explanation
Indices: 35305322--35305369 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
35305312 GTATATATTT
35305322 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
35305340 TAAATCTTATTTAGGTATA
1 TAAATTTTATTTAGGTAGA
*
35305359 TAAGTTTTATT
1 TAAATTTTATT
35305370 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:35309985 original size:19 final size:18
Alignment explanation
Indices: 35309956--35309995 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
35309946 GTATATATTT
35309956 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
35309974 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
35309993 TAA
1 TAA
35309996 GTTTTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:35316792 original size:33 final size:33
Alignment explanation
Indices: 35316755--35316819 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
35316745 CAATACAACC
35316755 AATGTCTCAATTTCATATATATTATCAACTTGA
1 AATGTCTCAATTTCATATATATTATCAACTTGA
35316788 AATGTCTCAATTTCATATATATTATCAACTTG
1 AATGTCTCAATTTCATATATATTATCAACTTG
35316820 TATGCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (33 bp):
AATGTCTCAATTTCATATATATTATCAACTTGA
Found at i:35333002 original size:30 final size:31
Alignment explanation
Indices: 35332956--35333019 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
35332946 ATTTCTTATG
35332956 CCAATATTTCGATACCCATATCTTTGAATTT
1 CCAATATTTCGATACCCATATCTTTGAATTT
* *
35332987 CCAATATTT-GATACCCTTATCTTTGACTTT
1 CCAATATTTCGATACCCATATCTTTGAATTT
35333017 CCA
1 CCA
35333020 TAATATGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (31 bp):
CCAATATTTCGATACCCATATCTTTGAATTT
Found at i:35338170 original size:50 final size:50
Alignment explanation
Indices: 35338063--35338191 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 50
35338053 AAAGAGATCC
* * **
35338063 CATGTAAGACCATGTCTGGAACATGGCGTTGGCACCAAGATGAGAGGTCCT
1 CATGTAAGACCATGTCTGG-ACATGGCATGGGCACCAAGATGAGAACTCCT
* * *
35338114 C-CGTAAGACCATGTCTGAGACATGGCATGGGCACCTATATGAGAACT-CT
1 CATGTAAGACCATGTCTG-GACATGGCATGGGCACCAAGATGAGAACTCCT
* *
35338163 CATGTAAGACCATATCTGGGATATGGCAT
1 CATGTAAGACCATGTCT-GGACATGGCAT
35338192 TAGCAGTACA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
49 3 0.05
50 59 0.91
51 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGACATGGCATGGGCACCAAGATGAGAACTCCT
Found at i:35349948 original size:27 final size:27
Alignment explanation
Indices: 35349420--35349937 Score: 610
Period size: 27 Copynumber: 19.3 Consensus size: 27
35349410 AGAGGCCAAT
* *
35349420 AAATGACCAAAATAACCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349447 AAATGACCAAAATACTCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349474 AAATGACCAAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
35349501 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
35349528 GAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349555 AAAT-AGCCAAAATAACCCCATAGGGTA
1 AAATGA-CCGAAATACCCCCATAGGGTA
*
35349582 AAATAACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
35349609 GAACGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
35349636 AAAGGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
35349663 ACATGACCAAAATACTCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
35349690 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
35349717 AAATAACCAAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349744 GAATGACAGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
***
35349770 AAATGACCGAAATACCCCCATAAAATA
1 AAATGACCGAAATACCCCCATAGGGTA
** * *
35349797 AAATGACTAAAATACCCCCATAAGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349824 AAATGACCGAAATACCCCTATAGTGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
35349851 AAATGATCGAAATAACCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
35349878 GAATGA-TGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
35349904 AAATAATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
35349931 AAATGAC
1 AAATGAC
35349938 TGTTATACCC
Statistics
Matches: 419, Mismatches: 68, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
26 46 0.11
27 372 0.89
28 1 0.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:35358818 original size:17 final size:16
Alignment explanation
Indices: 35358775--35358844 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
35358765 TTTTTGGTAC
* * *
35358775 TTTAGGGTTTATGTTT
1 TTTAGAGTTTAAGGTT
*
35358791 TTTAGATTTTAAGGTT
1 TTTAGAGTTTAAGGTT
*
35358807 TTTACGAGTTT-AGGACT
1 TTTA-GAGTTTAAGG-TT
*
35358824 TTTATGGGTTTAAGGTT
1 TTTA-GAGTTTAAGGTT
35358841 TTTA
1 TTTA
35358845 ACTGTTCTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
16 19 0.45
17 20 0.48
18 3 0.07
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTAGAGTTTAAGGTT
Found at i:35363516 original size:23 final size:23
Alignment explanation
Indices: 35363486--35363530 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35363476 TTTCTTAGTG
* *
35363486 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCAGGATATTACAA
35363509 TAGTAATTTTCAGGATATTACA
1 TAGTAATTTTCAGGATATTACA
35363531 GAGCCATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Found at i:35374843 original size:61 final size:59
Alignment explanation
Indices: 35374722--35374846 Score: 135
Period size: 61 Copynumber: 2.1 Consensus size: 59
35374712 TTTTATAAAA
* * * *
35374722 AATATAATATTTATCAAAATAAAATATTAGATTAAATTTAATATTAAATCTATTAAATT
1 AATATAATACTTATCAAAATAAAATATTAAATTAAATTTAATATTAAATCAATCAAATT
* * * * *
35374781 AATATAATACTTATCTACAATATAACTATTAAATTTAATTTAATATTAAGGT-AATCACATT
1 AATATAATACTTATC-AAAATA-AAATATTAAATTAAATTTAATATTAA-ATCAATCAAATT
35374842 AATAT
1 AATAT
35374847 TAAATTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 14 0.26
60 5 0.09
61 34 0.63
62 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (59 bp):
AATATAATACTTATCAAAATAAAATATTAAATTAAATTTAATATTAAATCAATCAAATT
Found at i:35375417 original size:27 final size:25
Alignment explanation
Indices: 35375362--35375429 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
35375352 CTTCCCTAAA
* *
35375362 CCCCCAAAACTTTTTTCCTTTTGCTTT
1 CCCCCAAAAC--TTTTACTTTTCCTTT
35375389 CCCCCAAAACTTTTACTTTCTCCTGTT
1 CCCCCAAAACTTTTACTTT-TCCT-TT
*
35375416 CCCTCAAAACTTTT
1 CCCCCAAAACTTTT
35375430 TTTTCAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 8 0.22
26 3 0.08
27 25 0.69
ACGTcount: A:0.19, C:0.35, G:0.03, T:0.43
Consensus pattern (25 bp):
CCCCCAAAACTTTTACTTTTCCTTT
Found at i:35375800 original size:19 final size:19
Alignment explanation
Indices: 35375776--35375813 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35375766 AAGTTAATAC
*
35375776 AAATTTGATTACGATGGGT
1 AAATTTGATGACGATGGGT
*
35375795 AAATTTGATGACGGTGGGT
1 AAATTTGATGACGATGGGT
35375814 GGCAGAGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (19 bp):
AAATTTGATGACGATGGGT
Found at i:35377085 original size:16 final size:16
Alignment explanation
Indices: 35377064--35377094 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35377054 ACCATGAATG
*
35377064 TCACAAGTGAATTAAT
1 TCACAAATGAATTAAT
35377080 TCACAAATGAATTAA
1 TCACAAATGAATTAA
35377095 GAATTAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (16 bp):
TCACAAATGAATTAAT
Found at i:35378116 original size:24 final size:24
Alignment explanation
Indices: 35378084--35378132 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35378074 CCTAAGAGTT
35378084 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
35378108 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
35378132 T
1 T
35378133 TCAATCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (24 bp):
TGATTTTCTCCCTTTTACATAGTC
Found at i:35378192 original size:25 final size:25
Alignment explanation
Indices: 35378158--35378220 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
35378148 AAGAAAGAAA
*
35378158 TAAAACAGAAAAAAGAAAATCTACTC
1 TAAAA-AGAAAAAAGAAAATCTAATC
*
35378184 TAAAAAGAAAAGAGAAAATCTAATC
1 TAAAAAGAAAAAAGAAAATCTAATC
*
35378209 TACAAATGAAAA
1 TA-AAAAGAAAA
35378221 GGAAAGGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.63, C:0.11, G:0.10, T:0.16
Consensus pattern (25 bp):
TAAAAAGAAAAAAGAAAATCTAATC
Found at i:35380487 original size:8 final size:8
Alignment explanation
Indices: 35380467--35380500 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
35380457 ATATTTCTGG
35380467 TTTAGGG-
1 TTTAGGGT
35380474 TTTAGGGT
1 TTTAGGGT
35380482 TTTAGGGT
1 TTTAGGGT
35380490 TTTAGGGT
1 TTTAGGGT
35380498 TTT
1 TTT
35380501 GAAAATATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (8 bp):
TTTAGGGT
Found at i:35384686 original size:21 final size:23
Alignment explanation
Indices: 35384644--35384689 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
35384634 TAATTAATCA
*
35384644 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
35384667 TAAA-AGAAG-AAATAT-TTTT-
1 TAAACAGAAGCAAATATCTTTTC
35384686 TAAA
1 TAAA
35384690 AAAAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 5 0.23
22 5 0.23
23 4 0.18
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:35387966 original size:14 final size:15
Alignment explanation
Indices: 35387936--35387967 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35387926 TCTCCAAATT
35387936 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
35387951 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
35387965 TTT
1 TTT
35387968 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:35391474 original size:35 final size:35
Alignment explanation
Indices: 35391428--35391498 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
35391418 CACACGGCCG
*
35391428 TGTGACCCCTGCAGTATGAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
*
35391463 TGTGATCCCTGCAGTATAAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
35391498 T
1 T
35391499 CTTAATGCTT
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:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (35 bp):
TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
Found at i:35392694 original size:42 final size:42
Alignment explanation
Indices: 35392644--35392726 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
35392634 ATTCATATGT
35392644 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
*
35392686 TTGGTTTAGTGGAATAGAGACTGTAATAGCATAAGGAAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAA
35392727 TGCTCAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (42 bp):
TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
Found at i:35393771 original size:16 final size:16
Alignment explanation
Indices: 35393750--35393790 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35393740 AATAACCTAT
35393750 ATTTAAAAGA-ATATA
1 ATTTAAAAGACATATA
35393765 CATTTAAAA-ACATATA
1 -ATTTAAAAGACATATA
*
35393781 ATTGAAAAGA
1 ATTTAAAAGA
35393791 TCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (16 bp):
ATTTAAAAGACATATA
Found at i:35394449 original size:66 final size:66
Alignment explanation
Indices: 35394271--35394449 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 66
35394261 CTAGTGAGCT
* * **
35394271 TACTGACTTGGGTCACACGGCCAAGCCACACGTCCATGTGCTAGGCTGTGTGAAAAATGATGGGC
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGATGGGC
35394336 A
66 A
* ** * *
35394337 TACTGACTTGTGACACACGGCCAAGCCACACACCCGTGAGCTAGGCCATGTGAAAATTGGA-GGG
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAAT-GATGGG
*
35394401 TA
65 CA
* ** * * *
35394403 TACTGACTTATGTCACACGGTTAAGTCACACGTCTGTGTGCCAGGCC
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCC
35394450 GTCTGAGACT
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
66 90 0.98
67 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (66 bp):
TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGATGGGC
A
Found at i:35395772 original size:36 final size:35
Alignment explanation
Indices: 35395722--35395793 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
35395712 ACATTTAATA
35395722 CATATCTCGGAAGATCA-TCTTCCATATTTGCCAAG
1 CATATCTCGGAAGATCACT-TTCCATATTTGCCAAG
* *
35395757 CATATCTTTGGAAGATCACTTTCCTTATTTGCCAAG
1 CATATC-TCGGAAGATCACTTTCCATATTTGCCAAG
35395793 C
1 C
35395794 TCCAGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 6 0.18
36 26 0.79
37 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (35 bp):
CATATCTCGGAAGATCACTTTCCATATTTGCCAAG
Found at i:35398308 original size:3 final size:3
Alignment explanation
Indices: 35398300--35398349 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
35398290 ATGACTCACC
35398300 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35398346 TAT T
1 TAT T
35398350 CTTTAACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:35398330 original size:23 final size:23
Alignment explanation
Indices: 35398300--35398349 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
35398290 ATGACTCACC
35398300 TATTATTATTATTATTATTATTT
1 TATTATTATTATTATTATTATTT
35398323 TATTATTATTATTATTATTATTT
1 TATTATTATTATTATTATTATTT
35398346 TATT
1 TATT
35398350 CTTTAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTATTATTATTATTATTT
Found at i:35398349 original size:20 final size:20
Alignment explanation
Indices: 35398302--35398341 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
35398292 GACTCACCTA
35398302 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
35398322 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
35398342 ATTTTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTATTATTATTATTATT
Done.