Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold383
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: 1247277
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.21
Warning! 434286 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1100172 original size:13 final size:13
Alignment explanation
Indices: 1100154--1100237 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1100144 AGCTTCCTAG
1100154 CGATACATTGTAT
1 CGATACATTGTAT
1100167 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1100186 CGATACATTGTAT
1 CGATACATTGTAT
1100199 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1100218 CGATACATTGTAT
1 CGATACATTGTAT
1100231 CGATACA
1 CGATACA
1100238 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1100186 original size:19 final size:18
Alignment explanation
Indices: 1100162--1100258 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1100152 AGCGATACAT
1100162 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1100181 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1100194 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1100213 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1100226 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1100245 TGTATCGATACAAA
1 TGTATCGATACAAA
1100259 TCGCTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1100195 original size:32 final size:32
Alignment explanation
Indices: 1100154--1100256 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1100144 AGCTTCCTAG
*
1100154 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1100186 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1100218 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1100250 CGATACA
1 CGATACA
1100257 AATCGCTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1101145 original size:55 final size:56
Alignment explanation
Indices: 1101060--1101955 Score: 959
Period size: 61 Copynumber: 15.3 Consensus size: 56
1101050 AATAAAGTGT
* * * *
1101060 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCCACTCGTGTGGGCTTTG-AAAGGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
* * *
1101115 GTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTG-GTGGGCTTTG-AAAGGT
1 ATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
* * * * * *
1101169 GTCCTGCTCTTTGGGGACTGAAAAGTGCCACAAACTCGTGTAGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101230 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGT
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
*
1101285 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101346 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG----AAAAGGC
1101406 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101467 ATCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101528 ATCTTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101589 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGT
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
* * *
1101644 GTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAGGT
1 ATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
* * * *
1101699 GTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGCCTTTG-AAAGGG
1 ATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
* *
1101754 GTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
* *
1101815 ATCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTTGGCTTTGAAAAGAAAAAGC
1 ATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GC
*
1101876 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAGAGGAACAGGC
1 ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--GA--AA-AGGC
1101937 ATCCTGCTCTTTGAGGACT
1 ATCCTGCTCTTTGAGGACT
1101956 AAAAAGCGGA
Statistics
Matches: 747, Mismatches: 54, Indels: 74
0.85 0.06 0.08
Matches are distributed among these distances:
53 4 0.01
54 48 0.06
55 227 0.30
56 23 0.03
60 62 0.08
61 369 0.49
62 4 0.01
63 2 0.00
65 6 0.01
66 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (56 bp):
ATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGC
Found at i:1101276 original size:61 final size:61
Alignment explanation
Indices: 1101170--1101955 Score: 1063
Period size: 61 Copynumber: 13.3 Consensus size: 61
1101160 TTGAAAGGTG
* * * * *
1101170 TCCTGCTCTTTGGGGACTGAAAAGTGCCACAAACTCGTGTAGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* **
1101231 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1101286 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
*
1101347 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAA-AAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1101407 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1101468 TCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1101529 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* **
1101590 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* **
1101645 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* * **
1101700 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGCCTTTG-AAAG-----GGG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
*
1101755 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* *
1101816 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTTGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
* * * *
1101877 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT-AAGAGGAACAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AAGAAAAAGCA
1101938 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1101956 AAAAAGCGGA
Statistics
Matches: 664, Mismatches: 41, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
54 4 0.01
55 188 0.28
56 8 0.01
57 3 0.00
58 9 0.01
60 65 0.10
61 383 0.58
62 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
Found at i:1101304 original size:116 final size:117
Alignment explanation
Indices: 1101061--1101955 Score: 1098
Period size: 116 Copynumber: 7.7 Consensus size: 117
1101051 ATAAAGTGTA
* * * * *
1101061 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCCACTCGTGTGGGCTTTG-AAAG-----GCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * *
1101120 GCTCTTTGAGGACTGGAAA-ATGCCACCAACTTG-GTGGGCTTTGAA-AGGTG
66 GCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* * * * *
1101170 TCCTGCTCTTTGGGGACTGAAAAGTGCCACAAACTCGTGTAGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
1101235 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
1101286 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * * *
1101351 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAAAAAAGCA
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----AAAGAGGCG
1101407 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * * *
1101472 GCTCTTTAAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* *
1101529 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
1101594 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
66 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
* **
1101645 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* *
1101703 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGCCTTTGAAAG-GG-G
65 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAGGCG
*
1101755 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * * *
1101820 GCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTTGGCTTTGAAAAGAAAAAGCA
66 GCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCG
* * * *
1101877 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT-AAGAGGAACAGGCATCC
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AAGAAAAAGCATCC
1101941 TGCTCTTTGAGGACT
65 TGCTCTTTGAGGACT
1101956 AAAAAGCGGA
Statistics
Matches: 702, Mismatches: 49, Indels: 57
0.87 0.06 0.07
Matches are distributed among these distances:
109 47 0.07
110 87 0.12
111 10 0.01
112 3 0.00
114 4 0.01
115 39 0.06
116 203 0.29
117 8 0.01
119 7 0.01
121 114 0.16
122 180 0.26
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (117 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCG
Found at i:1101336 original size:29 final size:29
Alignment explanation
Indices: 1101248--1101336 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
1101238 CTTTGAGGAC
1101248 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
1101277 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
1101303 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1101332 TGAAA
1 TGAAA
1101337 AGAAAAAGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 3 0.07
26 9 0.21
27 7 0.16
28 7 0.16
29 14 0.33
30 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:1101722 original size:27 final size:27
Alignment explanation
Indices: 1101640--1101722 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1101630 GGGCTTTAAG
1101640 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
1101667 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
1101695 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
1101722 A
1 A
1101723 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:1103047 original size:51 final size:51
Alignment explanation
Indices: 1102981--1103078 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
1102971 TGAAAATAAT
1102981 GGGGTTAAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCA
1 GGGGTTAAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCA
* ** * *
1103032 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAA
1 GGGGTTAAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAA
1103079 AACCGAGGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (51 bp):
GGGGTTAAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCA
Found at i:1103089 original size:51 final size:51
Alignment explanation
Indices: 1102983--1103097 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
1102973 AAAATAATGG
* ** *
1102983 GGTTAAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCAGG
1 GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAACAGA
** * * *
1103034 GGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAACCGA
1 GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAACAGA
1103085 GGTTGGAA-TATCC
1 GGTT-GAAGTATCC
1103098 TCTCGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 51 0.94
52 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (51 bp):
GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAACAGA
Found at i:1103197 original size:79 final size:79
Alignment explanation
Indices: 1103111--1103363 Score: 330
Period size: 79 Copynumber: 3.2 Consensus size: 79
1103101 CGAAAATAAT
* * * *
1103111 GGGGTTGGAGTAT-CCTTGATGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGT
1 GGGGTTGGAGTATCCCCTCA-GAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGT
* *
1103175 TTTGGAAATAAAATC
65 TTTAGAAATAAAACC
* *
1103190 GGAGTTGGAATATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATT-GATGT
1 GGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAG-TGT
1103254 TTTAGAAATAAAACC
65 TTTAGAAATAAAACC
* * * * * * *
1103269 GGGGTTGGAGTATCCCCTCAAAAATGACGGGGTTGTATTATCCCCGATTATGAGAAATTAATATT
1 GGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTT
*
1103334 TTAGAAATAAAGCC
66 TTAGAAATAAAACC
1103348 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1103364 TGATGAAAAA
Statistics
Matches: 153, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
78 1 0.01
79 148 0.97
80 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTT
TTAGAAATAAAACC
Found at i:1103222 original size:107 final size:107
Alignment explanation
Indices: 1103034--1103232 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 107
1103024 ATAAGGCAGG
* * *
1103034 GGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAACCGAGGTTGGAATATCCT
1 GGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACCGAGGTTGGAATATCCC
*
1103099 CTCGAAAATAATGGGGTTGGAGTATCCTTGATGAAATAACGA
66 CTCGAAAATAACGGGGTTGGAGTATCCTTGATGAAATAACGA
* * * * *
1103141 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCG-GAGTTGGAATATCC
1 GGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACCGAG-GTTGGAATATCC
1103205 CCTC-AGAAATAACGGGGTTGGAGTATCC
65 CCTCGA-AAATAACGGGGTTGGAGTATCC
1103233 CCGATTATGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
106 2 0.02
107 79 0.98
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (107 bp):
GGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACCGAGGTTGGAATATCCC
CTCGAAAATAACGGGGTTGGAGTATCCTTGATGAAATAACGA
Found at i:1105772 original size:20 final size:20
Alignment explanation
Indices: 1105747--1105797 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1105737 AAAATGCCTG
1105747 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
1105767 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTGTAA
*
1105787 ATTGTATCGAT
1 AATGTATCGAT
1105798 GCAATGAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:1105854 original size:20 final size:20
Alignment explanation
Indices: 1105817--1105873 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1105807 AACGTATCGA
**
1105817 TACAATGTATCGGCACAATG
1 TACAATGTATCGATACAATG
1105837 -AGCAATGTATCGATACAATG
1 TA-CAATGTATCGATACAATG
* *
1105857 CAAAATGTATCGATACA
1 TACAATGTATCGATACA
1105874 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (20 bp):
TACAATGTATCGATACAATG
Found at i:1105936 original size:13 final size:13
Alignment explanation
Indices: 1105889--1105918 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1105879 GTAAACCTAG
1105889 AATGTATCGATAC
1 AATGTATCGATAC
*
1105902 AATTTATCGATAC
1 AATGTATCGATAC
1105915 AATG
1 AATG
1105919 AACAATGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1106577 original size:40 final size:41
Alignment explanation
Indices: 1106533--1106632 Score: 123
Period size: 40 Copynumber: 2.4 Consensus size: 41
1106523 GTCCCACTTT
* * *
1106533 TTGAGGACAAAGGAAAAGAGAATGAA-ATAG-GTCCTGCTCC
1 TTGAGGACAAAGGAAAAAAGAA-AAAGAAAGTGTCCTGCTCC
*
1106573 TTGAGGACAAAGGAAAAAAGAAAAAGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAAAAAAGAAAAAGAAAGTGTCCTGCTCC
*
1106614 TTGAGGGCAAAGTGAAAAA
1 TTGAGGACAAAG-GAAAAA
1106633 GAGTACGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.04
40 24 0.46
41 20 0.38
42 6 0.12
ACGTcount: A:0.44, C:0.12, G:0.27, T:0.17
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAAAGAAAAAGAAAGTGTCCTGCTCC
Found at i:1106822 original size:42 final size:42
Alignment explanation
Indices: 1106667--1106832 Score: 152
Period size: 42 Copynumber: 3.9 Consensus size: 42
1106657 AAAGGAAAAA
* * * * *
1106667 AGGAAAACAAAATGCGTCTTGCTTTTTGAGGACAAAAGAAAG
1 AGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAG
** * *
1106709 AGGAAAATAAAGTATGTCCTGCTCTTTAAGGACAAAAGAGAA
1 AGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAG
** * * * *
1106751 AATAAGGGAATGAAGTGTGTCCTGCTCTTTGAGGACAAAGGGGAG
1 AGGAA---AATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAG
* *
1106796 AGGAAAATAAAGTGCGTCCTACTCTTTGAGGGCAAAA
1 AGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAA
1106833 AAGTGCCACC
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
42 63 0.65
45 34 0.35
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.22
Consensus pattern (42 bp):
AGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAG
Found at i:1106900 original size:61 final size:61
Alignment explanation
Indices: 1106812--1107048 Score: 246
Period size: 61 Copynumber: 3.9 Consensus size: 61
1106802 ATAAAGTGCG
* * *
1106812 TCCTACTCTTTGAGGGCAAAAAAGTGCCACCAACTCGTGTGGGCTATGAAAAAGAAAGGCA
1 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAGGCA
** * * * * *
1106873 TCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGAGCTTTGCAAAGAGAAA-GTA
1 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAAAGAAAGGCA
* * * * * *
1106934 TCCTGCTCTTTGAGGACTAGAAAA-TGCTACCAACTTGGGTGGGCTTTG-AAAGGAAAAGGCG
1 TCCTACTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAAG-AAAGGCA
* *
1106995 TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA
1 TCCTACTCTTTGAGGAC-TA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
1107049 GCATCCTGCA
Statistics
Matches: 144, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
59 3 0.02
60 3 0.02
61 98 0.68
62 17 0.12
63 20 0.14
64 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (61 bp):
TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAGGCA
Found at i:1107208 original size:93 final size:94
Alignment explanation
Indices: 1106993--1107236 Score: 350
Period size: 93 Copynumber: 2.6 Consensus size: 94
1106983 AAGGAAAAGG
* **
1106993 CGTCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA-GCATCCTG
1 CGTCCTGCTCTTTGAGGAC-TAG-GAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGCATCCTG
* *
1107057 CATTTTGAGGACTAAAGGGTGAAAGGAGAGAA
63 CATTTTGAGGACTAAAGGGTAAAAGAAGAGAA
* *
1107089 CGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGC-T
1 CGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCAT
*
1107153 CTTTGAGGACTAAAGGG-AAAAGAAGAGAG
66 -TTTGAGGACTAAAGGGTAAAAGAAGAGAA
*
1107182 TGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 CGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1107237 AGAAAGCATC
Statistics
Matches: 136, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
93 67 0.49
94 48 0.35
95 2 0.01
96 19 0.14
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (94 bp):
CGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCAT
TTTGAGGACTAAAGGGTAAAAGAAGAGAA
Found at i:1107265 original size:61 final size:58
Alignment explanation
Indices: 1107187--1107350 Score: 203
Period size: 55 Copynumber: 2.8 Consensus size: 58
1107177 GAGAGTGTCC
1107187 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCA
1 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTT-AAA-GA-AAAGCATCA
* * *
1107248 TGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTT---GAAAGGCATCC
1 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGCATCA
* *
1107303 TACACTTTGAGGACT--GAAGGGTGCCACCAACTTGTGTGGGCTTTAAAG
1 TGCTCTTTGAGGACTAGGAA--GTGCCACCAACTTGTGTGGGCTTTAAAG
1107351 GCGTCCTGCT
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
53 3 0.03
55 43 0.47
56 2 0.02
58 1 0.01
61 43 0.47
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (58 bp):
TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAGCATCA
Found at i:1107328 original size:55 final size:54
Alignment explanation
Indices: 1107269--1107377 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
1107259 GACTAGGAAA
*
1107269 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTACACTTTGAGGACTGAAGGG
1 TGCCACCAACTTGTGTGGGCTTT-AAAGGCATCCTACACTTTGAGGACTAAAGGG
* * *
1107324 TGCCACCAACTTGTGTGGGCTTTAAAGGCGTCCTGCTCTTTGAGGACTAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTAAAGGCATCCTACACTTTGAGGACTAAAGGG
1107378 CGAAATGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 27 0.54
55 23 0.46
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (54 bp):
TGCCACCAACTTGTGTGGGCTTTAAAGGCATCCTACACTTTGAGGACTAAAGGG
Found at i:1107330 original size:209 final size:210
Alignment explanation
Indices: 1107098--1107581 Score: 701
Period size: 209 Copynumber: 2.3 Consensus size: 210
1107088 ACGTCCTGCT
*
1107098 CTTTGAGGACTG--GGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGCTCTTTGAGG
1 CTTTGAGGACTGAAGG--GTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGG
**
1107161 ACTAAA-GG-GAAAAGAAGAGAGTGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGT
64 ACTAAAGGGCGAAAAG-AGAGAACGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGT
1107224 GGGCTTTAAAAGGAGAAAGCATCATGCTCTTTGAGGACTAGG-AAATGCCACCAACTTGTGTGGG
128 GGGCTTTAAAAGGAGAAAGCATCATGCTCTTTGAGGA-TAGGAAAATGCCACCAACTTGTGTGGG
1107288 CTTTGAAAGGCATCCTACA
192 CTTTGAAAGGCATCCTACA
*
1107307 CTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAGGCGTCCTGCTCTTTGAGGAC
1 CTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
* *
1107371 TAAAGGGCGAAATGAGAGAACGTCCTGCTCTTTGAGGACTAGGAATTGCCACCAACTTGTGTGGG
66 TAAAGGGCGAAAAGAGAGAACGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGG
* * *
1107436 CTTTAAAAGGAGAAAGCATCCTGCTCTTTGAGGATTGGAAAATGCTACCAACTTGTGTGGGCTTT
131 CTTTAAAAGGAGAAAGCATCATGCTCTTTGAGGATAGGAAAATGCCACCAACTTGTGTGGGCTTT
* * *
1107501 GAAAGGCGTCCTGCT
196 GAAAGGCATCCTACA
* *** * * ** *
1107516 CTTTGAGAACTGAAAAATGCCACCAACTTGTCTAGGCTTTATGAGGCATCCTGCTTTTTGAGGAC
1 CTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
1107581 T
66 T
1107582 GGAAAATGCC
Statistics
Matches: 247, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
208 29 0.12
209 190 0.77
210 26 0.11
211 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (210 bp):
CTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGAC
TAAAGGGCGAAAAGAGAGAACGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGG
CTTTAAAAGGAGAAAGCATCATGCTCTTTGAGGATAGGAAAATGCCACCAACTTGTGTGGGCTTT
GAAAGGCATCCTACA
Found at i:1107377 original size:54 final size:54
Alignment explanation
Indices: 1107238--1107373 Score: 179
Period size: 55 Copynumber: 2.5 Consensus size: 54
1107228 TTTAAAAGGA
* *
1107238 GAAA-GCATCATGCTCTTTGAGGACT-AGGAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAGGCATCCTGCTCTTTGAGGACTAAGG--GTGCCACCAACTTGTGTGGGCTTT
* *
1107292 GAAAGGCATCCTACACTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAGGCATCCTGCTCTTTGAGGACT-AAGGGTGCCACCAACTTGTGTGGGCTTT
*
1107347 -AAAGGCGTCCTGCTCTTTGAGGACTAA
1 GAAAGGCATCCTGCTCTTTGAGGACTAA
1107374 AGGGCGAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.03
54 26 0.36
55 41 0.57
57 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (54 bp):
GAAAGGCATCCTGCTCTTTGAGGACTAAGGGTGCCACCAACTTGTGTGGGCTTT
Found at i:1107445 original size:148 final size:152
Alignment explanation
Indices: 1106934--1107522 Score: 415
Period size: 154 Copynumber: 3.8 Consensus size: 152
1106924 AGAGAAAGTA
* * * * * *
1106934 TCCTGCTCTTTGAGGACTAGAAAATGCTACCAACTTGGGTGGGCTTTGAAAGGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-AGA-GCATCCT
* * * ** * *
1106999 GCTCTTTGAGGACTTAGAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGCATCCTGCAT-TTT
63 ACACTTTGAGGAC-TGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC-TCTTT
* *
1107063 GAGGACTAAAGGGTGAAAGGAGAGAACG
125 GAGGACTAAAGGGCGAAATGAGAGAACG
* * * * *
1107091 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT-AAA-AG-GCATCTTGCT
1 TCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGAGAGCATCCTACA
** * * ** * **
1107153 CTTTGAGGACTAAAGGGAAAA-G--AAGAGA-GTGTCCTGCTCTTTGAGGACTAGGAAGTGCCAC
66 CTTTGAGGACT----GGAAAATGCCACCA-ACTTGT-GTGGGCTTTGA--A--AGG-CGT-CCTG
* * * ** * *
1107214 CAACTTGTGTGGGCTTTA-----AAAGGAGA-AAGCA
119 C-TCTT-TGAGGACTAAAGGGCGAAATGAGAGAA-CG
* *
1107245 TCATGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTT-GAA-AG-GCATCCTACA
1 TCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGAGAGCATCCTACA
**
1107307 CTTTGAGGACT-GAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAGGCGTCCTGCTCTTTGAGGA
66 CTTTGAGGACTGGAA-AATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
1107370 CTAAAGGGCGAAATGAGAGAACG
130 CTAAAGGGCGAAATGAGAGAACG
*
1107393 TCCTGCTCTTTGAGGACTAGGAATTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCATCCT
1 TCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAA-GAG--AGCATCCT
* * * *
1107458 GCTCTTTGAGGATTGGAAAATGCTACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAG
63 ACACTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAG
1107523 AACTGAAAAA
Statistics
Matches: 335, Mismatches: 63, Indels: 70
0.72 0.13 0.15
Matches are distributed among these distances:
143 7 0.02
144 3 0.01
145 3 0.01
146 2 0.01
147 3 0.01
148 53 0.16
149 8 0.02
150 4 0.01
151 31 0.09
152 8 0.02
153 9 0.03
154 120 0.36
155 28 0.08
156 1 0.00
157 46 0.14
158 2 0.01
159 7 0.02
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (152 bp):
TCCTGCTCTTTGAGGACTAGGAAATGCCACCAACTTGTGTGGGCTTTAAAAGAGAGCATCCTACA
CTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGAC
TAAAGGGCGAAATGAGAGAACG
Found at i:1107488 original size:61 final size:57
Alignment explanation
Indices: 1107393--1107648 Score: 261
Period size: 55 Copynumber: 4.4 Consensus size: 57
1107383 TGAGAGAACG
*
1107393 TCCTGCTCTTTGAGGACTAGG-AATTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT---AGGA-AAAGCA
* * * *
1107454 TCCTGCTCTTTGAGGATTGGAAAATGCTACCAACTTGTGTGGGCTTT--GAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGGAAAAGCA
* * * * * *
1107509 TCCTGCTCTTTGAGAACTGAAAAATGCCACCAACTTGTCTAGGCTTTATG--AGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGGAAAAGCA
* *
1107564 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---AGGAAAA-GCA
* *
1107625 TCCTGCTTTTTGAGGACTAGAAAA
1 TCCTGCTCTTTGAGGACTGGAAAA
1107649 GTGAAAGGAG
Statistics
Matches: 165, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
55 91 0.55
56 2 0.01
57 1 0.01
58 2 0.01
60 3 0.02
61 66 0.40
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (57 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAGGAAAAGCA
Found at i:1108634 original size:1 final size:1
Alignment explanation
Indices: 1108628--1108719 Score: 58
Period size: 1 Copynumber: 92.0 Consensus size: 1
1108618 TTCTTTTCTC
* * * * * * * * * *
1108628 TTTTTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTATTATTTTTGTTTTTTTGTTGTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
1108693 TTTTTGTTGTTTTCTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1108720 AAAAAAGAAT
Statistics
Matches: 63, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:1108659 original size:8 final size:8
Alignment explanation
Indices: 1108629--1108716 Score: 72
Period size: 8 Copynumber: 10.9 Consensus size: 8
1108619 TCTTTTCTCT
*
1108629 TTTTTTTC
1 TTTTTTTG
1108637 TTTGTTTTG
1 TTT-TTTTG
*
1108646 TTTTTTTT
1 TTTTTTTG
*
1108654 TGTTTTTTA
1 T-TTTTTTG
1108663 TTATTTTTG
1 TT-TTTTTG
1108672 TTTTTTTG
1 TTTTTTTG
*
1108680 TTGTTTT-
1 TTTTTTTG
*
1108687 TTTGTTT-
1 TTTTTTTG
*
1108694 TTTTGTTG
1 TTTTTTTG
*
1108702 TTTTCTTG
1 TTTTTTTG
1108710 TTTTTTT
1 TTTTTTT
1108717 TTTAAAAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
7 10 0.15
8 34 0.52
9 21 0.32
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1108659 original size:27 final size:25
Alignment explanation
Indices: 1108629--1108719 Score: 110
Period size: 27 Copynumber: 3.4 Consensus size: 25
1108619 TCTTTTCTCT
1108629 TTTTTTTCTTTGTTTTGTTTTTTTTTG
1 TTTTTTT-TTT-TTTTGTTTTTTTTTG
*
1108656 TTTTTTATTATTTTTGTTTTTTTGTTG
1 TTTTTT-TTTTTTTTGTTTTTTT-TTG
*
1108683 TTTTTTTGTTTTTTTGTTGTTTTCTTG
1 TTTTTTT-TTTTTTTGTT-TTTTTTTG
1108710 TTTTTTTTTT
1 TTTTTTTTTT
1108720 AAAAAAGAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 16 0.28
27 36 0.63
28 5 0.09
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (25 bp):
TTTTTTTTTTTTTTGTTTTTTTTTG
Found at i:1108701 original size:19 final size:18
Alignment explanation
Indices: 1108628--1108716 Score: 101
Period size: 19 Copynumber: 4.9 Consensus size: 18
1108618 TTCTTTTCTC
*
1108628 TTTTTTTTCTTTGTTTTGT
1 TTTTTTTTGTTT-TTTTGT
*
1108647 TTTTTTTTG-TTTTTT-A
1 TTTTTTTTGTTTTTTTGT
*
1108663 TTATTTTTGTTTTTTTGT
1 TTTTTTTTGTTTTTTTGT
1108681 TGTTTTTTTGTTTTTTTGT
1 T-TTTTTTTGTTTTTTTGT
*
1108700 TGTTTTCTTGTTTTTTT
1 T-TTTTTTTGTTTTTTT
1108717 TTTAAAAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.13
17 10 0.16
18 3 0.05
19 40 0.66
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.84
Consensus pattern (18 bp):
TTTTTTTTGTTTTTTTGT
Found at i:1110309 original size:13 final size:13
Alignment explanation
Indices: 1110291--1110316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1110281 CAATTTTTTG
1110291 TGTATCGATACAT
1 TGTATCGATACAT
1110304 TGTATCGATACAT
1 TGTATCGATACAT
1110317 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1110381 original size:21 final size:21
Alignment explanation
Indices: 1110355--1110430 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1110345 CTGCCAAGAA
*
1110355 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1110376 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1110396 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1110417 ATGTATCGATACAT
1 ATGTATCGATACAT
1110431 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1110401 original size:20 final size:20
Alignment explanation
Indices: 1110376--1110448 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1110366 CATCTTTTTT
1110376 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1110396 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1110417 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1110437 ATGTATCGATAC
1 ATGTATCGATAC
1110449 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1110412 original size:41 final size:41
Alignment explanation
Indices: 1110355--1110448 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1110345 CTGCCAAGAA
*
1110355 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1110396 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1110437 ATGTATCGATAC
1 ATGTATCGATAC
1110449 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1111174 original size:126 final size:126
Alignment explanation
Indices: 1110949--1111200 Score: 504
Period size: 126 Copynumber: 2.0 Consensus size: 126
1110939 GATTTCAAAA
1110949 GTCAAAATTTTACATTTTTCCTTTATTTTTCCCTTAAAAGAACAAATTTTACGAATTTGTATATT
1 GTCAAAATTTTACATTTTTCCTTTATTTTTCCCTTAAAAGAACAAATTTTACGAATTTGTATATT
1111014 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAAT
66 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAAT
1111075 GTCAAAATTTTACATTTTTCCTTTATTTTTCCCTTAAAAGAACAAATTTTACGAATTTGTATATT
1 GTCAAAATTTTACATTTTTCCTTTATTTTTCCCTTAAAAGAACAAATTTTACGAATTTGTATATT
1111140 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAAT
66 CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAAT
1111201 CTCCCTAATT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.43
Consensus pattern (126 bp):
GTCAAAATTTTACATTTTTCCTTTATTTTTCCCTTAAAAGAACAAATTTTACGAATTTGTATATT
CTCCCCCTTAATAAGGTAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAAT
Found at i:1111217 original size:50 final size:50
Alignment explanation
Indices: 1111156--1111255 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1111146 CTTAATAAGG
1111156 TAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAATCTCCC
1 TAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAATCTCCC
1111206 TAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAATCTCCC
1 TAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAATCTCCC
1111256 CCTTAATCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (50 bp):
TAATTCACGCATTCTCTCATTTATCTCCCCCGTTTATTAATAAATCTCCC
Found at i:1113082 original size:13 final size:13
Alignment explanation
Indices: 1113064--1113102 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1113054 ATAATCACCC
*
1113064 TGTATCGATACAG
1 TGTATCGATACAA
1113077 TGTATCGATACAA
1 TGTATCGATACAA
1113090 TGTATCGATACAA
1 TGTATCGATACAA
1113103 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1113113 original size:20 final size:20
Alignment explanation
Indices: 1113088--1113166 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1113078 GTATCGATAC
1113088 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
1113108 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
1113133 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
1113152 ACATGTATCGATACA
1 A-ATGTATCGATACA
1113167 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:1115210 original size:15 final size:15
Alignment explanation
Indices: 1115174--1115211 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1115164 TACATCAATT
* *
1115174 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
1115189 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
1115204 TCATTTTG
1 TCATTTTG
1115212 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:1117268 original size:21 final size:22
Alignment explanation
Indices: 1117226--1117268 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1117216 TTTTCAATTT
* *
1117226 ATTGTCTTCTTTTAGTTTAATG
1 ATTGTCTTCTTATAGCTTAATG
1117248 ATTGTCTTCTTAT-GCTTAATG
1 ATTGTCTTCTTATAGCTTAATG
1117269 TTCATGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (22 bp):
ATTGTCTTCTTATAGCTTAATG
Found at i:1119294 original size:13 final size:13
Alignment explanation
Indices: 1119276--1119301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1119266 CAATTTTTTG
1119276 TGTATCGATACAT
1 TGTATCGATACAT
1119289 TGTATCGATACAT
1 TGTATCGATACAT
1119302 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1119366 original size:21 final size:21
Alignment explanation
Indices: 1119340--1119415 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1119330 CTGCCAAGAA
*
1119340 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1119361 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
*
1119381 ATCTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1119402 ATGTATCGATACAT
1 ATGTATCGATACAT
1119416 TGCAACATGT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1119389 original size:20 final size:20
Alignment explanation
Indices: 1119361--1119433 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1119351 CATCTTTTTT
1119361 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
* ****
1119381 ATCTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1119402 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1119422 ATGTATCGATAC
1 ATGTATCGATAC
1119434 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1119400 original size:41 final size:41
Alignment explanation
Indices: 1119343--1119433 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1119333 CCAAGAAATG
*
1119343 TATCGATACATCTTTTTTATGTATCGATACATTGCAACATC
1 TATCGATACATCTTTTTCATGTATCGATACATTGCAACATC
*
1119384 TATCGATACATCTTTTTCATGTATCGATACATTGCAACATG
1 TATCGATACATCTTTTTCATGTATCGATACATTGCAACATC
1119425 TATCGATAC
1 TATCGATAC
1119434 TTTGAATTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (41 bp):
TATCGATACATCTTTTTCATGTATCGATACATTGCAACATC
Found at i:1127680 original size:13 final size:13
Alignment explanation
Indices: 1127662--1127686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1127652 CAAAGATCAG
1127662 TGTATCGATACAA
1 TGTATCGATACAA
1127675 TGTATCGATACA
1 TGTATCGATACA
1127687 GTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1127765 original size:13 final size:13
Alignment explanation
Indices: 1127747--1127773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1127737 TACAAAACTT
1127747 ATGTATCGATACA
1 ATGTATCGATACA
1127760 ATGTATCGATACA
1 ATGTATCGATACA
1127773 A
1 A
1127774 CACTTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1127770 original size:32 final size:33
Alignment explanation
Indices: 1127729--1127793 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1127719 TAGCTTAAAT
1127729 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
1127761 TGTATCGATACAACACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
1127794 ATCGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:1134610 original size:28 final size:28
Alignment explanation
Indices: 1134575--1134645 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
1134565 ATAAAGCCGG
1134575 GGTTGGAGTATCCCTTCG-GAAATAACGA
1 GGTTGGAGTATCCC-TCGAGAAATAACGA
*
1134603 GGTTGGAGCATCCC-CGATGAAATAACGA
1 GGTTGGAGTATCCCTCGA-GAAATAACGA
1134631 GGTTGGAGTATCCCT
1 GGTTGGAGTATCCCT
1134646 GATTGTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 2 0.05
28 36 0.95
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCTCGAGAAATAACGA
Found at i:1134745 original size:51 final size:50
Alignment explanation
Indices: 1134631--1134747 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 50
1134621 GAAATAACGA
* *
1134631 GGTTGGAGTATCCCTGATTGTGAAAAATTAATGTTTTAGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAACCG
* * * * **
1134681 GAGTTGAAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCAG
1 G-GTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAACC-G
1134733 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1134748 TCAGAAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 1 0.02
51 52 0.95
52 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAACCG
Found at i:1134774 original size:79 final size:79
Alignment explanation
Indices: 1134690--1134978 Score: 377
Period size: 79 Copynumber: 3.7 Consensus size: 79
1134680 GGAGTTGAAA
* * * * *
1134690 TATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCCTCAGAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAA
1134755 TAATGAGGTTGGAG
66 TAATGAGGTTGGAG
*
1134769 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAA
* **
1134834 TGACAAGGTTGGAG
66 TAATGAGGTTGGAG
* * * * * * * * *
1134848 TATCCCCGATTATGAGAAATTAATATTTTACAAATAAAGCTGGGGTTAGAGTATCCCCTAAAAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAA
*
1134913 TAATGGGGTTGGAG
66 TAATGAGGTTGGAG
*
1134927 TATCCGCG---ATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
1134979 TCCGATTAAG
Statistics
Matches: 179, Mismatches: 31, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
76 37 0.21
79 142 0.79
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAA
TAATGAGGTTGGAG
Found at i:1134978 original size:48 final size:49
Alignment explanation
Indices: 1134917--1135031 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 49
1134907 AAAAAATAAT
**
1134917 GGGGTTGGAGTATCCGCGA-T-GAAAAATTGATGTTTTAGAAATAAAACC
1 GGGGTTGGAGTATCC-CGATTAGAAAAATTGACATTTTAGAAATAAAACC
* **
1134965 GGGGTTGGAGTATCTCCGATTAAGAAAAATTGACATTTTGGAAATGGAACC
1 GGGGTTGGAGTATC-CCGATT-AGAAAAATTGACATTTTAGAAATAAAACC
*
1135016 GGGATTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1135032 CGAGATAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
48 17 0.30
49 2 0.04
50 2 0.04
51 36 0.63
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (49 bp):
GGGGTTGGAGTATCCCGATTAGAAAAATTGACATTTTAGAAATAAAACC
Found at i:1137350 original size:20 final size:20
Alignment explanation
Indices: 1137325--1137439 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
1137315 AAAATGCTTG
*
1137325 AATGTATCGATACATTGTAA-
1 AATGTATCGATACAATG-AAC
1137345 AATGTATCGATACAAT-AAGC
1 AATGTATCGATACAATGAA-C
* *
1137365 AACGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAC
1137385 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
1137405 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
1137425 AATGTATCGATACAA
1 AATGTATCGATACAA
1137440 ATTGCAAAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
18 2 0.02
20 84 0.97
21 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:1143336 original size:85 final size:84
Alignment explanation
Indices: 1143180--1143406 Score: 249
Period size: 85 Copynumber: 2.6 Consensus size: 84
1143170 ATCCAACAAA
* * * *
1143180 GGATAAAGAGGATTTACCCAGGACTAAGCTGATGGGTAAACACAGGTATGAAAGGTTGACTAGGA
1 GGATAAA-AGG-TTTACCGAGGACTAAGC-AATAGGTAAACA-AGGGATGAAAGGTTGACTAGGA
* * *
1143245 ATTAAGCCGATAGGTCACTGACG
62 ACTAAGCCGACAAGTCACTGACG
* * *
1143268 GGATAAAAGGTTTACCGAGGACTAAGTCAATAGGTGAACAAGGGATGAAGGGTTG-CTCAGGGAC
1 GGATAAAAGGTTTACCGAGGACTAAG-CAATAGGTAAACAAGGGATGAAAGGTTGACT-AGGAAC
*
1143332 TAAGCCGACAAGTCACTGAGG
64 TAAGCCGACAAGTCACTGACG
* * *
1143353 GGATAAGAGGTTTACCGAGGACTGAGCCAATTGGTAAACAATGGGATGAAAGGT
1 GGATAAAAGGTTTACCGAGGACTAAG-CAATAGGTAAACAA-GGGATGAAAGGT
1143407 ATCAGATAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
84 2 0.02
85 71 0.60
86 35 0.29
87 4 0.03
88 7 0.06
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (84 bp):
GGATAAAAGGTTTACCGAGGACTAAGCAATAGGTAAACAAGGGATGAAAGGTTGACTAGGAACTA
AGCCGACAAGTCACTGACG
Found at i:1143633 original size:87 final size:87
Alignment explanation
Indices: 1143528--1144114 Score: 607
Period size: 87 Copynumber: 6.7 Consensus size: 87
1143518 AATTTCACCG
* *
1143528 GGGTGGTAACCATACGTCAAAT-AAGCATGAAAAGAATCTGACTAGGGTGGTAACCATACGTCAG
1 GGGTGGTAACCATACGTCAAATCAA-AATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAG
*
1143592 ATAGAAAGGAAAAGATTCGACTA
65 ATAGAAAGGAAAAGATTCGACCA
* * * *
1143615 GGGTGGTAACCATGCGTCAAATCAAAATGAAAAGAATTTGACCAGGATGGTAACCATACGTTAGA
1 GGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGA
*
1143680 CAGAAAGGAAAAGATTCGACCA
66 TAGAAAGGAAAAGATTCGACCA
* * * * * *
1143702 GGGTTGTAACCATATGTTAAATCCAAATGGAAAGAATCTGACCAGGGTGGTAACCATACATCAGA
1 GGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGA
*
1143767 TAGAAAGGAATAGATTCGACCA
66 TAGAAAGGAAAAGATTCGACCA
* * * *
1143789 GGGTGGTAACCATACGTCAAATCAAAAT-AGAAAGAATCTGACTAAGATGGTAACCATACATCAG
1 GGGTGGTAACCATACGTCAAATCAAAATGA-AAAGAATCTGACCAGGGTGGTAACCATACGTCAG
*
1143853 ATAGAAAGGAAAAGATTCAACCA
65 ATAGAAAGGAAAAGATTCGACCA
* * *
1143876 GGGTGGTAACCATGCGTTAAATCAAAATTG-AAAGAATCTGACCAGGGTGGTAACCATACGTCAA
1 GGGTGGTAACCATACGTCAAATCAAAA-TGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAG
* *
1143940 ATCA-AAATGG-AAAGAATTTGACTA
65 AT-AGAAA-GGAAAAG-ATTCGACCA
* * * * * * * * * *
1143964 AGGTCGTAACCATATGTCAGA-CAGAAAAGAAAAGATTC-AACCAAGGTGGTAACCATACGTTAA
1 GGGTGGTAACCATACGTCAAATCA-AAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAG
* **
1144027 ATCA-AAATGG-AAAGAATCTGACTG
65 AT-AGAAA-GGAAAAGATTC-GACCA
** * * * * *
1144051 GGGTGGTAACCATACGTCAAACTTGAAATGAGAAGAGTTTGACCAGAGTGGTATCCATACGTCA
1 GGGTGGTAACCATACGTCAAA-TCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCA
1144115 AACAGACACT
Statistics
Matches: 418, Mismatches: 69, Indels: 24
0.82 0.14 0.05
Matches are distributed among these distances:
86 2 0.00
87 350 0.84
88 47 0.11
89 19 0.05
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (87 bp):
GGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGA
TAGAAAGGAAAAGATTCGACCA
Found at i:1143734 original size:131 final size:129
Alignment explanation
Indices: 1143528--1144071 Score: 503
Period size: 131 Copynumber: 4.2 Consensus size: 129
1143518 AATTTCACCG
* * * * * *
1143528 GGGTGGTAACCATACGTCAAAT-AAGCATGAAAAGAATCTGACTAGGGTGGTAACCATACGTCAG
1 GGGTGGTAACCATACGTCAAATCAA-AAGGAAAAGATTC-GACTAAGGTCGTAACCATATGTCAG
* * * * *
1143592 ATAGAAAGGAAAAGATTCGACTAGGGTGGTAACCATGCGTCAAATCAAAATGAAAAGAATTTGAC
64 AT-CAAAGGAAAAGATTCAACCAGGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGAC
1143657 CA
128 CA
* * * * * * * *
1143659 GGATGGTAACCATACGTTAGA-CAGAAAGGAAAAGATTCGACCAGGGTTGTAACCATATGTTAAA
1 GGGTGGTAACCATACGTCAAATCA-AAAGGAAAAGATTCGACTAAGGTCGTAACCATATGTCAGA
* * * * * * *
1143723 TCCAAATGG-AAAGAATCTGACCAGGGTGGTAACCATACATCAGAT-AGAAAGGAATAGATTC-G
65 T-CAAA-GGAAAAGATTC-AACCAGGGTGGTAACCATACGTCAAATCA-AAATGAAAAGAATCTG
1143785 ACCA
126 ACCA
* * * * **
1143789 GGGTGGTAACCATACGTCAAATCAAAA-TAGAAAGAATCTGACTAAGATGGTAACCATACATCAG
1 GGGTGGTAACCATACGTCAAATCAAAAGGA-AAAGATTC-GACTAAGGTCGTAACCATATGTCAG
* * *
1143853 ATAGAAAGGAAAAGATTCAACCAGGGTGGTAACCATGCGTTAAATCAAAATTG-AAAGAATCTGA
64 AT-CAAAGGAAAAGATTCAACCAGGGTGGTAACCATACGTCAAATCAAAA-TGAAAAGAATCTGA
1143917 CCA
127 CCA
*
1143920 GGGTGGTAACCATACGTCAAATCAAAATGG-AAAGAATTTGACTAAGGTCGTAACCATATGTCAG
1 GGGTGGTAACCATACGTCAAATCAAAA-GGAAAAG-ATTCGACTAAGGTCGTAACCATATGTCAG
* * * *
1143984 A-CAGAAAAGAAAAGATTCAACCAAGGTGGTAACCATACGTTAAATCAAAATGGAAAGAATCTGA
64 ATC--AAAGGAAAAGATTCAACCAGGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGA
**
1144048 CTG
127 CCA
1144051 GGGTGGTAACCATACGTCAAA
1 GGGTGGTAACCATACGTCAAA
1144072 CTTGAAATGA
Statistics
Matches: 336, Mismatches: 59, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
129 1 0.00
130 101 0.30
131 231 0.69
132 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (129 bp):
GGGTGGTAACCATACGTCAAATCAAAAGGAAAAGATTCGACTAAGGTCGTAACCATATGTCAGAT
CAAAGGAAAAGATTCAACCAGGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACCA
Found at i:1162743 original size:165 final size:165
Alignment explanation
Indices: 1162438--1162758 Score: 377
Period size: 165 Copynumber: 1.9 Consensus size: 165
1162428 GAGAAAGAGG
*
1162438 ATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATCTTTGAAAACTTAATTAATATGAA
1 ATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATCTTTGAAAACTGAATTAATATGAA
* * * *
1162503 ATAAATAATAATATTTTATAAATTTTAAAAATAAAGAAAAGAAAAATTCCCCCGAAACATTTGCA
66 ATAAATAATAATATTTGATAAATTTCAAAAATAAAGAAAAGAAAAATTCCCCCGAAAAATTTACA
* * *
1162568 GAGTAGAAAACTTCGTATTTTAAAAAAAAAAGAAA
131 GAGAAGAAAACTACGTAATTTAAAAAAAAAAGAAA
* * *
1162603 ATTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAAT-TTTTAGAAACTGAATTAATATG-
1 ATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATCTTTGA-AAACTGAATTAATATGA
* * ** *
1162666 AA-AAA-AATAATATTTGATTAATTTCAAAAATTTTAA-ACTAGTGAAAA-TCCTCCCGAAAAAA
65 AATAAATAATAATATTTGATAAATTTCAAAAA--TAAAGAAAAG-AAAAATTCC-CCCG-AAAAA
*
1162727 TTTAC-GAAGAAGAAAACTACGTAATTTGAAAA
125 TTTACAG-AGAAGAAAACTACGTAATTTAAAAA
1162759 TAAGAGGAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
162 22 0.17
163 9 0.07
164 18 0.14
165 83 0.63
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (165 bp):
ATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATCTTTGAAAACTGAATTAATATGAA
ATAAATAATAATATTTGATAAATTTCAAAAATAAAGAAAAGAAAAATTCCCCCGAAAAATTTACA
GAGAAGAAAACTACGTAATTTAAAAAAAAAAGAAA
Found at i:1172972 original size:21 final size:21
Alignment explanation
Indices: 1172943--1173046 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
1172933 CAAAATTACA
* * *
1172943 CTAAAGTATCGATACATTAGG
1 CTAATGTATCAATACATTAGC
*
1172964 GTAATGTATCAATACATTAGC
1 CTAATGTATCAATACATTAGC
*
1172985 CTAATGTATCTATACATTA-C
1 CTAATGTATCAATACATTAGC
* * * **
1173005 CGTCATCTATCAATATA-CCGAC
1 C-TAATGTATCAATACATTAG-C
*
1173027 CTAATGTATCAATACTTTAG
1 CTAATGTATCAATACATTAG
1173047 AGCCCAAAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.03
21 56 0.92
22 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (21 bp):
CTAATGTATCAATACATTAGC
Found at i:1173110 original size:21 final size:21
Alignment explanation
Indices: 1173084--1173133 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1173074 CAAAGCCTTT
* *
1173084 TATCAATATATTTATAAAACA
1 TATCAATAGATTGATAAAACA
**
1173105 TATCAATAGATTGATAAAATG
1 TATCAATAGATTGATAAAACA
1173126 TATCAATA
1 TATCAATA
1173134 CTTTGAGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (21 bp):
TATCAATAGATTGATAAAACA
Found at i:1173857 original size:119 final size:119
Alignment explanation
Indices: 1173699--1173925 Score: 289
Period size: 119 Copynumber: 1.9 Consensus size: 119
1173689 ATTCGACTTG
* * * ** * *
1173699 TTTCTAGGAAAATATGTTTGACTTGAAAAAAAAATGACCTCGAGTTTGTTCTTTCGCTTAACCTA
1 TTTCTAGGAAAATATGGTTCACTTGAAAAAAAAAAGACCTCGAGTTCATTCATACGCTTAACCTA
* * * *
1173764 TTTCTGGGAAAATAGGTTTGACTTAAAAA-AGAGAAAAAACCTAAGGTTGACCTA
66 TTTCTAGGAAAATAGGTTCGACATAAAAAGA-AAAAAAAACCTAAGGTTGACCTA
*
1173818 TTTCTAGGAAAATA-GGTTCATCTT-AAAAAGAAAAAGACCTCGAGTTCATTCATAGGCTTAACC
1 TTTCTAGGAAAATATGGTTCA-CTTGAAAAA-AAAAAGACCTCGAGTTCATTCATACGCTTAACC
*
1173881 TATTTCTAGGAAAATTGGTTCGACATAAAAAGAAAAAAAAACCTA
64 TATTTCTAGGAAAATAGGTTCGACATAAAAAGAAAAAAAAACCTA
1173926 TAGTTTGTTC
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 9 0.10
119 82 0.89
120 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (119 bp):
TTTCTAGGAAAATATGGTTCACTTGAAAAAAAAAAGACCTCGAGTTCATTCATACGCTTAACCTA
TTTCTAGGAAAATAGGTTCGACATAAAAAGAAAAAAAAACCTAAGGTTGACCTA
Found at i:1175298 original size:31 final size:33
Alignment explanation
Indices: 1175263--1175323 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1175253 GTATTTCCTT
*
1175263 TTTAAAA-ATCCTCAATGGAAGAAA-ATTTACC
1 TTTAAAAGATCCTCAATGAAAGAAATATTTACC
*
1175294 TTTAAAAGATTCTCAATGAAAGAAATATTT
1 TTTAAAAGATCCTCAATGAAAGAAATATTT
1175324 TTTTTATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 7 0.27
32 15 0.58
33 4 0.15
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (33 bp):
TTTAAAAGATCCTCAATGAAAGAAATATTTACC
Found at i:1179633 original size:7 final size:6
Alignment explanation
Indices: 1179620--1179699 Score: 51
Period size: 7 Copynumber: 13.0 Consensus size: 6
1179610 ATTTCGTTTC
* *
1179620 ATTTTT ACTTTTT A-TTTT ATATTT ATTTCAT ATTTTT CA--TTT ATTTCTT
1 ATTTTT A-TTTTT ATTTTT ATTTTT ATTT-TT ATTTTT -ATTTTT ATTT-TT
*
1179669 ATTTCTT ATTTCCT A-TTTT ATTTTT ATTTTT
1 ATTT-TT ATTT-TT ATTTTT ATTTTT ATTTTT
1179700 TTCTTCTTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
4 1 0.02
5 10 0.17
6 21 0.35
7 28 0.47
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:1179677 original size:14 final size:13
Alignment explanation
Indices: 1179659--1179699 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1179649 ATATTTTTCA
1179659 TTTATTTCTTATT
1 TTTATTTCTTATT
*
1179672 TCTTATTTCCTA-T
1 T-TTATTTCTTATT
1179685 TTTATTT-TTATT
1 TTTATTTCTTATT
1179697 TTT
1 TTT
1179700 TTCTTCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 2 0.08
12 10 0.42
13 3 0.12
14 9 0.38
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTCTTATT
Found at i:1179679 original size:18 final size:17
Alignment explanation
Indices: 1179632--1179679 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
1179622 TTTTACTTTT
1179632 TATTTTATATTTATTTCA
1 TATTTT-TATTTATTTCA
*
1179650 TATTTTTCATTTATTTCT
1 TATTTTT-ATTTATTTCA
1179668 TATTTCTTATTT
1 TATTT-TTATTT
1179680 CCTATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.89
19 2 0.07
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTATTTATTTCA
Found at i:1179794 original size:16 final size:15
Alignment explanation
Indices: 1179775--1179824 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1179765 CAAAATTTTG
1179775 AAAAATTAAAAAAATT
1 AAAAATTAAAAAAA-T
*
1179791 AAAAATTAAAAATAT
1 AAAAATTAAAAAAAT
1179806 AAAAA-TATAAAAAAT
1 AAAAATTA-AAAAAAT
1179821 AAAA
1 AAAA
1179825 TAAAAAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 2 0.06
15 16 0.52
16 13 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATTAAAAAAAT
Found at i:1179820 original size:9 final size:8
Alignment explanation
Indices: 1179775--1179832 Score: 63
Period size: 7 Copynumber: 7.8 Consensus size: 8
1179765 CAAAATTTTG
1179775 AAAAAT-T
1 AAAAATAT
*
1179782 AAAAAAATT
1 AAAAATA-T
1179791 AAAAAT-T
1 AAAAATAT
1179798 AAAAATAT
1 AAAAATAT
1179806 AAAAATAT
1 AAAAATAT
1179814 AAAAA-AT
1 AAAAATAT
1179821 -AAAATA-
1 AAAAATAT
1179827 AAAAAT
1 AAAAAT
1179833 TGAGAGATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
6 4 0.09
7 20 0.45
8 14 0.32
9 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:1182553 original size:23 final size:23
Alignment explanation
Indices: 1182522--1182566 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1182512 CTAGCATATA
*
1182522 AATTATTAATTGCTTATTTGTTT
1 AATTATTAATTGCTTAATTGTTT
* *
1182545 AATTTTTAATTGTTTAATTGTT
1 AATTATTAATTGCTTAATTGTT
1182567 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (23 bp):
AATTATTAATTGCTTAATTGTTT
Found at i:1182562 original size:8 final size:8
Alignment explanation
Indices: 1182527--1182566 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1182517 ATATAAATTA
*
1182527 TTAATTGC
1 TTAATTGT
*
1182535 TTATTTGT
1 TTAATTGT
1182543 TTAATT-T
1 TTAATTGT
1182550 TTAATTGT
1 TTAATTGT
1182558 TTAATTGT
1 TTAATTGT
1182566 T
1 T
1182567 ATTTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (8 bp):
TTAATTGT
Found at i:1183130 original size:16 final size:16
Alignment explanation
Indices: 1183109--1183142 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1183099 TTGAGTTATT
*
1183109 AATCACACTTGGATAA
1 AATCACACCTGGATAA
1183125 AATCACACCTGGATAA
1 AATCACACCTGGATAA
1183141 AA
1 AA
1183143 ATTGTTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (16 bp):
AATCACACCTGGATAA
Found at i:1184248 original size:20 final size:20
Alignment explanation
Indices: 1184225--1184297 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1184215 ACAATTCAAA
1184225 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1184245 GTATCGATACATGAAAAAATT
1 GTATCGATACATGTTGCAA-T
1184266 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1184286 GTATCGATACAT
1 GTATCGATACAT
1184298 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1184270 original size:21 final size:20
Alignment explanation
Indices: 1184242--1184318 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
1184232 TACATGTTGC
1184242 AATGTATCGATACATGAAAA
1 AATGTATCGATACATGAAAA
****
1184262 AATTGTATCGATACATGTTGC
1 AA-TGTATCGATACATGAAAA
1184283 AATGTATCGATACAT-AAAA
1 AATGTATCGATACATGAAAA
1184302 AGGATGTATCGATACAT
1 A--ATGTATCGATACAT
1184319 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 30 0.65
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1184276 original size:41 final size:40
Alignment explanation
Indices: 1184225--1184318 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 40
1184215 ACAATTCAAA
1184225 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-ATT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGA-T
1184266 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAA-GAT
1184307 GTATCGATACAT
1 GTATCGATACAT
1184319 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
40 5 0.10
41 45 0.88
42 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
Found at i:1184375 original size:13 final size:13
Alignment explanation
Indices: 1184357--1184382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1184347 TACAGCAAGT
1184357 ATGTATCGATACA
1 ATGTATCGATACA
1184370 ATGTATCGATACA
1 ATGTATCGATACA
1184383 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1188463 original size:15 final size:15
Alignment explanation
Indices: 1188443--1188473 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1188433 TAAAAATGTC
*
1188443 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1188458 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1188473 C
1 C
1188474 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1190570 original size:13 final size:13
Alignment explanation
Indices: 1190552--1190590 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1190542 ACATTTTTCC
1190552 TTGTATCGATACA
1 TTGTATCGATACA
1190565 TTGTATCGATACA
1 TTGTATCGATACA
*
1190578 CTGTATCGATACA
1 TTGTATCGATACA
1190591 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1192485 original size:48 final size:48
Alignment explanation
Indices: 1192431--1192526 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1192421 GGGGAGATAA
1192431 AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1 AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1192479 AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1 AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
1192527 CGTAAAATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.08, G:0.29, T:0.25
Consensus pattern (48 bp):
AGGAGAGAATGCGTGAATTACCTTATTAAGGGGGAGAATGTACAAATT
Found at i:1193101 original size:20 final size:20
Alignment explanation
Indices: 1193078--1193150 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1193068 ACAATTCAAA
1193078 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1193098 GTATCGATACATGAAAAAATT
1 GTATCGATACATGTTGCAA-T
1193119 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1193139 GTATCGATACAT
1 GTATCGATACAT
1193151 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1193123 original size:21 final size:20
Alignment explanation
Indices: 1193095--1193171 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
1193085 TACATGTTGC
1193095 AATGTATCGATACATGAAAA
1 AATGTATCGATACATGAAAA
****
1193115 AATTGTATCGATACATGTTGC
1 AA-TGTATCGATACATGAAAA
1193136 AATGTATCGATACAT-AAAA
1 AATGTATCGATACATGAAAA
1193155 AGGATGTATCGATACAT
1 A--ATGTATCGATACAT
1193172 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 30 0.65
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:1193129 original size:41 final size:40
Alignment explanation
Indices: 1193078--1193171 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 40
1193068 ACAATTCAAA
1193078 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-ATT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGA-T
1193119 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAA-GAT
1193160 GTATCGATACAT
1 GTATCGATACAT
1193172 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
40 5 0.10
41 45 0.88
42 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
Found at i:1193228 original size:13 final size:13
Alignment explanation
Indices: 1193210--1193235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1193200 TACAGCAAGT
1193210 ATGTATCGATACA
1 ATGTATCGATACA
1193223 ATGTATCGATACA
1 ATGTATCGATACA
1193236 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1195163 original size:58 final size:58
Alignment explanation
Indices: 1195095--1195214 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
1195085 TTAAAGTTTT
*
1195095 ACTTATAGAATGTTTTATCAATCTTCTTAGAATTTTTAATTAAATAACAAACAATAGG
1 ACTTATAGAATGTTTTATCAATCTTCTTAGAATTTTTAACTAAATAACAAACAATAGG
1195153 ACTTATAGAATGTTTTATCAATCTTCTTAGAATTTTTAACTAAATAACAAACAATAGG
1 ACTTATAGAATGTTTTATCAATCTTCTTAGAATTTTTAACTAAATAACAAACAATAGG
1195211 ACTT
1 ACTT
1195215 TAATGAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (58 bp):
ACTTATAGAATGTTTTATCAATCTTCTTAGAATTTTTAACTAAATAACAAACAATAGG
Found at i:1196087 original size:7 final size:8
Alignment explanation
Indices: 1196059--1196105 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
1196049 TGCAACCTTG
1196059 AAAGAAAA
1 AAAGAAAA
1196067 AAAGAAAA
1 AAAGAAAA
1196075 ATAAG-AAA
1 A-AAGAAAA
1196083 AAAGAAAA
1 AAAGAAAA
1196091 AAATGAAAA
1 AAA-GAAAA
1196100 AGAAGA
1 A-AAGA
1196106 GAAAGTATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 3 0.09
8 19 0.54
9 11 0.31
10 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1196098 original size:25 final size:24
Alignment explanation
Indices: 1196059--1196105 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1196049 TGCAACCTTG
*
1196059 AAAGAAAAAAAGAAAAATAAGAAA
1 AAAGAAAAAAAGAAAAAGAAGAAA
1196083 AAAGAAAAAAATGAAAAAGAAGA
1 AAAGAAAAAAA-GAAAAAGAAGA
1196106 GAAAGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAGAAAAAAAGAAAAAGAAGAAA
Found at i:1196110 original size:24 final size:24
Alignment explanation
Indices: 1196058--1196110 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1196048 ATGCAACCTT
*
1196058 GAAAGAAAAAAAGAAAAATAAGAA
1 GAAAGAAAAAAAGAAAAAGAAGAA
*
1196082 AAAAGAAAAAAATGAAAAAGAAG-A
1 GAAAGAAAAAAA-GAAAAAGAAGAA
1196106 GAAAG
1 GAAAG
1196111 TATTGTTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (24 bp):
GAAAGAAAAAAAGAAAAAGAAGAA
Found at i:1197043 original size:30 final size:29
Alignment explanation
Indices: 1196974--1197103 Score: 83
Period size: 30 Copynumber: 4.4 Consensus size: 29
1196964 ACAGAATCTA
* *
1196974 AGGTTATTTTAGA--AATTTTCATCATTTT
1 AGGTCATTTTAGATTAATTTTCAT-AATTT
1197002 AAGGTCA-TTTAGATTAATTTTCATAATTT
1 -AGGTCATTTTAGATTAATTTTCATAATTT
**
1197031 AGGATCATTTTAGAATTTTTTTTTCAT--TTT
1 AGG-TCATTTTAG-A-TTAATTTTCATAATTT
* * * *
1197061 AGGAC-TATTTAGATTACTTTACATAATCTG
1 AGGTCAT-TTTAGATTAATTTTCATAAT-TT
1197091 AGGTCATTTTAGA
1 AGGTCATTTTAGA
1197104 AAATTCTATC
Statistics
Matches: 80, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
27 8 0.10
28 11 0.14
29 19 0.24
30 31 0.39
31 2 0.03
32 9 0.11
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (29 bp):
AGGTCATTTTAGATTAATTTTCATAATTT
Found at i:1197204 original size:117 final size:114
Alignment explanation
Indices: 1197095--1197331 Score: 259
Period size: 117 Copynumber: 2.0 Consensus size: 114
1197085 AATCTGAGGT
*
1197095 CATTTTAGAAAATTC-TATCATTTTATGG-CTATTCAAGTTATTTTATATAATCTAGGGACCATT
1 CATTTT-GAAAATTCATA-CATTTTA-GGACAATTCAAGTTATTTTATATAATCTA-GG-CCATT
1197158 TTA-CATTTTCCATACATTTTAGGT-ATATGTAAGTTATTTCATATAATCTAGAGAC
61 TTAGCA-TTTCCATACATTTTAGGTCAT-T-TAAGTTATTTCATATAATCTAGAGAC
* * * * * *
1197213 CGTTTTGCAATTTCATACATTTTAGGACAATTTAGGTTATTTTATATAATCTAGGTCATTTTAGC
1 CATTTTGAAAATTCATACATTTTAGGACAATTCAAGTTATTTTATATAATCTAGGCCATTTTAGC
* * * *
1197278 ATTTCCATACATTTTGGGTCATTTAAGTTATTCCATGTATAT-TAGAAAC
66 ATTTCCATACATTTTAGGTCATTTAAGTTATTTCATATA-ATCTAGAGAC
1197327 CATTT
1 CATTT
1197332 AGCAATTTTC
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
114 24 0.24
115 27 0.26
116 8 0.08
117 36 0.35
118 7 0.07
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (114 bp):
CATTTTGAAAATTCATACATTTTAGGACAATTCAAGTTATTTTATATAATCTAGGCCATTTTAGC
ATTTCCATACATTTTAGGTCATTTAAGTTATTTCATATAATCTAGAGAC
Found at i:1197254 original size:58 final size:59
Alignment explanation
Indices: 1197129--1197309 Score: 194
Period size: 58 Copynumber: 3.1 Consensus size: 59
1197119 ATGGCTATTC
* * *
1197129 AAGTTATTTTATATAATCTAGGGACCATTTTACATTTTCCATACATTTTAGGTATATGT
1 AAGTTATTTTATATAATCTAGAGACCATTTTACAATTTCCATACATTTTAGGTAAATGT
* * * *
1197188 AAGTTATTTCATATAATCTAGAGACCGTTTTGCAATTT-CATACATTTTAGG-ACAATTT
1 AAGTTATTTTATATAATCTAGAGACCATTTTACAATTTCCATACATTTTAGGTA-AATGT
* * * * *
1197246 AGGTTATTTTATATAATCTAG-G-TCATTTTAGC-ATTTCCATACATTTTGGGT-CATTT
1 AAGTTATTTTATATAATCTAGAGACCATTTTA-CAATTTCCATACATTTTAGGTAAATGT
1197302 AAGTTATT
1 AAGTTATT
1197310 CCATGTATAT
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
56 20 0.19
57 15 0.15
58 35 0.34
59 33 0.32
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (59 bp):
AAGTTATTTTATATAATCTAGAGACCATTTTACAATTTCCATACATTTTAGGTAAATGT
Found at i:1197369 original size:115 final size:117
Alignment explanation
Indices: 1197131--1197353 Score: 287
Period size: 115 Copynumber: 1.9 Consensus size: 117
1197121 GGCTATTCAA
1197131 GTTATTTTATATAATCTAGGGACCATTTTACATTTTCCATACATTTTAGGTATATGTAAGTTATT
1 GTTATTTTATATAATCTAGGGACCATTTTACATTTTCCATACATTTTAGGTATATGTAAGTTATT
* * * *
1197196 TCATATAATCTAGAGACCGTTTTGCAATTTCATACATTTTAGGACAATTTAG
66 CCATATAATCTAGAAACCATTTAGCAATTTCATACATTTTAGGACAATTTAG
* *
1197248 GTTATTTTATATAATCTA-GG-TCATTTTAGCA-TTTCCATACATTTTGGGTCAT-T-TAAGTTA
1 GTTATTTTATATAATCTAGGGACCATTTTA-CATTTTCCATACATTTTAGGT-ATATGTAAGTTA
* * *
1197308 TTCCATGTATAT-TAGAAACCATTTAGCAATTTTCTTGCATTTTAGG
64 TTCCATATA-ATCTAGAAACCATTTAGCAA-TTTCATACATTTTAGG
1197354 GTCTTTTAGT
Statistics
Matches: 93, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
114 28 0.30
115 41 0.44
116 6 0.06
117 18 0.19
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (117 bp):
GTTATTTTATATAATCTAGGGACCATTTTACATTTTCCATACATTTTAGGTATATGTAAGTTATT
CCATATAATCTAGAAACCATTTAGCAATTTCATACATTTTAGGACAATTTAG
Found at i:1197485 original size:58 final size:58
Alignment explanation
Indices: 1197129--1197488 Score: 220
Period size: 59 Copynumber: 6.2 Consensus size: 58
1197119 ATGGCTATTC
* * * * *
1197129 AAGTTATTTTATATAATCTAGGGACCATTTTACATTTTCCATACATTTTAGGTA-TATGT
1 AAGTTATTTCATATAATCTAGGAACCATTTTGCATTTT-CATACATTTTAGG-ACCATTT
* * *
1197188 AAGTTATTTCATATAATCTA-GAGACCGTTTTGCAATTTCATACATTTTAGGACAATTT
1 AAGTTATTTCATATAATCTAGGA-ACCATTTTGCATTTTCATACATTTTAGGACCATTT
* * * * **
1197246 AGGTTATTTTATATAATCTAGG--TCATTTTAGCATTTCCATACATTTT-GGGTCATTT
1 AAGTTATTTCATATAATCTAGGAACCATTTT-GCATTTTCATACATTTTAGGACCATTT
* * * * * * **
1197302 AAGTTATTCCATGTATAT-TAGAAACCATTTAGCAATTTTCTTGCATTTTAGGGTC-TTT
1 AAGTTATTTCATATA-ATCTAGGAACCATTTTGC-ATTTTCATACATTTTAGGACCATTT
* * * * * * **
1197360 TAGTTTATTTCATGCAT-AT-GAAGAATCATTTTACAATTTTCATGCATTTTAAGG-CTTTTT
1 AAG-TTATTTCAT--ATAATCTAGGAACCATTTTGC-ATTTTCATACATTTT-AGGACCATTT
* * * * *
1197420 CAGTTATTTTATATAATCTAGGAATCATTTTGCATTTTCTATGCA-TTTAAGACCATTT
1 AAGTTATTTCATATAATCTAGGAACCATTTTGCATTTTC-ATACATTTTAGGACCATTT
1197478 AAGTTATTTCA
1 AAGTTATTTCA
1197489 CATGATTTAG
Statistics
Matches: 235, Mismatches: 48, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
56 25 0.11
57 24 0.10
58 81 0.34
59 96 0.41
60 8 0.03
61 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (58 bp):
AAGTTATTTCATATAATCTAGGAACCATTTTGCATTTTCATACATTTTAGGACCATTT
Found at i:1202210 original size:10 final size:10
Alignment explanation
Indices: 1202192--1202249 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
1202182 CTAAGTAATT
*
1202192 TAAACATAAA
1 TAAAAATAAA
1202202 TAAAAATAAA
1 TAAAAATAAA
* *
1202212 TAAAATTAATT
1 TAAAAATAA-A
*
1202223 TAAAATTAAA
1 TAAAAATAAA
*
1202233 TAAAATCTAAA
1 TAAAA-ATAAA
1202244 TAAAAA
1 TAAAAA
1202250 CTCTAAGACT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:1202225 original size:31 final size:32
Alignment explanation
Indices: 1202187--1202248 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1202177 AACATCTAAG
1202187 TAATTTAAACA-TAAATAAAA-ATAAATAAAAT
1 TAATTTAAA-ATTAAATAAAATATAAATAAAAT
*
1202218 TAATTTAAAATTAAATAAAATCTAAATAAAA
1 TAATTTAAAATTAAATAAAATATAAATAAAA
1202249 ACTCTAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.04
31 18 0.64
32 9 0.32
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (32 bp):
TAATTTAAAATTAAATAAAATATAAATAAAAT
Found at i:1202243 original size:11 final size:10
Alignment explanation
Indices: 1202198--1202248 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
1202188 AATTTAAACA
*
1202198 TAAATAAAAA
1 TAAATAAAAT
1202208 TAAATAAAAT
1 TAAATAAAAT
*
1202218 TAATTTAAAAT
1 TAA-ATAAAAT
1202229 TAAATAAAAT
1 TAAATAAAAT
1202239 CTAAATAAAA
1 -TAAATAAAA
1202249 ACTCTAAGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 18 0.50
11 18 0.50
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAATAAAAT
Found at i:1202247 original size:21 final size:20
Alignment explanation
Indices: 1202198--1202249 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1202188 AATTTAAACA
1202198 TAAATAAAAATAAATAAAAT
1 TAAATAAAAATAAATAAAAT
* *
1202218 TAATTTAAAATTAAATAAAAT
1 TAA-ATAAAAATAAATAAAAT
1202239 CTAAATAAAAA
1 -TAAATAAAAA
1202250 CTCTAAGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAATAAAAATAAATAAAAT
Found at i:1207842 original size:16 final size:16
Alignment explanation
Indices: 1207818--1207848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1207808 AAAGACTTTC
*
1207818 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
1207834 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
1207849 GGAAATGTTG
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:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:1211911 original size:33 final size:33
Alignment explanation
Indices: 1211856--1211920 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1211846 AAGTGAAATG
* *
1211856 TATCGATACATAGGATAATGTATCGATACATTT
1 TATCGATACATAAGATAATGTATCAATACATTT
*
1211889 TATCGATACATGAAGA-ATTGTATCAATACATT
1 TATCGATACAT-AAGATAATGTATCAATACATT
1211921 GTGTCCAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (33 bp):
TATCGATACATAAGATAATGTATCAATACATTT
Found at i:1218775 original size:20 final size:20
Alignment explanation
Indices: 1218750--1218791 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1218740 AGCTTAGTTT
1218750 TTATTCATTA-TATCAATACA
1 TTATTCA-TAGTATCAATACA
1218770 TTATTCATAGTATCAATACA
1 TTATTCATAGTATCAATACA
1218790 TT
1 TT
1218792 GTATTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (20 bp):
TTATTCATAGTATCAATACA
Found at i:1225354 original size:13 final size:13
Alignment explanation
Indices: 1225336--1225361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1225326 CAATTTTTTG
1225336 TGTATCGATACAT
1 TGTATCGATACAT
1225349 TGTATCGATACAT
1 TGTATCGATACAT
1225362 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1225373 original size:32 final size:33
Alignment explanation
Indices: 1225316--1225379 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1225306 TACAAGCCAA
**
1225316 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1225349 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1225380 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1227465 original size:21 final size:20
Alignment explanation
Indices: 1227436--1227478 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1227426 GACTAGTGTG
* *
1227436 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1227457 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1227477 GG
1 GG
1227479 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1227928 original size:13 final size:13
Alignment explanation
Indices: 1227910--1227960 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
1227900 ATAATCCCCC
1227910 TGTATCGATACAG
1 TGTATCGATACAG
1227923 TGTATCGATACAG
1 TGTATCGATACAG
*
1227936 TGTATCGATACAA
1 TGTATCGATACAG
1227949 TGTATCGATACA
1 TGTATCGATACA
1227961 AAGAAAAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1234151 original size:13 final size:13
Alignment explanation
Indices: 1234133--1234158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1234123 CAATTTTTTG
1234133 TGTATCGATACAT
1 TGTATCGATACAT
1234146 TGTATCGATACAT
1 TGTATCGATACAT
1234159 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1234170 original size:32 final size:33
Alignment explanation
Indices: 1234113--1234176 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1234103 TACAAGCTAA
**
1234113 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1234146 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1234177 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1237608 original size:88 final size:88
Alignment explanation
Indices: 1237523--1237689 Score: 271
Period size: 88 Copynumber: 1.9 Consensus size: 88
1237513 CCTTCAGAGT
* * * *
1237523 AATGGGGATAGAGTTTCCTTAAGGATAAAATTATATGAAGGAAAATTTAAATCTTTGTTAGAATG
1 AATGGGGATAGAGTTTCCCTAAGGATAAAATTATACGAAGAAAAATTTAAATCTTTGTTAGAATA
*
1237588 AGGTTGGAATATCCTCTCAGAAC
66 AGGTTAGAATATCCTCTCAGAAC
* *
1237611 AATGGGGATGGAGTTTCCCTAAGGATAAAATTATACGAAGAAAAATTTAAATTTTTGTTAGAATA
1 AATGGGGATAGAGTTTCCCTAAGGATAAAATTATACGAAGAAAAATTTAAATCTTTGTTAGAATA
1237676 AGGTTAGAATATCC
66 AGGTTAGAATATCC
1237690 CTTTAGAGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (88 bp):
AATGGGGATAGAGTTTCCCTAAGGATAAAATTATACGAAGAAAAATTTAAATCTTTGTTAGAATA
AGGTTAGAATATCCTCTCAGAAC
Found at i:1243270 original size:14 final size:14
Alignment explanation
Indices: 1243251--1243298 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1243241 TTAAAGATTA
1243251 ATATATTAATATTT
1 ATATATTAATATTT
1243265 ATATATTAATATTT
1 ATATATTAATATTT
* *
1243279 TTA-ATTATATAATT
1 ATATATTA-ATATTT
1243293 ATATAT
1 ATATAT
1243299 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 23 0.79
15 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTAATATTT
Found at i:1243357 original size:17 final size:18
Alignment explanation
Indices: 1243326--1243360 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1243316 ATATTTATTT
*
1243326 TTTAGTATAATATAAAAA
1 TTTAGTATAAAATAAAAA
1243344 TTTA-TATAAAATAAAAA
1 TTTAGTATAAAATAAAAA
1243361 AAATAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAGTATAAAATAAAAA
Done.