Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_pilon, whole genome shotgun sequence
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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 17
Found at i:777193 original size:26 final size:25
Alignment explanation
Indices: 777164--777253 Score: 96
Period size: 26 Copynumber: 3.6 Consensus size: 25
777154 TATTTTAAAA
*
777164 TATGGATTAATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATT-TAGTTG
* **
777190 TATGGATTTATTTATT-TTTA--AA
1 TATGGATTGATTTATTATTTAGTTG
*
777212 TATAGATTGATTTATTATTATAGTTG
1 TATGGATTGATTTATTATT-TAGTTG
777238 TATGGATTGATTTATT
1 TATGGATTGATTTATT
777254 TTAAATAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.27
23 2 0.04
24 4 0.08
25 2 0.04
26 30 0.58
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (25 bp):
TATGGATTGATTTATTATTTAGTTG
Found at i:777198 original size:22 final size:22
Alignment explanation
Indices: 777173--777245 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
777163 ATATGGATTA
*
777173 ATTTATTATTGTAGTTGTATGG
1 ATTTATTATTATAGTTGTATGG
* * *
777195 ATTTATTTATTTTTAAATATAG-ATTG
1 ATTTA-TTA-TTAT-AGT-T-GTATGG
777221 ATTTATTATTATAGTTGTATGG
1 ATTTATTATTATAGTTGTATGG
777243 ATT
1 ATT
777246 GATTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.03
22 12 0.31
23 5 0.13
24 6 0.15
25 5 0.13
26 9 0.23
27 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (22 bp):
ATTTATTATTATAGTTGTATGG
Found at i:777203 original size:48 final size:48
Alignment explanation
Indices: 777141--777258 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 48
777131 TAATTTATTA
* * *
777141 GTATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTT
1 GTATGGATTGATTTATTTTAAAATATAGATTAATTTATTATTATAGTT
* * *
777189 GTATGGATTTATTTATTTTTAAATATAGATTGATTTATTATTATAGTT
1 GTATGGATTGATTTATTTTAAAATATAGATTAATTTATTATTATAGTT
777237 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
777259 TAATTTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.53
Consensus pattern (48 bp):
GTATGGATTGATTTATTTTAAAATATAGATTAATTTATTATTATAGTT
Found at i:777320 original size:14 final size:14
Alignment explanation
Indices: 777301--777353 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
777291 ATATGGATTG
777301 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
777315 ATTTATTAGTATGGAATG
1 ATTTATT--T-T-AAATA
777333 ATTTATTTTAAATA
1 ATTTATTTTAAATA
777347 ATTTATT
1 ATTTATT
777354 AGTATAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:777385 original size:22 final size:22
Alignment explanation
Indices: 777360--777420 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
777350 TATTAGTATA
777360 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
*
777382 GATTGATTTATTTTAAAATTTG
1 GATTGATTTATTTTAAAATATG
777404 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
777421 TAATTTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:777507 original size:242 final size:242
Alignment explanation
Indices: 777078--777689 Score: 783
Period size: 242 Copynumber: 2.5 Consensus size: 242
777068 TATTTTAAAA
*
777078 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AA-AA--TA-T-G-
* * * *
777143 ATGAATTGATTTATTTTAAAATATGGATTAATTTA--TT--AT--TGTAGTTGTATGGATTTATT
59 --G-ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTTGTATAGATTGATT
* *
777202 TATTTTTAAATATAGATTGATTTATTATTATAGTTGTATGGATTGATTTATTTTAAATAATTTAT
121 TATTTTAAAATATAGATTGATTTATTATTATAGTTGTATGAATTGATTTATTTTAAATAATTTAT
777267 TAGTATGTATTGGA-TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
186 TAGTATGTATT-GATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
*
777324 TATGGAATGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
* *
777389 TTATTTTAAAATTTGGATTGATTTATTTTAAATAATTTA-TTAGTATATATTGATTTATTTTAAA
66 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTT-GTATAGATTGATTTATTTTAAA
*
777453 ATATAGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGTA
130 ATATAGATTGATTTATTATTATAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGTA
777518 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
195 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * * * * *
777566 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGA
1 TATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGA
*
777626 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT-A---A-TTGTATGGATTGATTTATTT
61 TTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTTGTATAGATTGATTTATTT
777686 TAAA
126 TAAA
777690 TAATTTATTA
Statistics
Matches: 332, Mismatches: 21, Indels: 35
0.86 0.05 0.09
Matches are distributed among these distances:
236 29 0.09
237 21 0.06
238 5 0.02
240 3 0.01
241 6 0.02
242 192 0.58
243 5 0.02
244 4 0.01
245 2 0.01
246 59 0.18
247 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (242 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTTGTATAGATTGATTTATTTTAAAA
TATAGATTGATTTATTATTATAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGTAT
TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:777528 original size:22 final size:22
Alignment explanation
Indices: 777512--777554 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
777502 AATTTATTAG
*
777512 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
777534 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
777555 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:777591 original size:22 final size:23
Alignment explanation
Indices: 777566--777689 Score: 99
Period size: 22 Copynumber: 4.9 Consensus size: 23
777556 AATTTATTAG
777566 TATGGATTGATTTATTTTAAAA-
1 TATGGATTGATTTATTTTAAAAT
777588 TATGGATTGATTTATTTTAAATAATT
1 TATGGATTGATTTATTTT-AA-AA-T
* *
777614 TATTAGTATGGATTGATTTATTTTAAAA-
1 TA-T-GGATTGA----TTTATTTTAAAAT
777642 TATGGATTGATTTATTTTAAATAATT
1 TATGGATTGATTTATTTT-AA-AA-T
777668 GTATGGATTGATTTATTTTAAA
1 -TATGGATTGATTTATTTTAAA
777690 TAATTTATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 27
0.73 0.04 0.24
Matches are distributed among these distances:
22 26 0.31
23 4 0.05
24 4 0.05
25 1 0.01
26 9 0.11
27 20 0.24
28 7 0.08
30 2 0.02
31 2 0.02
32 8 0.10
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (23 bp):
TATGGATTGATTTATTTTAAAAT
Found at i:777689 original size:81 final size:80
Alignment explanation
Indices: 777566--777751 Score: 308
Period size: 81 Copynumber: 2.4 Consensus size: 80
777556 AATTTATTAG
777566 TATGGATTGATTTATTTT-AA-AA--TATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
1 TATGGATTGATTTATTTTAAATAATTTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
*
777627 TGATTTATTTTAAAA
66 TAATTTATTTTAAAA
*
777642 TATGGATTGATTTATTTTAAATAATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTA
1 TATGGATTGATTTATTTTAAATAATT-TATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
*
777707 TTAATTTATTTTATAA
65 TTAATTTATTTTAAAA
777723 TATGGATTGATTTATTTTAAATAATTTAT
1 TATGGATTGATTTATTTTAAATAATTTAT
777752 TATTGTAGTT
Statistics
Matches: 102, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
76 18 0.18
77 2 0.02
78 2 0.02
80 3 0.03
81 77 0.75
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAT
TAATTTATTTTAAAA
Found at i:777717 original size:22 final size:22
Alignment explanation
Indices: 777701--777745 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
777691 AATTTATTAG
*
777701 TATGTATTAATTTATTTTATAA
1 TATGGATTAATTTATTTTATAA
*
777723 TATGGATTGATTTATTTTA-AA
1 TATGGATTAATTTATTTTATAA
777744 TA
1 TA
777746 ATTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (22 bp):
TATGGATTAATTTATTTTATAA
Found at i:777825 original size:31 final size:31
Alignment explanation
Indices: 777768--777826 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
777758 AGTTGTATGG
* * **
777768 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTACAAAACTAAA
777799 ATTATTTAAATCTCAGTATTACAAAACT
1 ATTATTTAAATCTCAGTATTACAAAACT
777827 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTACAAAACTAAA
Found at i:787775 original size:12 final size:12
Alignment explanation
Indices: 787758--787797 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
787748 CTCCTTGGTC
787758 TAATTTCATTAG
1 TAATTTCATTAG
787770 TAATTTCATTAG
1 TAATTTCATTAG
787782 TAATTTCATTAG
1 TAATTTCATTAG
787794 TAAT
1 TAAT
787798 CCCTTGCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (12 bp):
TAATTTCATTAG
Found at i:787939 original size:215 final size:216
Alignment explanation
Indices: 787559--787980 Score: 801
Period size: 215 Copynumber: 2.0 Consensus size: 216
787549 AGAAAATCTG
787559 TCATTCAGCAATTTCATTAGTAATACCTTGCAGTACAGTGTTTTATTTCTTTATTGGTATTGATT
1 TCATTCAGCAATTTCATTAGTAATACCTTGCAGTACAGTGTTTTATTTCTTTATTGGTATTGATT
787624 TCTCTAAATTAATCCAATTGACAGTCCTGTACAAAACAATCTAACTGCCTGCGTTGGTATCATCT
66 TCTCTAAATTAATCCAATTGACAGTCCTGTACAAAACAATCTAACTGCCTGCGTTGGTATCATCT
787689 TATCCTTCTTGGGCTCCACAATTGGGCTTCCCTCCATTCTCCCACATGTTGAAATTGAGCTCCTT
131 TATCCTTCTTGGGCTCCACAATTGGGCTTCCCTCCATTCTCCCACATGTTGAAATTGAGCTCCTT
787754 GGTCTAATTTCATTAGTAATT
196 GGTCTAATTTCATTAGTAATT
* *
787775 TCATT-AGTAATTTCATTAGTAATCCCTTGCAGTACAGTGTTTTATTTCTTTATTGGTATTGATT
1 TCATTCAGCAATTTCATTAGTAATACCTTGCAGTACAGTGTTTTATTTCTTTATTGGTATTGATT
*
787839 TCTCTAAATTAATCCAATTGGCAGTCCTGTACAAAACAATCTAACTGCCTGCGTTGGTATCATCT
66 TCTCTAAATTAATCCAATTGACAGTCCTGTACAAAACAATCTAACTGCCTGCGTTGGTATCATCT
787904 TATCCTTCTTGGGCTCCACAATTGGGCTTCCCTCCATTCTCCCACATGTTGAAATTGAGCTCCTT
131 TATCCTTCTTGGGCTCCACAATTGGGCTTCCCTCCATTCTCCCACATGTTGAAATTGAGCTCCTT
*
787969 GGTTTAATTTCA
196 GGTCTAATTTCA
787981 CCCGTGCCTC
Statistics
Matches: 202, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
215 197 0.98
216 5 0.02
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (216 bp):
TCATTCAGCAATTTCATTAGTAATACCTTGCAGTACAGTGTTTTATTTCTTTATTGGTATTGATT
TCTCTAAATTAATCCAATTGACAGTCCTGTACAAAACAATCTAACTGCCTGCGTTGGTATCATCT
TATCCTTCTTGGGCTCCACAATTGGGCTTCCCTCCATTCTCCCACATGTTGAAATTGAGCTCCTT
GGTCTAATTTCATTAGTAATT
Found at i:791471 original size:127 final size:125
Alignment explanation
Indices: 791247--791502 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 125
791237 TTTTCCATGG
791247 GTCTTGGTCTCATTCTTTTAGATGTTTTTTTTACTTTGATATCGATTTTAACTTTTCAATTAGTG
1 GTCTTGGTCTCATTCTTTTAGATGTTTTTTTTACTTTGATATCGATTTTAACTTTTCAATTAGTG
791312 GATTCATAACGTTATCCTTTGATCTTATAAAATTAATAGTGACACCATTTGAGATCAATT
66 GATTCATAACGTTATCCTTTGATCTTATAAAATTAATAGTGACACCATTTGAGATCAATT
*
791372 GTCTTGGTCTCATTCTTTTAGATGTTTTTTTTTTACTTTGATATCGATTTTAACTTTTCAGTTAG
1 GTCTTGGTCTCATTCTTTTAGATG--TTTTTTTTACTTTGATATCGATTTTAACTTTTCAATTAG
*
791437 TGGATTCATAACGTTATCCTTTGATCTTATAAAATTAATAGTGACACCATTTGAGATCAGTT
64 TGGATTCATAACGTTATCCTTTGATCTTATAAAATTAATAGTGACACCATTTGAGATCAATT
791499 GTCT
1 GTCT
791503 AACGGTATTA
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
125 24 0.19
127 103 0.81
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (125 bp):
GTCTTGGTCTCATTCTTTTAGATGTTTTTTTTACTTTGATATCGATTTTAACTTTTCAATTAGTG
GATTCATAACGTTATCCTTTGATCTTATAAAATTAATAGTGACACCATTTGAGATCAATT
Found at i:806007 original size:6 final size:6
Alignment explanation
Indices: 805992--806026 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
805982 ACCAATTGTT
* *
805992 TTCTTC TTCTTG TTCTTG TTCTTG TTCTTC TTCTT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCTTG TTCTT
806027 TTGTTACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.69
Consensus pattern (6 bp):
TTCTTG
Found at i:806013 original size:12 final size:12
Alignment explanation
Indices: 805992--806026 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
805982 ACCAATTGTT
805992 TTCTTCTTCTTG
1 TTCTTCTTCTTG
*
806004 TTCTTGTTCTTG
1 TTCTTCTTCTTG
806016 TTCTTCTTCTT
1 TTCTTCTTCTT
806027 TTGTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.69
Consensus pattern (12 bp):
TTCTTCTTCTTG
Found at i:807285 original size:19 final size:19
Alignment explanation
Indices: 807261--807305 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
807251 TCAACATGCT
807261 TGGATTGTCCATGATAAAC
1 TGGATTGTCCATGATAAAC
807280 TGGATTGTCCATGATAAAC
1 TGGATTGTCCATGATAAAC
807299 TGGATTG
1 TGGATTG
807306 GCGCTCGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (19 bp):
TGGATTGTCCATGATAAAC
Found at i:810274 original size:54 final size:54
Alignment explanation
Indices: 810208--810496 Score: 377
Period size: 54 Copynumber: 5.4 Consensus size: 54
810198 TTTATTAAGA
* * * * ** *
810208 TGCACACGTAGTGCCTATACGGTCGTTCATCAACTCATGATTAATTTTGTGGGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGAT
* *
810262 TGCACACATAGTGCCTGTACGATTGTTCATCAA-TACATGATGAATTCCGT-TAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACT-CATGATGAATTCCGTGGA-T
* *
810316 TGCACACATAGTTCCTGTACGGTTGTTCATCAACACATGATGAATTCCGT-GACT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGA-T
* * * *
810370 TGCACACATAGTGCATGTACCGTTGTTCATCAACTCATAATGAATTACGTGGAT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGAT
* *
810424 TGCACACATAGTGCCTGTATGGTTGTTTATCAACTCATGATGAATTCCGTGGAT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGAT
810478 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
810497 GTACACATAG
Statistics
Matches: 205, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.00
54 202 0.99
55 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGAT
Found at i:815251 original size:2 final size:2
Alignment explanation
Indices: 815244--815274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
815234 ATTGTTTATC
815244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
815275 TAAATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:815745 original size:2 final size:2
Alignment explanation
Indices: 815738--815765 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
815728 TAATAATTTA
815738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815766 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:815770 original size:2 final size:2
Alignment explanation
Indices: 815765--815793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
815755 TATATATATA
815765 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
815794 TAAAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:827740 original size:19 final size:20
Alignment explanation
Indices: 827704--827743 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
827694 TTGGAAACTA
*
827704 ATGTTAGAATGTTGAAATTG
1 ATGTTACAATGTTGAAATTG
827724 ATGTTACAATG-TGAAATTG
1 ATGTTACAATGTTGAAATTG
827743 A
1 A
827744 ATCACTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.38
Consensus pattern (20 bp):
ATGTTACAATGTTGAAATTG
Found at i:828299 original size:23 final size:23
Alignment explanation
Indices: 828273--828318 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
828263 ATATAATTTA
828273 TGATTAGATGAAAATGCAAATTG
1 TGATTAGATGAAAATGCAAATTG
828296 TGATTAGATGAAAATGCAAATTG
1 TGATTAGATGAAAATGCAAATTG
828319 GTGAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (23 bp):
TGATTAGATGAAAATGCAAATTG
Found at i:829097 original size:25 final size:24
Alignment explanation
Indices: 829046--829098 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
829036 GAGTGTTGGT
*
829046 ATAAATAGCACTTTTCAGTGCGATG
1 ATAAATAGCACTTTT-AGTGCAATG
829071 ATAAATAGCACTTCTT-GTGCAAGTG
1 ATAAATAGCACTT-TTAGTGCAA-TG
829096 ATA
1 ATA
829099 TATGGAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 18 0.72
26 2 0.08
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (24 bp):
ATAAATAGCACTTTTAGTGCAATG
Found at i:830454 original size:31 final size:31
Alignment explanation
Indices: 830416--830475 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
830406 ATTAAAATTC
830416 ATTTAACTTAATTTGTTATATCGAAATATTT
1 ATTTAACTTAATTTGTTATATCGAAATATTT
830447 ATTTAACTTAATTTGTTATATCGAAATAT
1 ATTTAACTTAATTTGTTATATCGAAATAT
830476 CAAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (31 bp):
ATTTAACTTAATTTGTTATATCGAAATATTT
Found at i:833558 original size:30 final size:30
Alignment explanation
Indices: 833522--833586 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
833512 TAAAGTTTGG
* * *
833522 AAAAGTTTAGGGATCAAAAGGGTAATTTTT
1 AAAAGTTCAGGGACCAAAAGGGTAATCTTT
*
833552 AAAAGTTCAGGGACCAAAAGTGTAATCTTT
1 AAAAGTTCAGGGACCAAAAGGGTAATCTTT
833582 AAAAG
1 AAAAG
833587 CTATATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAAGTTCAGGGACCAAAAGGGTAATCTTT
Found at i:834787 original size:19 final size:20
Alignment explanation
Indices: 834744--834789 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
834734 ATCTATGATG
*
834744 GAAATTAATGTTAGAATGTT
1 GAAATTGATGTTAGAATGTT
834764 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
834783 GAAATTG
1 GAAATTG
834790 GATCACTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:836093 original size:26 final size:26
Alignment explanation
Indices: 836064--836170 Score: 142
Period size: 26 Copynumber: 4.1 Consensus size: 26
836054 GAGTCTTGGT
* *
836064 ATAATTAGCACTTTCGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGCAAGTG
* *
836090 ATAAATAACAATTTCGAGTGCAAGTG
1 ATAAATAGCACTTTCGAGTGCAAGTG
* * *
836116 ATAAATAGAACTTTTGAGTGCGAGTG
1 ATAAATAGCACTTTCGAGTGCAAGTG
*
836142 ATAAATGGCACTTTCGAGTGCAAGTG
1 ATAAATAGCACTTTCGAGTGCAAGTG
836168 ATA
1 ATA
836171 TATGACATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 68 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (26 bp):
ATAAATAGCACTTTCGAGTGCAAGTG
Found at i:836157 original size:52 final size:52
Alignment explanation
Indices: 836064--836170 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
836054 GAGTCTTGGT
* *
836064 ATAATTAGCACTTTCGAGTGCGAGTGATAAATAACAATTTCGAGTGCAAGTG
1 ATAAATAGAACTTTCGAGTGCGAGTGATAAATAACAATTTCGAGTGCAAGTG
* ** *
836116 ATAAATAGAACTTTTGAGTGCGAGTGATAAATGGCACTTTCGAGTGCAAGTG
1 ATAAATAGAACTTTCGAGTGCGAGTGATAAATAACAATTTCGAGTGCAAGTG
836168 ATA
1 ATA
836171 TATGACATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (52 bp):
ATAAATAGAACTTTCGAGTGCGAGTGATAAATAACAATTTCGAGTGCAAGTG
Found at i:837470 original size:37 final size:37
Alignment explanation
Indices: 837420--837493 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
837410 TACTATACTG
837420 TATGAATTCATTAAATGATCACACTAACAAATAAAAT
1 TATGAATTCATTAAATGATCACACTAACAAATAAAAT
*
837457 TATGAATTCATTAAATGATCATACTAACAAATAAAAT
1 TATGAATTCATTAAATGATCACACTAACAAATAAAAT
837494 CATGTGCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.31
Consensus pattern (37 bp):
TATGAATTCATTAAATGATCACACTAACAAATAAAAT
Found at i:841982 original size:2 final size:2
Alignment explanation
Indices: 841975--842006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
841965 TATTTTGACT
841975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
842007 AAGTGTAAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:842217 original size:22 final size:22
Alignment explanation
Indices: 842189--842234 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
842179 CCTGGTTATT
842189 ATATATATGACGTTTATCATGA
1 ATATATATGACGTTTATCATGA
*
842211 ATATATATGATGTTTATCATGA
1 ATATATATGACGTTTATCATGA
842233 AT
1 AT
842235 GTTATTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (22 bp):
ATATATATGACGTTTATCATGA
Found at i:842567 original size:17 final size:16
Alignment explanation
Indices: 842540--842571 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
842530 TAATAATAAT
842540 TATTATTATTAATATA
1 TATTATTATTAATATA
842556 TATTATTTATTAATAT
1 TATTA-TTATTAATAT
842572 TATAAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATTAATATA
Found at i:844630 original size:22 final size:19
Alignment explanation
Indices: 844588--844642 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 19
844578 TTCTTTTAAA
*
844588 TTTTTA-TTACTTATTATTT
1 TTTTTATTTA-TTAATATTT
844607 TTATATTATGTTATTAATATTT
1 TT-T-TTAT-TTATTAATATTT
844629 TTTTTATTTATTAA
1 TTTTTATTTATTAA
844643 AGTATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.29
20 5 0.16
21 4 0.13
22 10 0.32
23 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTATTTATTAATATTT
Found at i:846081 original size:8 final size:7
Alignment explanation
Indices: 846057--846098 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
846047 TTTTCATACA
846057 TGCA-TT
1 TGCATTT
846063 TGCATTT
1 TGCATTT
846070 TGCATCTT
1 TGCAT-TT
846078 TGCATTT
1 TGCATTT
* *
846085 TTCATTG
1 TGCATTT
846092 TGCATTT
1 TGCATTT
846099 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:846081 original size:15 final size:14
Alignment explanation
Indices: 846057--846098 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
846047 TTTTCATACA
846057 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
846070 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
846085 TTCATTGTGCATTT
1 TGCATTTTGCATTT
846099 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:854088 original size:50 final size:53
Alignment explanation
Indices: 853890--854090 Score: 194
Period size: 54 Copynumber: 3.8 Consensus size: 53
853880 AGAAATCTTG
* *** ** *
853890 GCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAACACTTTATGAACGTCTGA
1 GCAGAAACCACAGAAAA-GATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* *
853944 GCAAAAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCAC-AGAAAAGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
* * * * *
853998 GCAGAAGCCACAGAAAAGGATAAATGTGTTGCCAAGTGTTTTAC-ATC-TC-GA
1 GCAGAAACCACAGAAAA-GATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
**
854049 -CAGAAACCACAGGAAAAGATGAATGCATTGTCAAATGTTTTA
1 GCAGAAACCACA-GAAAAGATGAATGTGTTGTCAAATGTTTTA
854091 TGAACCAGTG
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
50 30 0.25
51 7 0.06
52 2 0.02
53 7 0.06
54 71 0.58
55 5 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (53 bp):
GCAGAAACCACAGAAAAGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
Found at i:854492 original size:22 final size:22
Alignment explanation
Indices: 854463--854517 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
854453 ATCTGCACTC
854463 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
854485 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
854507 TTCAAAGATGA
1 TTCAAAGATGA
854518 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:855216 original size:124 final size:122
Alignment explanation
Indices: 855075--855483 Score: 484
Period size: 124 Copynumber: 3.3 Consensus size: 122
855065 TGCCAGAAGT
**
855075 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTA
* * *
855140 ACCTTTTGCTCGACGCTATCACATAAGGAGATAGATCGGCATCAACTTTTCCAGAGAAA
66 ACCTTTTGCT-GACTCTATCACAGAAGGAGATAGATC-GCATCAACATTTCCAGAGAAA
* *
855199 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTA
* * * * * * **
855264 ACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGA-AGT
66 ACCTTTTGC-TGACTCTATCACAGAAGGAGATAGA-TCGCATCAACATTTCCAGAGAAA
* * *
855322 GTTCATAATGAGAAGAACTCATCTGAAGGAGAAAAGAAGAAGTTCATAATGAGAAGAGCTTATTT
1 GTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTT
* * * * * **
855387 AACATTTTGAATGACTCTATCACAGAAGGAAATAGGTC-CA-CATCATCCCCAGCAGAAA
65 AACCTTTTG-CTGACTCTATCACAGAAGGAGATAGATCGCATCAACATTTCCAG-AGAAA
* *
855445 GTTCATAATGAGAAGAACTCATCTAAAGAAAG-AGAAGAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
855484 TTTATTCAAC
Statistics
Matches: 241, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
121 14 0.06
122 3 0.01
123 61 0.25
124 161 0.67
125 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (122 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTTA
ACCTTTTGCTGACTCTATCACAGAAGGAGATAGATCGCATCAACATTTCCAGAGAAA
Found at i:855628 original size:3 final size:3
Alignment explanation
Indices: 855622--855690 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
855612 TTACCCATTT
* *
855622 TTA TTA TTA TTTA TTA TAA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
855668 ATA TATA TTA TTTA TTA ATA TTA
1 TTA T-TA TTA -TTA TTA TTA TTA
855691 CAAAACCCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
3 46 0.84
4 9 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:863564 original size:183 final size:181
Alignment explanation
Indices: 863112--863578 Score: 638
Period size: 183 Copynumber: 2.6 Consensus size: 181
863102 CCATTCAAAT
* * * ** *
863112 ATGTATCGATACATAATAATATATCAGGCAAAAATATGACAAAACCGGGTTCAATATGAC-AACC
1 ATGTATCGATACATAACAATATAACA-GTAAAAATATGACAAAACCGATTTCATTATGACAAACC
* *
863176 GGTAAAGCGCTACCACATATGTTGAAGGTATTC-ATACCATTCAAATAAGTATCGATACTTTTGG
65 GGTAAAGCGCAAACACATATGTTGAAGGTA-TCGATACCATTCAAATAAGTATCGATACTTTTGG
* ** *
863240 AATTTAAAAGAAAAGTAATAATAGTGCCTATAAAGTATCGATACTTTATAAAC
129 AATTTAAAAGAAAAGCAATAATAGCACCTATAAAGTACCGATACTTTATAAAC
*
863293 ATGTATCGATACATAACAATATAACAGTTAAAAATATGACAAAACC-AGTTTCATTATGAGAAAA
1 ATGTATCGATACATAACAATATAACAG-TAAAAATATGACAAAACCGA-TTTCATTATGA-CAAA
* * *
863357 CCGGTAAAGAG-ATACTATATATGTTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTT
63 CCGGTAAAGCGCAAAC-ACATATGTTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTT
863421 GGAATTTAAAAGAACAA-CAATAATAGCACCTATAAAGTACCGATACTTTATAAAC
127 GGAATTTAAAAGAA-AAGCAATAATAGCACCTATAAAGTACCGATACTTTATAAAC
*
863476 ATGTATCGATACATAACAATATAACATGTAAAAATATGAAAAAACCGATTTCATTATGACCAAAC
1 ATGTATCGATACATAACAATATAACA-GTAAAAATATGACAAAACCGATTTCATTATGA-CAAAC
** *
863541 CGGTAAAGCGCAAACGGATATGTTGAAAGTATCGATAC
64 CGGTAAAGCGCAAACACATATGTTGAAGGTATCGATAC
863579 TTTAATAAGT
Statistics
Matches: 252, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
180 1 0.00
181 50 0.20
182 3 0.01
183 191 0.76
184 7 0.03
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (181 bp):
ATGTATCGATACATAACAATATAACAGTAAAAATATGACAAAACCGATTTCATTATGACAAACCG
GTAAAGCGCAAACACATATGTTGAAGGTATCGATACCATTCAAATAAGTATCGATACTTTTGGAA
TTTAAAAGAAAAGCAATAATAGCACCTATAAAGTACCGATACTTTATAAAC
Found at i:865701 original size:46 final size:45
Alignment explanation
Indices: 865609--865823 Score: 328
Period size: 46 Copynumber: 4.8 Consensus size: 45
865599 ATAAATTGGC
*
865609 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
865653 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGTA
* *
865699 AAATAAGCTTACGAGCTTATGGAAT-AATGGAAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
865743 AAATAATCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
865789 AAATAAGCTTACGAGCTTAT-GAGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGA-ATAAATGGTAAG
865824 AGATTTTATC
Statistics
Matches: 156, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
44 62 0.40
45 17 0.11
46 77 0.49
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:865725 original size:90 final size:90
Alignment explanation
Indices: 865609--865809 Score: 357
Period size: 90 Copynumber: 2.2 Consensus size: 90
865599 ATAAATTGGC
* *
865609 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATTAGTAAAATAAGCTTACGAGCTTATG
865674 GAATTAAATGGTAAGTATATTGGTA
66 GAATTAAATGGTAAGTATATTGGTA
*
865699 AAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATTAGTAAAATAATCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATTAGTAAAATAAGCTTACGAGCTTATG
* *
865764 GGATTAAATGGTAAGTATTTTGGTA
66 GAATTAAATGGTAAGTATATTGGTA
865789 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
865810 AGATAAATGG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 106 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGAAAGTATATTAGTAAAATAAGCTTACGAGCTTATG
GAATTAAATGGTAAGTATATTGGTA
Found at i:868143 original size:444 final size:443
Alignment explanation
Indices: 867108--868426 Score: 1921
Period size: 447 Copynumber: 3.0 Consensus size: 443
867098 AGTTTCAATA
* * * *
867108 TAAATAACTTAATAGGTAAAAAATTGACAAAACCGATTTCCATAACTGCGCCTATAAAGTATCGA
1 TAAATAACATAATAGGTAAAAAATTGACAAAACCAATTTCCATAATTGTGCCTATAAAGTATCGA
* ** * * *
867173 TGCAAATATGAAGAGTATTGATTCTTAAAACTTCGAAACCGATTACTTTAAAGTAATAGATAAAT
66 TACACGTATGAAAAGTATTGATTCTTAAAACTTCGAAACCTATTACTTTAAAGTAATAGGTAAAT
*
867238 ATATAATGTAAGCTGTAAAAATATATCAGTTTAATGGTAAAATATGTTTATATAAAGTATCGATA
131 ATACAATGTAAGCTGTAAAAATATATCAGTTTAATGGTAAAATATGTTTATATAAAGTATCGATA
* * * * *
867303 GTTTTGGTATATGTATTGATACTTTTTGTTCAGTATGCTTCCC-AAACTAGATGCACGTAGGAAG
196 CTTTTGGTATATGTATCGATACTTTTTGTCCA-TACGCTTCCCAAAACTAGATGCACGTATGAAG
* * * *
867367 TATCGATACCTATGATACATGTATCGATACATGA-CATTATAACATGTTAAAAATTGATAAAACT
260 TATCGATACCTATGATACATGTATCGATACATGATGA-TATAAAAGGTTAAAAATTGATAAAACC
* * * *
867431 GATTTCAATATGATAAAAATGGTAAATAGCTACCGATTTTGAAAAAAAATGAAACGTCTCGAAAG
324 GATTTCAATATGACAAAAAAGGTAAATAGCTACCG-TTTTG-AAAAAAACGAAACGTCTCGCAAG
* * *
867496 TATTGATACCGTACATAAAAGTATCGATACTTCTGTAAGGGTAATGGTATCAATTTT
387 TATCGATACCGTACATAAAAGTATTGATACTTTTGTAAGGGTAATGGTATCAATTTT
* * *** *
867553 AAAATAACATAATAGGTTCATATTTTTGACAAAACCAGTTTCCATAATTGTGCCTATAAAGTATC
1 TAAATAACATAATAGG-T-AAAAAATTGACAAAACCAATTTCCATAATTGTGCCTATAAAGTATC
* *
867618 GATACACGTATGAAAAGTATTGATTCTTAAAACTTCGAAATCTATTACTTTAAAGTAATATGTAA
64 GATACACGTATGAAAAGTATTGATTCTTAAAACTTCGAAACCTATTACTTTAAAGTAATAGGTAA
*
867683 ATATACAATGTAAGCTGTAAAAATATA-CTAGTTTAATGGTAAAATAAGTTTATATAAAGTATCG
129 ATATACAATGTAAGCTGTAAAAATATATC-AGTTTAATGGTAAAATATGTTTATATAAAGTATCG
* * *
867747 ATACTTTTGCTATATGTATCGATACTTTTTTGTCCATACGCTTCCCAAAACTAGATGCACTTATA
193 ATACTTTTGGTATATGTATCGATAC-TTTTTGTCCATACGCTTCCCAAAACTAGATGCACGTATG
* *
867812 AAGTATCGATACCTATGGTACATGTATCGATACATGATGACATAAAAGGTTAAAAATTGATAAAA
257 AAGTATCGATACCTATGATACATGTATCGATACATGATGATATAAAAGGTTAAAAATTGATAAAA
* *
867877 CCGATTTCAATATGACAAAAAAGGTAAATACCTACCAGTTTTG-AAAAAACGAAATGTCTCGCAA
322 CCGATTTCAATATGACAAAAAAGGTAAATAGCTACC-GTTTTGAAAAAAACGAAACGTCTCGCAA
* * *
867941 GTATCAATATCGTACATAAAAGTATTGATACTTTTGTAAGGGTAATGGTATCGATTTT
386 GTATCGATACCGTACATAAAAGTATTGATACTTTTGTAAGGGTAATGGTATCAATTTT
* * * *
867999 TAAATAACATAACAGGTAAAAAATTGACAAATCCAATTTCCATAATTGTGCCTATAAAGTTTGGA
1 TAAATAACATAATAGGTAAAAAATTGACAAAACCAATTTCCATAATTGTGCCTATAAAGTATCGA
* *
868064 TACACGTATGAAAAGTATCGATTCTTAAAACTTTGAAACCTATTACTTTAAAGTAATAGGTAAAT
66 TACACGTATGAAAAGTATTGATTCTTAAAACTTCGAAACCTATTACTTTAAAGTAATAGGTAAAT
* * *
868129 ATACAATGTAAGCTGTAAAAATATGTCGGCTTAATGGTAAAATATGTTTATATAAAGTATCGATA
131 ATACAATGTAAGCTGTAAAAATATATCAGTTTAATGGTAAAATATGTTTATATAAAGTATCGATA
868194 CTTTTGGTATATGTATCGATACTTTTTGTCCATACGCTTCCCAAAACTAGATGCACGTATGAAGT
196 CTTTTGGTATATGTATCGATACTTTTTGTCCATACGCTTCCCAAAACTAGATGCACGTATGAAGT
*
868259 ATCGATACCTATGATACATGTATCGATACATGATGATATAAAAGGTTAAAAATTGATAAAACCGG
261 ATCGATACCTATGATACATGTATCGATACATGATGATATAAAAGGTTAAAAATTGATAAAACCGA
**
868324 TTTCAATAT-ACAATGTAACCGGTAAATAGCTACCGGTTTTGAAAAAAACGAAACGTCTC-CAAA
326 TTTCAATATGACAA---AAAAGGTAAATAGCTACC-GTTTTGAAAAAAACGAAACGTCTCGC-AA
* * *
868387 GTATCGATACCATACACAAAAGTATTGATACTTTGGTAAG
386 GTATCGATACCGTACATAAAAGTATTGATACTTTTGTAAG
868427 AGTTTCAATA
Statistics
Matches: 781, Mismatches: 80, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
442 4 0.01
443 112 0.14
444 181 0.23
445 38 0.05
446 139 0.18
447 186 0.24
448 119 0.15
449 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (443 bp):
TAAATAACATAATAGGTAAAAAATTGACAAAACCAATTTCCATAATTGTGCCTATAAAGTATCGA
TACACGTATGAAAAGTATTGATTCTTAAAACTTCGAAACCTATTACTTTAAAGTAATAGGTAAAT
ATACAATGTAAGCTGTAAAAATATATCAGTTTAATGGTAAAATATGTTTATATAAAGTATCGATA
CTTTTGGTATATGTATCGATACTTTTTGTCCATACGCTTCCCAAAACTAGATGCACGTATGAAGT
ATCGATACCTATGATACATGTATCGATACATGATGATATAAAAGGTTAAAAATTGATAAAACCGA
TTTCAATATGACAAAAAAGGTAAATAGCTACCGTTTTGAAAAAAACGAAACGTCTCGCAAGTATC
GATACCGTACATAAAAGTATTGATACTTTTGTAAGGGTAATGGTATCAATTTT
Found at i:871100 original size:226 final size:226
Alignment explanation
Indices: 870698--871205 Score: 718
Period size: 226 Copynumber: 2.2 Consensus size: 226
870688 TTTACATTTA
* * *
870698 GTTGATAATACTGATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCTAAGGCCC
1 GTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCCAAAGCCC
* * *
870763 CGTCATCTTTAATAATGTGCAACATATTACGTTACATAAGCGCTACCTAGTATGTTATTATGCTT
66 CATCATCTTTAATAAAGTGCAACATATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTT
* *
870828 GATAATGTTTCCAGTAATTAACCGGTTATGTTATCATCGAATTTCTAAGGCTCTATCAGCTTAAA
131 GATAATGTTTCCAGTAATTAACCGGTTATGTTATCATCGAATTTCTAAGACTCTATCAACTTAAA
870893 ATGTGGTAACATTTTAAGTGTTACCTAATAT
196 ATGTGGTAACATTTTAAGTGTTACCTAATAT
* * *
870924 GTTGATAATACAAATAACAAATTAAGTAATTAACCTATTTTTTTATCGTC-AGATTTCCAAAGCC
1 GTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGA-ATTTCCAAAGCC
*
870988 CCATCATCTTTAA-AAAG-GCAATATCTATTACGTTACATAAGCGCTACCTAATATGTTATTATG
65 CCATCATCTTTAATAAAGTGCAACA--TATTACGTTACATAAGCGCTACCTAATATGTTATTATG
* * * *
871051 CTTGATAATGTTTCCAGTAATTAACTGGTTATGTTATCGTTGGATTTCTAAGACTCTATCAACTT
128 CTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCATCGAATTTCTAAGACTCTATCAACTT
* * * *
871116 AAACTTTGGTAATATTTTATGTGTTACCTAATAT
193 AAAATGTGGTAACATTTTAAGTGTTACCTAATAT
* * ** * *
871150 GTTGATAATATTAATAAC-AATATAAGTAATTAATCGGTTATGTTATCGTCGAATTT
1 GTTGATAATACTAATAACAAAT-TAAGTAATTAACCTATTTTGTTATCATCGAATTT
871206 TTAAGGCTCT
Statistics
Matches: 250, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
224 5 0.02
225 7 0.03
226 237 0.95
227 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (226 bp):
GTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCATCGAATTTCCAAAGCCC
CATCATCTTTAATAAAGTGCAACATATTACGTTACATAAGCGCTACCTAATATGTTATTATGCTT
GATAATGTTTCCAGTAATTAACCGGTTATGTTATCATCGAATTTCTAAGACTCTATCAACTTAAA
ATGTGGTAACATTTTAAGTGTTACCTAATAT
Found at i:871225 original size:108 final size:107
Alignment explanation
Indices: 871066--871307 Score: 385
Period size: 108 Copynumber: 2.2 Consensus size: 107
871056 TAATGTTTCC
* * * *
871066 AGTAATTAACTGGTTATGTTATCGTTGGATTTCTAAGACTCTATCAACTTAAACTTTGGTAATAT
1 AGTAATTAAC-GGTTATGTTATCGTCGAATTTCTAAGACTCTATCAACTTAAACTTCGGTAACAT
871131 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
65 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
* * *
871174 AGTAATTAATCGGTTATGTTATCGTCGAATTTTTAAGGCTCTATCAGCTTAAACTTCGGTAACAT
1 AGTAATTAA-CGGTTATGTTATCGTCGAATTTCTAAGACTCTATCAACTTAAACTTCGGTAACAT
871239 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
65 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
*
871282 AGTAATTAACCGATTATGTTATCGTC
1 AGTAATTAA-CGGTTATGTTATCGTC
871308 AGATTTCCAA
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 123 0.99
109 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (107 bp):
AGTAATTAACGGTTATGTTATCGTCGAATTTCTAAGACTCTATCAACTTAAACTTCGGTAACATT
TTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
Found at i:871328 original size:108 final size:106
Alignment explanation
Indices: 871066--871334 Score: 376
Period size: 108 Copynumber: 2.5 Consensus size: 106
871056 TAATGTTTCC
* * * * * *
871066 AGTAATTAACTGGTTATGTTATCGTTGGATTTCTAAGACTCTATCAACTTAAACTTTGGTAATAT
1 AGTAATTAACCGGTTATGTTATCG-TCGATTTCAAAG-CTCTATCAGCTTAAACTTCGGTAACAT
871131 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
64 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
* * *
871174 AGTAATTAATCGGTTATGTTATCGTCGAATTTTTAAGGCTCTATCAGCTTAAACTTCGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCG-A-TTTCAAAGCTCTATCAGCTTAAACTTCGGTAACAT
871239 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
64 TTTATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
* * *
871282 AGTAATTAACCGATTATGTTATCGTCAGATTTCCAAAGCCCCATCAGCTTAAA
1 AGTAATTAACCGGTTATGTTATCGTC-GATTT-CAAAGCTCTATCAGCTTAAA
871335 AAGGCGCTAC
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
107 5 0.04
108 131 0.92
109 6 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (106 bp):
AGTAATTAACCGGTTATGTTATCGTCGATTTCAAAGCTCTATCAGCTTAAACTTCGGTAACATTT
TATGTGTTACCTAATATGTTGATAATATTAATAACAATATA
Found at i:879662 original size:59 final size:59
Alignment explanation
Indices: 879591--879999 Score: 577
Period size: 59 Copynumber: 6.9 Consensus size: 59
879581 AAATTCAATA
* * * * *
879591 GGAAATTCATACAATTAGTGTGATTTCCTTATCTTTTTAGCACACGAAGTGCCATATCT
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* *
879650 GGAAATTCATACACTTAGTATAATTTCCTTTTCATTTTAGCACACGAAGTGTCCTATCT
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * * * *
879709 AGAAATTCATACACTTAGTATGATTTCCTTATTATTTTAGCACAAGAAGTGCCCTATCA
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * * *
879768 GGAAATTCATAAACTTAGTATAATTTACTTATCATTTTAGCACACGAAGTGTCCTATTT
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
*
879827 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACATGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * * *
879886 GGAAATAT-ATACACTTAGTATGATTTCCTTAACATTTTAGCGCACGAAGTGCCCTATTT
1 GGAAAT-TCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * **
879945 GGAAATTTATACGCTTAGTATAATTTCCTTATCATTTTAGCACACTTAGTGCCCT
1 GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCT
880000 TTTGGTAATC
Statistics
Matches: 309, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
58 1 0.00
59 307 0.99
60 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATAATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
Found at i:880361 original size:22 final size:21
Alignment explanation
Indices: 880319--880375 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
880309 TGGCTCTTTA
*
880319 GTATCAATAC-CCCTACCATG
1 GTATCGATACTCCCTACCATG
*
880339 GTATCGATACTACCCTACTATG
1 GTATCGATACT-CCCTACCATG
*
880361 GTATTGATACTCCCT
1 GTATCGATACTCCCT
880376 TTCAGTATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.28
21 4 0.12
22 19 0.59
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (21 bp):
GTATCGATACTCCCTACCATG
Found at i:882505 original size:18 final size:18
Alignment explanation
Indices: 882482--882527 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
882472 AGGCATTTGA
* *
882482 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
*
882500 TCCTCTGCTCGTTCTTGT
1 TCCTCTGCTCGTGCTTGT
882518 TCCTCGTGCT
1 TCCTC-TGCT
882528 ATTCTGGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.00, C:0.30, G:0.22, T:0.48
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:882532 original size:18 final size:19
Alignment explanation
Indices: 882495--882542 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
882485 TCTGGTTGTG
*
882495 CTTGTTCCTC-TGCTCGTT
1 CTTGTTCCTCGTGCTCATT
882513 CTTGTTCCTCGTGCT-ATT
1 CTTGTTCCTCGTGCTCATT
* *
882531 CTGGTTCATCGT
1 CTTGTTCCTCGT
882543 CGGAGTCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.04, C:0.29, G:0.19, T:0.48
Consensus pattern (19 bp):
CTTGTTCCTCGTGCTCATT
Found at i:884190 original size:22 final size:23
Alignment explanation
Indices: 884099--884204 Score: 137
Period size: 23 Copynumber: 4.7 Consensus size: 23
884089 CCAGAACCCT
* * *
884099 AGGGGGTATCGATTCCCC-T-AC
1 AGGGGGAATCGGTTCCCCTTCAA
*
884120 AGGGGGAACCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
884143 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
884166 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
884188 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
884205 TCTGCACTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
21 15 0.20
22 17 0.22
23 44 0.58
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:895057 original size:2 final size:2
Alignment explanation
Indices: 895045--895106 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
895035 CCTAAATACT
895045 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
895086 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
895107 GTGTGTGTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:896726 original size:30 final size:29
Alignment explanation
Indices: 896696--896860 Score: 109
Period size: 29 Copynumber: 5.7 Consensus size: 29
896686 ATTGTCTCCT
896696 TTTATTATAATTTATAAAAGGTTTTATCC
1 TTTATTATAATTTATAAAAGGTTTTATCC
* * * * *
896725 TTTAATGTAATTTGTAAATAGTTTTGTAT-T
1 TTTATTATAATTTATAAA-AGGTTT-TATCC
** * *
896755 TTTATTATAATTTATAAATTGTTTTGTAC
1 TTTATTATAATTTATAAAAGGTTTTATCC
* *** * *
896784 TTTATTGTAATTTATAAATTATTTTGTAC
1 TTTATTATAATTTATAAAAGGTTTTATCC
* * * *
896813 TTTATTGTAATTTGTAACAA-TTTTTTTCC
1 TTTATTATAATTTATAA-AAGGTTTTATCC
*
896842 TTTATTATAACTTATAAAA
1 TTTATTATAATTTATAAAA
896861 TAATCTTCCT
Statistics
Matches: 109, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
28 4 0.04
29 81 0.74
30 21 0.19
31 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTATTATAATTTATAAAAGGTTTTATCC
Found at i:896787 original size:59 final size:58
Alignment explanation
Indices: 896695--896825 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 58
896685 AATTGTCTCC
* *
896695 TTTTATTATAATTTATAAAAGGTTTTATCCTTTAATGTAATTTGTAAA-TAGTTTTGTA
1 TTTTATTATAATTTATAAAAGGTTTTATACTTTAATGTAATTTATAAATTA-TTTTGTA
** * *
896753 TTTTTATTATAATTTATAAATTGTTTTGTACTTTATTGTAATTTATAAATTATTTTGTA
1 -TTTTATTATAATTTATAAAAGGTTTTATACTTTAATGTAATTTATAAATTATTTTGTA
* *
896812 CTTTATTGTAATTT
1 TTTTATTATAATTT
896826 GTAACAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
58 12 0.19
59 49 0.78
60 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (58 bp):
TTTTATTATAATTTATAAAAGGTTTTATACTTTAATGTAATTTATAAATTATTTTGTA
Found at i:896846 original size:58 final size:57
Alignment explanation
Indices: 896696--896859 Score: 161
Period size: 59 Copynumber: 2.8 Consensus size: 57
896686 ATTGTCTCCT
* * * * *
896696 TTTATTATAATTTATAAAAGGTTTTATCCTTTAATGTAATTTGTAAATAGTTTTGTATT
1 TTTATTATAATTTAT-AAA-TTTTTTTCCTTTATTGTAATTTATAAATAGTTTTGTATC
*
896755 TTTATTATAATTTATAAATTGTTTTGTACTTTATTGTAATTTATAAATTA-TTTTGTA-C
1 TTTATTATAATTTATAAATT-TTTT-TCCTTTATTGTAATTTATAAA-TAGTTTTGTATC
* * * *
896813 TTTATTGTAATTTGTAACAATTTTTTTCCTTTATTATAACTTATAAA
1 TTTATTATAATTTAT-A-AATTTTTTTCCTTTATTGTAATTTATAAA
896860 ATAATCTTCC
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 37 0.42
59 45 0.51
60 6 0.07
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (57 bp):
TTTATTATAATTTATAAATTTTTTTCCTTTATTGTAATTTATAAATAGTTTTGTATC
Found at i:904118 original size:20 final size:20
Alignment explanation
Indices: 904089--904141 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
904079 GATTTTCCAT
* *
904089 AATCACAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
*
904109 AATCGTAACGCGAACATATA
1 AATCGCAACGCGAACATATA
904129 AATCGCAACGCGA
1 AATCGCAACGCGA
904142 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:904166 original size:20 final size:21
Alignment explanation
Indices: 904128--904302 Score: 136
Period size: 20 Copynumber: 8.6 Consensus size: 21
904118 GCGAACATAT
904128 AAATCGCAACGCG-ATTCTG-A
1 AAATCGCAACGCGTA-TCTGTA
** *
904148 CTATCGCAACGAGTATCTGTA
1 AAATCGCAACGCGTATCTGTA
*
904169 AAATCGCAACGCGTATCCGT-
1 AAATCGCAACGCGTATCTGTA
*
904189 AAATCGTAACGCGTATCTGT-
1 AAATCGCAACGCGTATCTGTA
* *
904209 AAATCGCAACGAGAATAC-GT-
1 AAATCGCAACGCGTAT-CTGTA
* * *
904229 AAATCGCAATGTGTATCCGT-
1 AAATCGCAACGCGTATCTGTA
*
904249 AAATCGCAACGAC-AATAC-GTA
1 AAATCGCAACG-CGTAT-CTGTA
*
904270 AAATCGCAACGCGTATCCGT-
1 AAATCGCAACGCGTATCTGTA
904290 AAATCGCAACGCG
1 AAATCGCAACGCG
904303 ATTTTTAAAG
Statistics
Matches: 127, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.01
20 91 0.72
21 35 0.28
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
AAATCGCAACGCGTATCTGTA
Found at i:904230 original size:40 final size:40
Alignment explanation
Indices: 904150--904300 Score: 194
Period size: 40 Copynumber: 3.7 Consensus size: 40
904140 GATTCTGACT
* * * * *
904150 ATCGCAACGAGTATCTGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATACGTAA
* *
904191 ATCGTAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* * *
904231 ATCGCAATGTGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
904272 ATCGCAACGCGTATCCGTAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCGCAACG
904301 CGATTTTTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 52 0.54
41 45 0.46
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:904920 original size:21 final size:21
Alignment explanation
Indices: 904859--904937 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
904849 TTCTATACTT
904859 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
904879 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
904899 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
904920 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
904938 TCACAACGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:904952 original size:33 final size:33
Alignment explanation
Indices: 904915--904994 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
904905 GCAACGAGAG
904915 AAATGAAAATCGCAACGAGAGAATCACAACGCA
1 AAATGAAAATCGCAACGAGAGAATCACAACGCA
* * *
904948 AAATGAAAATCGCAACGAGATAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCACAACGCA
**
904981 AAACCAAAATCGCA
1 AAATGAAAATCGCA
904995 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCACAACGCA
Found at i:905068 original size:20 final size:20
Alignment explanation
Indices: 905039--905093 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
905029 TGCGATTTTA
905039 ATTT-CGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGTC
905058 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGTC
*
905078 A-TTCTCTCGTTGCGAT
1 ATTTC-CGCGTTGCGAT
905094 TTTTATTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTCCGCGTTGCGATAGTC
Found at i:905975 original size:21 final size:22
Alignment explanation
Indices: 905951--905993 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
905941 AATTTCTATA
905951 TAATGTTTTCAA-AATTA-TAAT
1 TAAT-TTTTCAACAATTACTAAT
*
905972 TAATTTTTTAACAATTACTAAT
1 TAATTTTTCAACAATTACTAAT
905994 GTTTGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTTTTCAACAATTACTAAT
Found at i:908476 original size:14 final size:14
Alignment explanation
Indices: 908457--908492 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
908447 ATTGTTTAAT
908457 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
908471 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
908485 TGATTTGT
1 TGATTTGT
908493 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:908621 original size:19 final size:18
Alignment explanation
Indices: 908599--908657 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
908589 AAAAATGACT
908599 ATCGCAATTCGAAATGAAA
1 ATCGCAA-TCGAAATGAAA
*
908618 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
908632 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
908651 ATCGCAA
1 ATCGCAA
908658 CGCGAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:908662 original size:19 final size:19
Alignment explanation
Indices: 908608--908683 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
908598 TATCGCAATT
908608 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAACG
* *
908625 CG--A-GAGAATCGCAATG
1 CGAAATGAAAATCGCAACG
908641 CGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCAACG
*
908660 CGAAACT-AAAATGGCAACG
1 CGAAA-TGAAAATCGCAACG
908679 CGAAA
1 CGAAA
908684 CTAAATTCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 32 0.65
20 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
CGAAATGAAAATCGCAACG
Found at i:908684 original size:19 final size:19
Alignment explanation
Indices: 908631--908693 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
908621 GCAACGAGAG
*
908631 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
908650 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
908669 AATGGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
908688 ATTCGC
1 AATCGC
908694 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 38 0.97
20 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:908711 original size:19 final size:19
Alignment explanation
Indices: 908689--908846 Score: 129
Period size: 19 Copynumber: 8.7 Consensus size: 19
908679 CGAAACTAAA
908689 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
908708 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
908723 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
908741 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
908756 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
908774 TTCGCATTGTGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
908793 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATTTTCAT
908813 ATTCGCGTTGCGATTTTCAT
1 -TTCGCGTTGCGATTTTCAT
*
908833 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
908847 CTCTCGTTGC
Statistics
Matches: 108, Mismatches: 19, Indels: 24
0.72 0.13 0.16
Matches are distributed among these distances:
14 17 0.16
16 6 0.06
17 6 0.06
19 47 0.44
20 30 0.28
21 2 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:908735 original size:33 final size:33
Alignment explanation
Indices: 908693--908782 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
908683 ACTAAATTCG
*
908693 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
908726 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
908759 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
908783 TGATAGTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:908878 original size:53 final size:56
Alignment explanation
Indices: 908759--908879 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 56
908749 GCGATTCTCT
* * *
908759 CGTTGCGATTTTCATTTCGCATTGTGATAGTCATTTCCGCGTTGCGATATTCATATTCG
1 CGTTGCGATTTTCATTTCGCATTGCGATA-TC--TTCCGCGTTGCGATAGTAATATTCG
*
908818 CGTTGCGATTTTCATTTCGCATTGCGAT-TC-T-CTCGTTGCGATAGTAAT-TTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATT-CG
908871 CGTTGCGAT
1 CGTTGCGAT
908880 AGACATTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
52 2 0.04
53 25 0.44
54 1 0.02
57 2 0.04
59 27 0.47
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (56 bp):
CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATTCG
Found at i:908925 original size:20 final size:20
Alignment explanation
Indices: 908852--908925 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
908842 CGATTCTCTC
* *
908852 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
908872 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
908892 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
908913 GTTGCGATAGTCA
1 GTTGCGATAGTCA
908926 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:911428 original size:24 final size:24
Alignment explanation
Indices: 911394--911447 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
911384 CTGAAAAATC
*
911394 ATCAAAATCCGAGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
911418 ATCAAAGTCCGGGTATTGACGAAG
1 ATCAAAATCCGAGTATTGACCAAG
911442 ATCAAA
1 ATCAAA
911448 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:912356 original size:21 final size:21
Alignment explanation
Indices: 912332--912377 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
912322 TATTCGCATT
912332 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * * *
912353 GCGAATTTGGGAAATTGCAAT
1 GCGAATTAGGAAAATCGCAAC
912374 GCGA
1 GCGA
912378 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:918917 original size:14 final size:14
Alignment explanation
Indices: 918888--918944 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
918878 CATTCGTGAA
918888 CGTTCAATTATATGTT
1 CGTTC-ATT-TATGTT
918904 CGTTCATTTATGTT
1 CGTTCATTTATGTT
***
918918 CGTTTGGTTATGTT
1 CGTTCATTTATGTT
*
918932 TGTTCA-TTATGTT
1 CGTTCATTTATGTT
918945 TAATCCAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
13 7 0.20
14 20 0.57
15 3 0.09
16 5 0.14
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:919717 original size:9 final size:9
Alignment explanation
Indices: 919703--919792 Score: 63
Period size: 10 Copynumber: 9.3 Consensus size: 9
919693 AGGGCTGGAA
919703 ACCGGTTTG
1 ACCGGTTTG
*
919712 ACCGGTTTTCA
1 ACCGG-TTT-G
919723 ACCGGTTCTG
1 ACCGGTT-TG
*
919733 ACCGGTTTT
1 ACCGGTTTG
*
919742 ACCAGTTTCG
1 ACCGGTTT-G
*
919752 ACCGGTTCG
1 ACCGGTTTG
*
919761 AACCGGTCTG
1 -ACCGGTTTG
*
919771 AACCGGTCTG
1 -ACCGGTTTG
*
919781 ACCGGTCTG
1 ACCGGTTTG
919790 ACC
1 ACC
919793 CGACCCGACT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
9 26 0.39
10 35 0.52
11 6 0.09
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:919736 original size:21 final size:20
Alignment explanation
Indices: 919702--919758 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
919692 GAGGGCTGGA
919702 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
919722 AACCGGTTCTGACCGGTTTT-
1 AACCGGTT-TGACCGGTTTTC
*
919742 -ACCAGTTTCGACCGGTT
1 AACCGGTTT-GACCGGTT
919759 CGAACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 14 0.41
20 8 0.24
21 11 0.32
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:919738 original size:10 final size:10
Alignment explanation
Indices: 919703--919792 Score: 59
Period size: 9 Copynumber: 9.3 Consensus size: 10
919693 AGGGCTGGAA
919703 ACCGGTT-TG
1 ACCGGTTCTG
* *
919712 ACCGGTTTTCA
1 ACCGGTTCT-G
919723 ACCGGTTCTG
1 ACCGGTTCTG
*
919733 ACCGGTT-TT
1 ACCGGTTCTG
*
919742 ACCAGTT-TCG
1 ACCGGTTCT-G
919752 ACCGGTTC-G
1 ACCGGTTCTG
919761 AACCGG-TCTG
1 -ACCGGTTCTG
919771 AACCGG-TCTG
1 -ACCGGTTCTG
919781 ACCGG-TCTG
1 ACCGGTTCTG
919790 ACC
1 ACC
919793 CGACCCGACT
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
9 30 0.44
10 30 0.44
11 8 0.12
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.28
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:919755 original size:29 final size:30
Alignment explanation
Indices: 919702--919767 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
919692 GAGGGCTGGA
*
919702 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCAGTTTTCAACCGGTTC-G
* *
919733 -ACCGGTTTTACCAG-TTTCGACCGGTTCG
1 AACCGGTTTGACCAGTTTTCAACCGGTTCG
919761 AACCGGT
1 AACCGGT
919768 CTGAACCGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 18 0.58
30 12 0.39
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCAGTTTTCAACCGGTTCG
Found at i:919799 original size:5 final size:5
Alignment explanation
Indices: 919789--919854 Score: 84
Period size: 5 Copynumber: 13.8 Consensus size: 5
919779 TGACCGGTCT
* *
919789 GACCC GACCC GA-CT GACCC GACCC GACCC GA-CT GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
*
919837 GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACC
919855 GTTGACCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
4 9 0.17
5 43 0.83
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:919804 original size:14 final size:14
Alignment explanation
Indices: 919787--919853 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
919777 TCTGACCGGT
919787 CTGACCCGACCCGA
1 CTGACCCGACCCGA
919801 CTGACCCGA-CC--
1 CTGACCCGACCCGA
*
919812 C-GACCCGA-CTGA
1 CTGACCCGACCCGA
*
919824 CCCGACCCGACCCGA
1 -CTGACCCGACCCGA
919839 CTGACCCGACCCGA
1 CTGACCCGACCCGA
919853 C
1 C
919854 CGTTGACCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 8 0.18
11 1 0.02
13 3 0.07
14 30 0.67
15 3 0.07
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.06
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:919813 original size:19 final size:19
Alignment explanation
Indices: 919789--919854 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
919779 TGACCGGTCT
919789 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
919808 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
919827 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
919846 GACCCGACC
1 GACCCGACC
919855 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.05
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:919875 original size:6 final size:7
Alignment explanation
Indices: 919851--919880 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
919841 GACCCGACCC
919851 GACCGTT
1 GACCGTT
919858 GACCGTT
1 GACCGTT
919865 GACCG-T
1 GACCGTT
919871 GACCGTT
1 GACCGTT
919878 GAC
1 GAC
919881 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:919875 original size:13 final size:14
Alignment explanation
Indices: 919851--919880 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
919841 GACCCGACCC
919851 GACCGTTGACCGTT
1 GACCGTTGACCGTT
919865 GACCG-TGACCGTT
1 GACCGTTGACCGTT
919878 GAC
1 GAC
919881 TTCCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:921871 original size:22 final size:22
Alignment explanation
Indices: 921843--921884 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
921833 TCAACATGTT
*
921843 TTTATAAGTTATTAA-TATACGA
1 TTTATAA-TTATAAATTATACGA
921865 TTTATAATTATAAATTATAC
1 TTTATAATTATAAATTATAC
921885 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTATAATTATAAATTATACGA
Found at i:925173 original size:23 final size:23
Alignment explanation
Indices: 925147--925236 Score: 99
Period size: 23 Copynumber: 3.9 Consensus size: 23
925137 GTTTGTGCTG
925147 GTTCGTTTATGTTTATTTATTGT
1 GTTCGTTTATGTTTATTTATTGT
* *
925170 GTTCGTTTATGTTTGTTCATTTGT
1 GTTCGTTTATGTTTATTTA-TTGT
* * **
925194 GTTCGTTTACGTTTGTTTATTAC
1 GTTCGTTTATGTTTATTTATTGT
* *
925217 GTTCATTTATGTTCATTTAT
1 GTTCGTTTATGTTTATTTAT
925237 CGTTTAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 35 0.62
24 21 0.38
ACGTcount: A:0.13, C:0.09, G:0.17, T:0.61
Consensus pattern (23 bp):
GTTCGTTTATGTTTATTTATTGT
Found at i:927225 original size:29 final size:30
Alignment explanation
Indices: 927177--927233 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
927167 TCCCTTAATT
*
927177 TTTCTAAAGTTTATACTTTGATCACTAAAC
1 TTTCTAAAGTTTACACTTTGATCACTAAAC
* *
927207 TTTCTAAA-TTTACATTTTGGTCACTAA
1 TTTCTAAAGTTTACACTTTGATCACTAA
927234 CCAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTCTAAAGTTTACACTTTGATCACTAAAC
Found at i:928515 original size:80 final size:80
Alignment explanation
Indices: 928382--928541 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
928372 GGATTTAATT
928382 CCATGTTTAATATGGACCGTTGGATTAAAGTGGCAAGATTGTTATTTTTGGAAAAAGGCAAGGGC
1 CCATGTTTAATATGGACCGTTGGATTAAAGTGGCAAGATTGTTATTTTTGGAAAAAGGCAAGGGC
928447 AAATCGGTAAAGTAA
66 AAATCGGTAAAGTAA
928462 CCATGTTTAATATGGACCGTTGGATTAAAGTGGCAAGATTGTTATTTTTGGAAAAAGGCAAGGGC
1 CCATGTTTAATATGGACCGTTGGATTAAAGTGGCAAGATTGTTATTTTTGGAAAAAGGCAAGGGC
928527 AAATCGGTAAAGTAA
66 AAATCGGTAAAGTAA
928542 GATTTTGTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (80 bp):
CCATGTTTAATATGGACCGTTGGATTAAAGTGGCAAGATTGTTATTTTTGGAAAAAGGCAAGGGC
AAATCGGTAAAGTAA
Found at i:930705 original size:2 final size:2
Alignment explanation
Indices: 930698--930759 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
930688 TTTGATTGGG
930698 AT AT AT AT AT -T AT AT AT AT AT AT -T AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
930737 AT AT AT AT AT A- AT A- AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
930760 GTTTTAAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
1 5 0.09
2 49 0.91
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:932801 original size:13 final size:13
Alignment explanation
Indices: 932783--932807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
932773 TGTTATTTTG
932783 TTGGAAAAATTCC
1 TTGGAAAAATTCC
932796 TTGGAAAAATTC
1 TTGGAAAAATTC
932808 ATGGATTTGA
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:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGGAAAAATTCC
Found at i:937519 original size:46 final size:47
Alignment explanation
Indices: 937433--937525 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 47
937423 AATTTCATGC
937433 ATGATTTGTATTGCACTGTTTATTATGTTTAATTGCCTCACTAAGTA
1 ATGATTTGTATTGCACTGTTTATTATGTTTAATTGCCTCACTAAGTA
* * *
937480 ATGATTTGTATTGCACTG-TTATTGTTTTTAATTTCCTCACTAAGTA
1 ATGATTTGTATTGCACTGTTTATTATGTTTAATTGCCTCACTAAGTA
937526 TATATTTAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 25 0.58
47 18 0.42
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (47 bp):
ATGATTTGTATTGCACTGTTTATTATGTTTAATTGCCTCACTAAGTA
Found at i:938993 original size:41 final size:41
Alignment explanation
Indices: 938948--939305 Score: 538
Period size: 41 Copynumber: 8.7 Consensus size: 41
938938 GAATTGGTTT
* * * *
938948 GTGAATTATTGTTTTCTACCATGATTGAATAAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
*
938989 GTGAATTATTGTATGCTACCATGATCAAATCAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
* *
939030 GCGAATTATTGTATGCTACGATGATCGAATCAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
939071 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
* * *
939112 GTGCATTAATGTATGCTACCATGATTGAATCAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
* *
939153 GTGGATTATTGTATGCTACCATGATCGAATCAAGTTAAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
* **
939194 GTGGATTATTGTATGCTACCATGATCGAATCAAGTTGTGTG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
939235 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
1 GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
* * *
939276 GTGAAGTATTGCT-TGCTTCCATGATTGAAT
1 GTGAATTATTG-TATGCTACCATGATCGAAT
939306 TGAAACGAAT
Statistics
Matches: 290, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 289 1.00
42 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.35
Consensus pattern (41 bp):
GTGAATTATTGTATGCTACCATGATCGAATCAAGTTGAATG
Found at i:944520 original size:177 final size:179
Alignment explanation
Indices: 944224--944580 Score: 700
Period size: 177 Copynumber: 2.0 Consensus size: 179
944214 TAGGGTGTGT
944224 ATTTCAAACAATGATGACTTGAAGAAGGAAATTTTACAAGAAGCTCATCAAAGTCCATTCTTGAT
1 ATTTCAAACAATGATGACTTGAAGAAGGAAATTTTACAAGAAGCTCATCAAAGTCCATTCTTGAT
944289 TTATCTTGAATCTTTCAAGATGTATAAAGCCCTTAAATCCCTATATTGGTGGCCTCACATAAAGT
66 TTATCTTGAATCTTTCAAGATGTATAAAGCCCTTAAATCCCTATATTGGTGGCCTCACATAAAGT
944354 ATGCC-TTACAGATTATTTGTTTAGA-GACTGAATTGTCAAAGAATCAA
131 ATGCCATTACAGATTATTTGTTTAGATGACTGAATTGTCAAAGAATCAA
944401 ATTTCAAACAATGATGACTTGAAGAAGGAAATTTTACAAGAAGCTCATCAAAGTCCATTCTTGAT
1 ATTTCAAACAATGATGACTTGAAGAAGGAAATTTTACAAGAAGCTCATCAAAGTCCATTCTTGAT
944466 TTATCTTGAATCTTTCAAGATGTATAAAGCCCTTAAATCCCTATATTGGTGGCCTCACATAAAGT
66 TTATCTTGAATCTTTCAAGATGTATAAAGCCCTTAAATCCCTATATTGGTGGCCTCACATAAAGT
944531 ATGCCATTACAGATTATTTGTTTAGATGACTGAATTGTCAAAGAATCAA
131 ATGCCATTACAGATTATTTGTTTAGATGACTGAATTGTCAAAGAATCAA
944580 A
1 A
944581 GTCGAACATC
Statistics
Matches: 178, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
177 135 0.76
178 20 0.11
179 23 0.13
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (179 bp):
ATTTCAAACAATGATGACTTGAAGAAGGAAATTTTACAAGAAGCTCATCAAAGTCCATTCTTGAT
TTATCTTGAATCTTTCAAGATGTATAAAGCCCTTAAATCCCTATATTGGTGGCCTCACATAAAGT
ATGCCATTACAGATTATTTGTTTAGATGACTGAATTGTCAAAGAATCAA
Found at i:952834 original size:22 final size:21
Alignment explanation
Indices: 952807--952850 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
952797 AAGGGACAAT
*
952807 CTTTTTCCTCAAGGGATCGATC
1 CTTTTT-CTAAAGGGATCGATC
*
952829 CTTTTTGTAAAGGGATCGATC
1 CTTTTTCTAAAGGGATCGATC
952850 C
1 C
952851 CAAACTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (21 bp):
CTTTTTCTAAAGGGATCGATC
Found at i:952914 original size:21 final size:20
Alignment explanation
Indices: 952868--952915 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
952858 GACGGAATAC
*
952868 AAGGGATCGATATTTTATCA
1 AAGGGATCGATATTTGATCA
* * *
952888 AGGGGATCGATCCTTTGGTCA
1 AAGGGATCGAT-ATTTGATCA
952909 AAGGGAT
1 AAGGGAT
952916 TGATTATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
AAGGGATCGATATTTGATCA
Found at i:956813 original size:54 final size:54
Alignment explanation
Indices: 956748--957196 Score: 655
Period size: 54 Copynumber: 8.3 Consensus size: 54
956738 TCATTTACCA
* * *
956748 TATTGGCACTATGCGTGCAACCTAAGCAATTTATAATGAGTTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
* * *
956802 TATTGACACTATGTGTGCAACATAAGAAATTCATAATGAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
* **
956856 TATTGGCACTATGTCTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTTG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
* * *
956910 TATTGGAACTATGTGTGCGACCTAAGAAATTCATAATGAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
956964 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
*
957018 TATTGGCACTATGTCTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
** * *
957072 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAACAAGTTTTTGAATTTCCA
1 TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
* * * * * **
957126 TATTGGCACTATGTGTGCAACCCCACGTAATTCATAATGGGTTTGTGTTTTTCCG
1 TATTGGCACTATGTGTGCAA-CCTAAGAAATTCATAATGAGTTTATGAATTTCCG
* *
957181 CATCGGCACTATGTGT
1 TATTGGCACTATGTGT
957197 AAGAAACCAT
Statistics
Matches: 359, Mismatches: 35, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
54 321 0.89
55 38 0.11
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCG
Found at i:957580 original size:24 final size:25
Alignment explanation
Indices: 957540--957586 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
957530 ACATAATATA
* *
957540 AAATAATGAACGTTTTATTATTATC
1 AAATAATGAAAGTTTTATGATTATC
957565 AAATAA-GAAAGTTTTATGATTA
1 AAATAATGAAAGTTTTATGATTA
957587 AAAGCATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (25 bp):
AAATAATGAAAGTTTTATGATTATC
Found at i:963337 original size:21 final size:20
Alignment explanation
Indices: 963289--963337 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
963279 AAATGTGTAT
963289 TTAATATTAATATATATATGA
1 TTAAT-TTAATATATATATGA
*
963310 -TATATTTATATATATATGTGA
1 TTA-ATTTA-ATATATATATGA
963331 TTAATTT
1 TTAATTT
963338 TAATTACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAATTTAATATATATATGA
Found at i:965908 original size:12 final size:12
Alignment explanation
Indices: 965891--965915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
965881 ATTTCACATT
965891 AATTCAATTTTA
1 AATTCAATTTTA
965903 AATTCAATTTTA
1 AATTCAATTTTA
965915 A
1 A
965916 TAGATTAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTCAATTTTA
Found at i:968053 original size:20 final size:20
Alignment explanation
Indices: 968028--968091 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
968018 GAAGAAAAAA
968028 GGTTTAAAATGCTTTAGTTT
1 GGTTTAAAATGCTTTAGTTT
* *
968048 GGTTTATAATCCTTTCA---T
1 GGTTTAAAATGCTTT-AGTTT
* *
968066 GTTTTAAAATGTTTTAGTTT
1 GGTTTAAAATGCTTTAGTTT
968086 GGTTTA
1 GGTTTA
968092 TATGCCTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
17 1 0.03
18 12 0.36
20 19 0.58
21 1 0.03
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.53
Consensus pattern (20 bp):
GGTTTAAAATGCTTTAGTTT
Found at i:990341 original size:20 final size:22
Alignment explanation
Indices: 990304--990360 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
990294 CAGAACCCTA
* *
990304 GGGGGTATCGATTCCCCT-GTG
1 GGGGGAATCGATTCCCCTCATG
*
990325 GGGGGAATCGGTT-CCCTCATG
1 GGGGGAATCGATTCCCCTCATG
*
990346 GGGGG-ATTGATTCCC
1 GGGGGAATCGATTCCC
990361 TCTGCACCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.12, C:0.23, G:0.39, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTCATG
Found at i:997216 original size:24 final size:22
Alignment explanation
Indices: 997179--997257 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 22
997169 TTATATATTT
997179 TTATTTTCTTCTTTTAGTTTTTCA
1 TTATTTT-TTCTTTTA-TTTTTCA
*
997203 TTATTTTTTACTTTATTATTTTTTCC
1 TTATTTTTT-C-TT-TTA-TTTTTCA
* *
997229 TTTTTTTTTC-TTT-TTTTTCT
1 TTATTTTTTCTTTTATTTTTCA
997249 TTATTTTTT
1 TTATTTTTT
997258 GTAGTTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 14 0.30
22 2 0.04
23 3 0.06
24 8 0.17
25 3 0.06
26 17 0.36
ACGTcount: A:0.10, C:0.10, G:0.01, T:0.78
Consensus pattern (22 bp):
TTATTTTTTCTTTTATTTTTCA
Found at i:997220 original size:15 final size:15
Alignment explanation
Indices: 997202--997231 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
997192 TTAGTTTTTC
997202 ATTATTTTTTACTTT
1 ATTATTTTTTACTTT
*
997217 ATTATTTTTTCCTTT
1 ATTATTTTTTACTTT
997232 TTTTTTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATTTTTTACTTT
Found at i:997273 original size:8 final size:7
Alignment explanation
Indices: 997203--997442 Score: 67
Period size: 8 Copynumber: 31.7 Consensus size: 7
997193 TAGTTTTTCA
997203 TTATTTT
1 TTATTTT
*
997210 TTACTTTA
1 TTA-TTTT
997218 TTATTTT
1 TTATTTT
*
997225 TTCCTTTT
1 TT-ATTTT
*
997233 TTTTTCTT
1 TTATT-TT
*
997241 TTTTTTCT
1 TTATTT-T
997249 TTATTTT
1 TTATTTT
* *
997256 TTGTAGTT
1 TTAT-TTT
997264 TTATATTT
1 TTAT-TTT
997272 TTATTTT
1 TTATTTT
* *
997279 TTCTTCAT
1 TTATT-TT
* **
997287 CT-TTAC
1 TTATTTT
997293 TTATTTT
1 TTATTTT
*
997300 CTATTTCCT
1 TTATTT--T
**
997309 TTA-TAC
1 TTATTTT
997315 TTATTTT
1 TTATTTT
997322 TTATTTAT
1 TTATTT-T
997330 TT-TTCTT
1 TTATT-TT
997337 TTATTTT
1 TTATTTT
*
997344 TGTTTTTGT
1 T-TATTT-T
*
997353 TTATTATA
1 TTATT-TT
*
997361 TTA-TTA
1 TTATTTT
997367 TTATTTTT
1 TTA-TTTT
997375 TTATTTTAT
1 TTA-TTT-T
997384 TTATTTT
1 TTATTTT
**
997391 TT-TTAA
1 TTATTTT
997397 TTATTTT
1 TTATTTT
997404 ATTACTTTT
1 -TTA-TTTT
997413 TTATTTGTT
1 TTA-TT-TT
997422 TTATTTATT
1 TTA-TT-TT
997431 TTATTTT
1 TTATTTT
997438 TTATT
1 TTATT
997443 ACTTTCATTA
Statistics
Matches: 178, Mismatches: 32, Indels: 46
0.70 0.12 0.18
Matches are distributed among these distances:
6 14 0.08
7 59 0.33
8 78 0.44
9 27 0.15
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (7 bp):
TTATTTT
Found at i:997331 original size:11 final size:11
Alignment explanation
Indices: 997315--997442 Score: 77
Period size: 11 Copynumber: 11.1 Consensus size: 11
997305 TCCTTTATAC
997315 TTATTTTTTAT
1 TTATTTTTTAT
997326 TTATTTTTCT-T
1 TTATTTTT-TAT
*
997337 TTA-TTTTTGT
1 TTATTTTTTAT
*
997347 TT-TTGTTTAT
1 TTATTTTTTAT
997357 TATATTATTATTATT
1 T-TATT-TT-TTA-T
*
997372 TTTTTATTTTAT
1 TTATT-TTTTAT
997384 TTATTTTTT-T
1 TTATTTTTTAT
*
997394 TAATTATTTTA-
1 TTATT-TTTTAT
997405 TTACTTTTTTAT
1 TTA-TTTTTTAT
*
997417 TTGTTTTATTTATT
1 TT-ATTT-TTTA-T
997431 TTATTTTTTAT
1 TTATTTTTTAT
997442 T
1 T
997443 ACTTTCATTA
Statistics
Matches: 93, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
9 1 0.01
10 18 0.19
11 30 0.32
12 19 0.20
13 11 0.12
14 12 0.13
15 2 0.02
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:997343 original size:5 final size:5
Alignment explanation
Indices: 997320--997437 Score: 63
Period size: 5 Copynumber: 23.8 Consensus size: 5
997310 TATACTTATT
* * *
997320 TTTTA -TTTA TTTTTC TTTTA TTTT- TGTTTT TGTTTA TTATA TTATTA
1 TTTTA TTTTA -TTTTA TTTTA TTTTA T-TTTA T-TTTA TTTTA TT-TTA
* *
997367 TTATTT TTTTA TTTTA -TTTA TTTT- TTTTA -ATTA TTTTA TTACTT-
1 TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT--TTA
*
997411 TTTTA -TTTG TTTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
997438 TTATTACTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 26
0.71 0.09 0.21
Matches are distributed among these distances:
4 25 0.28
5 42 0.47
6 20 0.22
7 2 0.02
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:997386 original size:9 final size:9
Alignment explanation
Indices: 997320--997436 Score: 73
Period size: 9 Copynumber: 12.9 Consensus size: 9
997310 TATACTTATT
997320 TTTTATTTA
1 TTTTATTTA
*
997329 TTTTTCTTTTA
1 -TTTT-ATTTA
*
997340 TTTT-TGT-
1 TTTTATTTA
*
997347 TTTTGTTTA
1 TTTTATTTA
*
997356 TTATA-TTA
1 TTTTATTTA
997364 TTATTATTT-
1 TT-TTATTTA
997373 TTTTATTT-
1 TTTTATTTA
*
997381 TATTTATTTT
1 T-TTTATTTA
*
997391 TTTTAATTA
1 TTTTATTTA
*
997400 TTTTATTACTT
1 TTTTATT--TA
*
997411 TTTTATTTG
1 TTTTATTTA
997420 TTTTATTTA
1 TTTTATTTA
997429 TTTTATTT
1 TTTTATTT
997437 TTTATTACTT
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
7 4 0.05
8 16 0.19
9 43 0.50
10 11 0.13
11 12 0.14
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:997391 original size:41 final size:42
Alignment explanation
Indices: 997335--997437 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 42
997325 TTTATTTTTC
* *
997335 TTTTATTTTTGTTTTTGTTTATTATATTATTA-TTATTTT-TTTA
1 TTTTATTTAT-TTTTT-TTAATTATATTATTACTT-TTTTATTTA
* *
997378 TTTTATTTATTTTTTTTAATTATTTTATTACTTTTTTATTTG
1 TTTTATTTATTTTTTTTAATTATATTATTACTTTTTTATTTA
997420 TTTTATTTATTTTATTTT
1 TTTTATTTATTTT-TTTT
997438 TTATTACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
41 17 0.32
42 23 0.43
43 13 0.25
ACGTcount: A:0.18, C:0.01, G:0.03, T:0.78
Consensus pattern (42 bp):
TTTTATTTATTTTTTTTAATTATATTATTACTTTTTTATTTA
Found at i:997415 original size:29 final size:30
Alignment explanation
Indices: 997366--997435 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
997356 TTATATTATT
* * *
997366 ATTATTTTTTTATTTTATTTATTTTTTTTA
1 ATTATTTTATTACTTTATTTATTTGTTTTA
997396 ATTATTTTATTACTTT-TTTATTTGTTTTA
1 ATTATTTTATTACTTTATTTATTTGTTTTA
*
997425 TTTATTTTATT
1 ATTATTTTATT
997436 TTTTATTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.77
Consensus pattern (30 bp):
ATTATTTTATTACTTTATTTATTTGTTTTA
Found at i:997433 original size:38 final size:37
Alignment explanation
Indices: 997359--997447 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
997349 TTGTTTATTA
* *
997359 TATTATTATTATTTTTTTATTTTATTTATTTTTTTTAAT
1 TATT-TTATTACTTTTTTATTTTATTTATTTATTTT-AT
997398 TATTTTATTACTTTTTTATTTGT-TTTATTTATTTTAT
1 TATTTTATTACTTTTTTATTT-TATTTATTTATTTTAT
997435 T-TTTTATTACTTT
1 TATTTTATTACTTT
997448 CATTACCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
36 12 0.26
37 3 0.06
38 27 0.57
39 5 0.11
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.76
Consensus pattern (37 bp):
TATTTTATTACTTTTTTATTTTATTTATTTATTTTAT
Found at i:997442 original size:41 final size:39
Alignment explanation
Indices: 997315--997442 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 39
997305 TCCTTTATAC
*
997315 TTATTTT-TTATTTATTTTTCTT-TTATT-TTTGTTTTTGTTT
1 TTATTTTATTA-TTATTTTT-TTATT-TTATTTATTTTT-TTT
*
997355 ATTATATTATTATTATTTTTTTATTTTATTTATTTTTTTT
1 -TTATTTTATTATTATTTTTTTATTTTATTTATTTTTTTT
*
997395 AATTATTTTATTACTT-TTTTATTTGTTTTATTTATTTTATTTT
1 --TTATTTTATTA-TTATTTT-TTTATTTTATTTATTTT-TTTT
997438 TTATT
1 TTATT
997443 ACTTTCATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
40 7 0.09
41 44 0.58
42 21 0.28
43 4 0.05
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (39 bp):
TTATTTTATTATTATTTTTTTATTTTATTTATTTTTTTT
Found at i:997458 original size:46 final size:46
Alignment explanation
Indices: 997367--997459 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 46
997357 TATATTATTA
* *
997367 TTATTTTTTTATTTTATTTATTTTTTTTAATTATTTTATTACTTTT
1 TTATTTTTTTATTTTATTTATATTTTTTAATTATTTCATTACTTTT
*
997413 TTATTTGTTTTA-TTTATTT-TATTTTTT-ATTACTTTCATTACCTTT
1 TTATTT-TTTTATTTTATTTATATTTTTTAATTA-TTTCATTACTTTT
997458 TT
1 TT
997460 CCTCTAACGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 4 0.10
45 20 0.48
46 13 0.31
47 5 0.12
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (46 bp):
TTATTTTTTTATTTTATTTATATTTTTTAATTATTTCATTACTTTT
Found at i:1002539 original size:12 final size:13
Alignment explanation
Indices: 1002522--1002555 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1002512 GGCTATCTCT
1002522 TCTTCTTCAT-CA
1 TCTTCTTCATCCA
1002534 TCTTCTTCATCCA
1 TCTTCTTCATCCA
1002547 TC-TCTTCAT
1 TCTTCTTCAT
1002556 TTGAATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (13 bp):
TCTTCTTCATCCA
Found at i:1003582 original size:20 final size:22
Alignment explanation
Indices: 1003532--1003588 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
1003522 ATGCACAGGT
*
1003532 AGTGCATCGATGCACATGTTAG
1 AGTGCATCGATACACATGTTAG
*
1003554 GGATGCATCGATACAC-TG-TAG
1 AG-TGCATCGATACACATGTTAG
1003575 AGTGCATCGATACA
1 AGTGCATCGATACA
1003589 TACCTTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 12 0.39
21 4 0.13
22 3 0.10
23 12 0.39
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
AGTGCATCGATACACATGTTAG
Found at i:1004369 original size:18 final size:18
Alignment explanation
Indices: 1004342--1004394 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1004332 AGGGTCTACA
1004342 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
1004360 TGGTCATTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
1004378 TGGTCCTTCGAGACATA
1 TGGTCCTTCGGGACATA
1004395 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:1004720 original size:17 final size:18
Alignment explanation
Indices: 1004685--1004723 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1004675 ATATGAACAA
1004685 GATAATAGAAATATGAAT
1 GATAATAGAAATATGAAT
1004703 GATAATA-AAATGAT-AAT
1 GATAATAGAAAT-ATGAAT
1004720 GATA
1 GATA
1004724 GGAATAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (18 bp):
GATAATAGAAATATGAAT
Found at i:1008951 original size:18 final size:18
Alignment explanation
Indices: 1008928--1008981 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
1008918 GAGGGTCTAC
*
1008928 GTGGTCCTTCGGGACGTA
1 GTGGTCCTTCGGGACATA
1008946 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1008964 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
1008982 TGTGTTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1011422 original size:14 final size:14
Alignment explanation
Indices: 1011403--1011435 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1011393 GAAAAGTATC
1011403 GGTATTGTTCATGA
1 GGTATTGTTCATGA
1011417 GGTATTGTTCATGA
1 GGTATTGTTCATGA
1011431 GGTAT
1 GGTAT
1011436 CGGTACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (14 bp):
GGTATTGTTCATGA
Found at i:1012575 original size:19 final size:18
Alignment explanation
Indices: 1012544--1012596 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1012534 TAAAAAAGGG
1012544 TTGCAACATAAAAAGGAA
1 TTGCAACATAAAAAGGAA
1012562 TTGCAACATAAAAAGGAA
1 TTGCAACATAAAAAGGAA
*
1012580 TTGCAACTTGAAAAAGG
1 TTGCAACAT-AAAAAGG
1012597 GTGTAACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (18 bp):
TTGCAACATAAAAAGGAA
Found at i:1014117 original size:2 final size:2
Alignment explanation
Indices: 1014112--1014158 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1014102 TAAAGAAATG
1014112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1014154 AT AT A
1 AT AT A
1014159 AAGATTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1016566 original size:12 final size:12
Alignment explanation
Indices: 1016549--1016574 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1016539 GTTTACCCTC
1016549 CAGAAACAAGAT
1 CAGAAACAAGAT
1016561 CAGAAACAAGAT
1 CAGAAACAAGAT
1016573 CA
1 CA
1016575 TTTACTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (12 bp):
CAGAAACAAGAT
Done.