Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003417.1 Hibiscus syriacus cultivar Beakdansim tig00007195_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: 80583
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:9842 original size:36 final size:36
Alignment explanation
Indices: 9797--9867 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
9787 ACTAAATTAC
* *
9797 AAGATTTTAAAATGATTAAAATTAGAGAATAAAAAT
1 AAGAGTTTAAAATGATGAAAATTAGAGAATAAAAAT
9833 AAGAGTTTAAAATGATGAAAATTAGAGAATAAAAA
1 AAGAGTTTAAAATGATGAAAATTAGAGAATAAAAA
9868 CTAAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (36 bp):
AAGAGTTTAAAATGATGAAAATTAGAGAATAAAAAT
Found at i:9997 original size:13 final size:12
Alignment explanation
Indices: 9958--9998 Score: 57
Period size: 11 Copynumber: 3.3 Consensus size: 12
9948 TTTATTCTTA
9958 AATTGAAATATTT
1 AATT-AAATATTT
9971 AA-TAAATATTT
1 AATTAAATATTT
9982 AATTAAATAGTTT
1 AATTAAATA-TTT
9995 AATT
1 AATT
9999 TCTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.38
12 7 0.27
13 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (12 bp):
AATTAAATATTT
Found at i:12359 original size:16 final size:16
Alignment explanation
Indices: 12340--12382 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
12330 CAATTAGTAA
*
12340 TTAGCGGTTAGAAAAG
1 TTAGTGGTTAGAAAAG
*
12356 TTAGTTGTTAGAAAAG
1 TTAGTGGTTAGAAAAG
12372 TTAGTGGTTAG
1 TTAGTGGTTAG
12383 CAGAGTCCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (16 bp):
TTAGTGGTTAGAAAAG
Found at i:12589 original size:4 final size:4
Alignment explanation
Indices: 12580--12608 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12570 TATTATAAAC
12580 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
12609 CAATGGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:12667 original size:142 final size:142
Alignment explanation
Indices: 12452--12739 Score: 400
Period size: 142 Copynumber: 2.0 Consensus size: 142
12442 TCAAATATAT
**
12452 TAAATAAATAAATAAACAATGGTTAGAATGCGATAAAATAAAAATCAGTAGTTACAGAATCTGAA
1 TAAATAAATAAATAAACAATGGTTAGAATGAAATAAAATAAAAATCAGTAGTTACAGAATCTGAA
* * *
12517 CCATAATAATGCATATCATACCCCAGATCAGGTCACCACAAGACCGAATCGAATATTATAAACAA
66 CCATAATAATGCAGATCATACCCCAGATCAGGTCACCACAAGACCGAATCGAATAATAGAAACAA
12582 TAAATAAATAAA
131 TAAATAAATAAA
* * * *
12594 TAAATAAATAAAT-AACAATGGTTA-AAGTGAAATAAAATAAAAGTTAGTAGTTAGTAGAGTCTG
1 TAAATAAATAAATAAACAATGGTTAGAA-TGAAATAAAATAAAAATCAGTAGTTA-CAGAATCTG
** * * * * *
12657 AACCATAATAATGTGGATTATACCCCGGATCGGGTCACCACAAGGCCGAATCGAATAATAGAAAT
64 AACCATAATAATGCAGATCATACCCCAGATCAGGTCACCACAAGACCGAATCGAATAATAGAAAC
12722 AATAAATAAATAAA
129 AATAAATAAATAAA
12736 TAAA
1 TAAA
12740 CAATGGTTAG
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
140 2 0.02
141 33 0.26
142 93 0.73
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (142 bp):
TAAATAAATAAATAAACAATGGTTAGAATGAAATAAAATAAAAATCAGTAGTTACAGAATCTGAA
CCATAATAATGCAGATCATACCCCAGATCAGGTCACCACAAGACCGAATCGAATAATAGAAACAA
TAAATAAATAAA
Found at i:12777 original size:29 final size:29
Alignment explanation
Indices: 12745--12809 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
12735 ATAAACAATG
*
12745 GTTAGAATGTAATAAAATAAAAATCAGTA
1 GTTAGAATGCAATAAAATAAAAATCAGTA
* * * *
12774 GTTA-ATATGCAGTAAAATAAAAGTTAGTT
1 GTTAGA-ATGCAATAAAATAAAAATCAGTA
12803 GTTAGAA
1 GTTAGAA
12810 ATAAATAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.03
29 27 0.93
30 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (29 bp):
GTTAGAATGCAATAAAATAAAAATCAGTA
Found at i:13804 original size:20 final size:20
Alignment explanation
Indices: 13779--13816 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13769 TTTGGTTCAC
13779 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
13799 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
13817 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:19219 original size:15 final size:15
Alignment explanation
Indices: 19199--19227 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19189 AGAACACTAG
19199 TTATCAATTTGTCAA
1 TTATCAATTTGTCAA
19214 TTATCAATTTGTCA
1 TTATCAATTTGTCA
19228 GTTTTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (15 bp):
TTATCAATTTGTCAA
Found at i:24057 original size:20 final size:20
Alignment explanation
Indices: 24032--24079 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
24022 GCGAAATAAA
24032 AATCGCAACGCGATCCCCAG
1 AATCGCAACGCGATCCCCAG
24052 AATCGCAACGCGATCCCCAG
1 AATCGCAACGCGATCCCCAG
24072 AATCGCAA
1 AATCGCAA
24080 ATCAGTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.38, G:0.19, T:0.10
Consensus pattern (20 bp):
AATCGCAACGCGATCCCCAG
Found at i:24116 original size:21 final size:20
Alignment explanation
Indices: 24010--24187 Score: 81
Period size: 20 Copynumber: 8.8 Consensus size: 20
24000 AAATGACCAA
**
24010 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
24029 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ***
24049 CAGAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
24069 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
24089 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
24110 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
24131 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
24151 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
24172 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
24188 ACACATAAAT
Statistics
Matches: 122, Mismatches: 31, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
19 16 0.13
20 60 0.49
21 46 0.38
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:24216 original size:20 final size:20
Alignment explanation
Indices: 24193--24324 Score: 167
Period size: 20 Copynumber: 6.5 Consensus size: 20
24183 CGCGAACACA
24193 TAAATCGCAACACGTATCCG
1 TAAATCGCAACACGTATCCG
* **
24213 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACACGTATCCG
*
24233 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACACGTATCCG
**
24253 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACACGTATCCG
* *
24273 TAAATCGCAACGAC-AATACG
1 TAAATCGCAAC-ACGTATCCG
24293 TAAAATCGCAACACGTATCCG
1 T-AAATCGCAACACGTATCCG
24314 TAAATCGCAAC
1 TAAATCGCAAC
24325 GCGATTTTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
20 81 0.84
21 16 0.16
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACACGTATCCG
Found at i:24295 original size:60 final size:59
Alignment explanation
Indices: 24155--24324 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 59
24145 GATTTTCCAG
* * * *
24155 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACACGTATCCGTA
1 AATCGCAACGC-AATACGTAAATCGCAACGCGTATC-CGTAAATCGCAACACGTATCCGTA
* ** * **
24215 AACCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACG-CAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACACGTATCCGTA
*
24275 AATCGCAACGACAATACGTAAAATCGCAACACGTATCCGTAAATCGCAAC
1 AATCGCAACG-CAATACGT-AAATCGCAACGCGTATCCGTAAATCGCAAC
24325 GCGATTTTTA
Statistics
Matches: 90, Mismatches: 17, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
60 60 0.67
61 30 0.33
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.18
Consensus pattern (59 bp):
AATCGCAACGCAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACACGTATCCGTA
Found at i:24300 original size:21 final size:21
Alignment explanation
Indices: 24155--24325 Score: 124
Period size: 20 Copynumber: 8.5 Consensus size: 21
24145 GATTTTCCAG
* *
24155 AATCGCAACG-CGAATATGAA
1 AATCGCAACGACGAATACGTA
* *
24175 AATCGCAACG-CGAACACATA
1 AATCGCAACGACGAATACGTA
* *
24195 AATCGCAAC-ACGTATCCGTA
1 AATCGCAACGACGAATACGTA
* * * *
24215 AACCGCAACG-TGTATCCGTA
1 AATCGCAACGACGAATACGTA
* *
24235 AATCGCAACG-CGTATCCGTA
1 AATCGCAACGACGAATACGTA
* * *
24255 AATCGCAATG-CGTATCCGTA
1 AATCGCAACGACGAATACGTA
24275 AATCGCAACGAC-AATACGTAA
1 AATCGCAACGACGAATACGT-A
* *
24296 AATCGCAAC-ACGTATCCGTA
1 AATCGCAACGACGAATACGTA
24316 AATCGCAACG
1 AATCGCAACG
24326 CGATTTTTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
20 111 0.87
21 16 0.13
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (21 bp):
AATCGCAACGACGAATACGTA
Found at i:24311 original size:41 final size:40
Alignment explanation
Indices: 24155--24328 Score: 172
Period size: 40 Copynumber: 4.3 Consensus size: 40
24145 GATTTTCCAG
* * * * *
24155 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGTAAATCGCAACACGTATC-CGTA
* * * * **
24195 AATCGCAACACGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACACGTATCCGTA
* * **
24235 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACACGTATCCGTA
24275 AATCGCAACGAC-AATACGTAAAATCGCAACACGTATCCGTA
1 AATCGCAACG-CGAATACGT-AAATCGCAACACGTATCCGTA
24316 AATCGCAACGCGA
1 AATCGCAACGCGA
24329 TTTTTAAAGC
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
40 80 0.71
41 33 0.29
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGAATACGTAAATCGCAACACGTATCCGTA
Found at i:24746 original size:33 final size:33
Alignment explanation
Indices: 24707--24777 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
24697 TTCACTTAGA
24707 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
24740 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
24773 TTTCA
1 TTTCA
24778 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:24883 original size:21 final size:21
Alignment explanation
Indices: 24857--24933 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
24847 TGCAGAAGAG
24857 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
24878 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
24898 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
24920 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
24934 TCACAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:24948 original size:33 final size:33
Alignment explanation
Indices: 24911--24990 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
24901 GCAACGAGAA
24911 AAATGAAAATCGCAACGAGAGAATCACAACGCG
1 AAATGAAAATCGCAACGAGAGAATCACAACGCG
*
24944 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCACAACGCG
**
24977 AAACCAAAATCGCA
1 AAATGAAAATCGCA
24991 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCACAACGCG
Found at i:24970 original size:14 final size:14
Alignment explanation
Indices: 24918--24974 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
24908 GAAAAATGAA
24918 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
24932 AATCACAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
24951 AATCGCAACGAGAG
1 AATCGCAACGAGAG
24965 AATCGCAACG
1 AATCGCAACG
24975 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:25008 original size:19 final size:18
Alignment explanation
Indices: 24986--25049 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
24976 GAAACCAAAA
*
24986 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
25005 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
25019 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
25037 TCGCGTTGCGATT
1 TCGCGTTGCGATT
25050 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.26
15 3 0.08
17 3 0.08
18 12 0.32
19 10 0.26
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:25027 original size:14 final size:14
Alignment explanation
Indices: 25008--25063 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
24998 TTTCATTTCG
25008 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
25022 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
25040 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
25054 CGTTGCGATT
1 CGTTGCGATT
25064 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
17 3 0.08
18 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:25038 original size:32 final size:33
Alignment explanation
Indices: 24991--25112 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 33
24981 CAAAATCGCA
24991 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
25024 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
25056 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
25097 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
25113 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
32 32 0.41
33 11 0.14
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:25074 original size:21 final size:21
Alignment explanation
Indices: 25048--25112 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
25038 CGCGTTGCGA
25048 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
25069 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
25089 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
25110 TTC
1 TTC
25113 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:25109 original size:20 final size:20
Alignment explanation
Indices: 25047--25110 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
25037 TCGCGTTGCG
25047 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
25067 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
25088 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
25108 ATT
1 ATT
25111 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:26073 original size:12 final size:12
Alignment explanation
Indices: 26056--26080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26046 TCTTCGGGGA
26056 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26068 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26080 C
1 C
26081 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:26289 original size:24 final size:24
Alignment explanation
Indices: 26255--26301 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26245 CTGAAACATC
26255 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26279 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26302 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27023 original size:20 final size:20
Alignment explanation
Indices: 26995--27224 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
26985 AAATTTCAGT
* * *
26995 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27015 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27035 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27055 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
27075 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27095 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27115 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27135 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* * *
27155 ATTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27175 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27195 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27215 GTTGCGATTT
1 GTTGCGATTT
27225 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27241 original size:21 final size:21
Alignment explanation
Indices: 27211--27293 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
27201 ATTTTCATAT
*
27211 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
27232 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
27253 TCGTATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
27274 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
27294 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:28474 original size:2 final size:2
Alignment explanation
Indices: 28467--28511 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28457 AAAAATAAAG
28467 TA TA TA 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
28509 TA T
1 TA T
28512 TAAACATGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30223 original size:3 final size:3
Alignment explanation
Indices: 30217--30269 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
30207 TATTTATTAT
* * *
30217 TAA TAA TAA TAA -AA TAA TAA TAT TAA TAT TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30264 TAA TAA
1 TAA TAA
30270 AAGATCGAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:30609 original size:42 final size:42
Alignment explanation
Indices: 30525--30890 Score: 288
Period size: 43 Copynumber: 8.6 Consensus size: 42
30515 CTTTAACAGT
30525 TCTTACAGATGACCCGAAGGATTTCAACATCTTGCACTGAAGG
1 TCTTACAGATGACCCGAAGGATTT-AACATCTTGCACTGAAGG
*
30568 TCTTACAGATGACCCGAAGGCTTTAACATCTTGCACTGAAGG
1 TCTTACAGATGACCCGAAGGATTTAACATCTTGCACTGAAGG
* * * * *
30610 GCTTACAGATGACCCGAAGGATTTATAGAT-TAAGAAACCCCCGGAAGATTAG
1 TCTTACAGATGACCCGAAGGATTTA-ACATCT-TG-----CACTGAAG----G
* * * ** * * *
30662 TTTCTA-AAAT--CTC-ATTTGA--AAACATCCTGCATTGAAGG
1 TCT-TACAGATGACCCGA-AGGATTTAACATCTTGCACTGAAGG
**
30700 TCTTATGGATGACCCGAAGGCA--T---ATCTTGCACTGAAGG
1 TCTTACAGATGACCCGAAGG-ATTTAACATCTTGCACTGAAGG
* * *
30738 GCTTACAAATGACCCGAAGGATTTTAACATCTTGCATTGAAGG
1 TCTTACAGATGACCCGAAGGA-TTTAACATCTTGCACTGAAGG
*
30781 TCTTACAGATGACCCGAAAGATTTCAACATCTTGCACTGAAGG
1 TCTTACAGATGACCCGAAGGATTT-AACATCTTGCACTGAAGG
* *
30824 TCTTACAGATGACCCGAAGGCTTTAACATCTTGCACTGAAAG
1 TCTTACAGATGACCCGAAGGATTTAACATCTTGCACTGAAGG
*
30866 TCTTACAAATGACCCGAAGGATTTA
1 TCTTACAGATGACCCGAAGGATTTA
30891 TAGATTAAGA
Statistics
Matches: 254, Mismatches: 43, Indels: 53
0.73 0.12 0.15
Matches are distributed among these distances:
37 3 0.01
38 34 0.13
40 4 0.02
41 2 0.01
42 90 0.35
43 98 0.39
47 4 0.02
48 7 0.03
49 1 0.00
50 4 0.02
52 5 0.02
53 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
TCTTACAGATGACCCGAAGGATTTAACATCTTGCACTGAAGG
Found at i:30889 original size:85 final size:86
Alignment explanation
Indices: 30723--30889 Score: 264
Period size: 85 Copynumber: 2.0 Consensus size: 86
30713 CCGAAGGCAT
* * *
30723 ATCTTGCACTGAAGGGCTTACAAATGACCCGAAGGATTTTAACATCTTGCATTGAAGGTCTTACA
1 ATCTTGCACTGAAGGGCTTACAAATGACCCGAAGGACTTTAACATCTTGCACTGAAAGTCTTACA
*
30788 GATGACCCGAAAGATTTCAAC
66 AATGACCCGAAAGATTTCAAC
* *
30809 ATCTTGCACTGAAGGTCTTACAGATGACCCGAAGG-CTTTAACATCTTGCACTGAAAGTCTTACA
1 ATCTTGCACTGAAGGGCTTACAAATGACCCGAAGGACTTTAACATCTTGCACTGAAAGTCTTACA
*
30873 AATGACCCGAAGGATTT
66 AATGACCCGAAAGATTT
30890 ATAGATTAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 41 0.55
86 33 0.45
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (86 bp):
ATCTTGCACTGAAGGGCTTACAAATGACCCGAAGGACTTTAACATCTTGCACTGAAAGTCTTACA
AATGACCCGAAAGATTTCAAC
Found at i:31017 original size:12 final size:12
Alignment explanation
Indices: 31000--31037 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
30990 CTGCACTGAA
31000 GGTCTTATGGAT
1 GGTCTTATGGAT
*
31012 GGTCTTATAGAT
1 GGTCTTATGGAT
31024 GGTCTTATGGAT
1 GGTCTTATGGAT
31036 GG
1 GG
31038 CCCGTAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.18, C:0.08, G:0.34, T:0.39
Consensus pattern (12 bp):
GGTCTTATGGAT
Found at i:31758 original size:22 final size:22
Alignment explanation
Indices: 31700--31759 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
31690 AATAAAGCTT
*
31700 TCATCTTTGAA-AAGAGAATCTA
1 TCATCTTTGAAGAA-TGAATCTA
31722 TCATCTTTGAAGAATGAATCTA
1 TCATCTTTGAAGAATGAATCTA
31744 TCATCTTTGAAGAATG
1 TCATCTTTGAAGAATG
31760 TAGATGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAATGAATCTA
Found at i:32235 original size:55 final size:55
Alignment explanation
Indices: 32121--32263 Score: 218
Period size: 55 Copynumber: 2.6 Consensus size: 55
32111 ATAATTACTG
* * *
32121 GTTCGTAGAATATTTGACAACACATTCA-TTATTTCTTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTTTCTTGTGGTTTCTGCACAGAT
32175 GTTCGTAAAACATTTGACAACACATTCATTTTTTTCTTGTGGCTTT-TGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTTTCTTGTGG-TTTCTGCACAGAT
* *
32230 GTTCGTAAAACATTTCACAACACATTCATCTTTT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTT
32264 CCTATAGCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 26 0.32
55 53 0.65
56 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (55 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTTTCTTGTGGTTTCTGCACAGAT
Found at i:33459 original size:580 final size:581
Alignment explanation
Indices: 32356--34682 Score: 4469
Period size: 580 Copynumber: 4.0 Consensus size: 581
32346 TAAGAACAGA
*
32356 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAACCATCAGAATAATGCAACTG
1 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
*
32421 TATAATGAGCAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
66 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
*
32486 ATTCCTTTCTGTCTTACTGGAAATATTTTCTCAAATCAATGATCTTGACACAGGATGATATGGAC
131 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTGA-ACAGGATGATATGGAC
32551 CTTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGAT
195 CTTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGAT
* **
32616 TGAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTGTTGTTGTTGTGAGCTTTCAAAAATGC
260 TGAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTT-TTATTGACGTGAGCTTTCAAAAATGC
32681 CCCACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAA
324 CCCACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAA
32746 AATGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAG
389 AATGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAG
32811 AATGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAA
454 AATGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAA
32876 TTAGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
519 TTAGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
32939 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
1 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
33004 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
66 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
33069 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTG-ACAGGATGATATGGACC
131 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTGAACAGGATGATATGGACC
33133 TTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGATT
196 TTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGATT
33198 GAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTATTGACGTGAGCTTTCAAAAATGCCC
261 GAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTATTGACGTGAGCTTTCAAAAATGCCC
33263 CACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAAAA
326 CACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAAAA
33328 TGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAGAA
391 TGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAGAA
*
33393 TGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATAGACCATTTCTGTTTGAATT
456 TGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAATT
*
33458 AGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATATCCCAC
521 AGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
33519 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
1 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
33584 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
66 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
33649 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTG-ACAGGATGATATGGACC
131 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTGAACAGGATGATATGGACC
33713 TTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGATT
196 TTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGATT
33778 GAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTATTGACGTGAGCTTTCAAAAATGCCC
261 GAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTATTGACGTGAGCTTTCAAAAATGCCC
33843 CACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAAAA
326 CACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAAAA
33908 TGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAGAA
391 TGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAGAA
33973 TGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAATT
456 TGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAATT
34038 AGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
521 AGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
34099 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
1 ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
**
34164 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCATTGCTTCACCATTTTCATTCTTC
66 TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
*
34229 ATTCCTTTCTGTCTTACTGGAAATATTTTCTCAAATCAATGATCTTGACACAGGATGATATGGAC
131 ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTGA-ACAGGATGATATGGAC
* *
34294 CTTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCAACAACATTCATGATTATGAT
195 CTTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGAT
*
34359 TGAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTTGTTGACGTGAGCTTTCAAAAATGC
260 TGAAATGGGCTTTCAGCATGCCCCAACATTTG-TTTTTTTTATTGACGTGAGCTTTCAAAAATGC
*
34424 CCCACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCCTTTAA
324 CCCACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAA
34489 AATGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAG
389 AATGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAG
34554 AATGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAA
454 AATGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAA
34619 TTAGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
519 TTAGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
34682 A
1 A
34683 TGGATCTGTC
Statistics
Matches: 1724, Mismatches: 17, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
580 1031 0.60
581 119 0.07
582 111 0.06
583 463 0.27
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (581 bp):
ACTCAATAGGAATACAAGGGGATGCATTGGTTTGCCAGCATCAAATCATCAGAATAATGCAACTG
TATAATGAACAAAGCAATTATATATAGTCAGCTCCATTGTCACGGCTTCACCATTTTCATTCTTC
ATTCCTTTCTATCTTACTGGAAATATTTTCTCAAATCAATGATCTTGAACAGGATGATATGGACC
TTCAATATGCCCCAATATTTGCTAATACAAATGTTCAAAATGCGACAACATTCATAATTATGATT
GAAATGGGCTTTCAGCATGCCCCAACATTTGTTTTTTTTATTGACGTGAGCTTTCAAAAATGCCC
CACCTTTTCATACTGATGTGCCTTCAAAATACCCCACATGGATATGTCTGAAGTGGCTTTTAAAA
TGCCCCAACATTTGCTGATACAGATGTTAAAAACATTAATTCTTGCTGAGATGAGCCTCCAAGAA
TGCCCAAATATTCATATTGCTGTGAGCCTTCAAAATGTCCCACATGGACCATTTCTGTTTGAATT
AGGCATTCAAAATGCCCCAGTATTCTATTTCTGGTTAAAATGGGCCTTCAAGATGTCCCAC
Found at i:36587 original size:7 final size:7
Alignment explanation
Indices: 36575--36619 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
36565 GTCAAAGAAA
36575 GTCAACG
1 GTCAACG
36582 GTCAACG
1 GTCAACG
36589 GTCAACG
1 GTCAACG
36596 GTCAACG
1 GTCAACG
36603 GTCAACG
1 GTCAACG
36610 GTCAACG
1 GTCAACG
36617 GTC
1 GTC
36620 GGGTCGGGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:36631 original size:17 final size:17
Alignment explanation
Indices: 36609--36649 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
36599 AACGGTCAAC
*
36609 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
36626 GGTCAACAGTTGGGTCG
1 GGTCAACAGTCGGGTCG
36643 GGTCAAC
1 GGTCAAC
36650 CCGGTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:36667 original size:19 final size:19
Alignment explanation
Indices: 36643--36714 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
36633 AGTTGGGTCG
*
36643 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
36662 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
36681 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
36700 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
36715 AAACTAGTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
18 1 0.02
19 49 0.98
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:36692 original size:38 final size:39
Alignment explanation
Indices: 36643--36732 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
36633 AGTTGGGTCG
* *
36643 GGTCAACCCGGTTC-AGACCGGTCAAACCGGTTC-AGACC
1 GGTCAAACCGGTTCGA-ACCGGTCAAACCGGTTCAAAACC
*
36681 GGTCAAACCGGTTCGAACCGGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCGAACCGGTCAAACCGGTTCAAAACC
*
36720 AGTCAAACCGGTT
1 GGTCAAACCGGTT
36733 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 30 0.65
39 16 0.35
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (39 bp):
GGTCAAACCGGTTCGAACCGGTCAAACCGGTTCAAAACC
Found at i:36715 original size:10 final size:10
Alignment explanation
Indices: 36645--36716 Score: 87
Period size: 10 Copynumber: 7.5 Consensus size: 10
36635 TTGGGTCGGG
*
36645 TCAACCCGGT
1 TCAAACCGGT
*
36655 TCAGACCGG-
1 TCAAACCGGT
36664 TCAAACCGGT
1 TCAAACCGGT
*
36674 TCAGACCGG-
1 TCAAACCGGT
36683 TCAAACCGGT
1 TCAAACCGGT
*
36693 TCGAACCGG-
1 TCAAACCGGT
36702 TCAAACCGGT
1 TCAAACCGGT
36712 TCAAA
1 TCAAA
36717 ACTAGTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 24 0.46
10 28 0.54
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:43852 original size:7 final size:7
Alignment explanation
Indices: 43840--43870 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
43830 GTCAAAGAAA
43840 GTCAACG
1 GTCAACG
43847 GTCAACG
1 GTCAACG
43854 GTCAACG
1 GTCAACG
43861 GTCAACG
1 GTCAACG
43868 GTC
1 GTC
43871 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:43882 original size:17 final size:17
Alignment explanation
Indices: 43860--43900 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
43850 AACGGTCAAC
*
43860 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
43877 GGTCAACAGTTGGGTCG
1 GGTCAACAGTCGGGTCG
43894 GGTCAAC
1 GGTCAAC
43901 CCGGTTCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.41, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:43918 original size:19 final size:20
Alignment explanation
Indices: 43894--43964 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
43884 AGTTGGGTCG
*
43894 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
43913 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
43932 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
43952 GGTCAAACCGGTT
1 GGTCAAACCGGTT
43965 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:43931 original size:10 final size:10
Alignment explanation
Indices: 43896--43964 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
43886 TTGGGTCGGG
*
43896 TCAACCCGGT
1 TCAAACCGGT
*
43906 TCAGACCGG-
1 TCAAACCGGT
43915 TCAAACCGGT
1 TCAAACCGGT
*
43925 TCGAACCGG-
1 TCAAACCGGT
43934 TCAAACCGGT
1 TCAAACCGGT
*
43944 TCAAAACTGG-
1 TC-AAACCGGT
43954 TCAAACCGGT
1 TCAAACCGGT
43964 T
1 T
43965 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:45659 original size:72 final size:72
Alignment explanation
Indices: 45542--45680 Score: 226
Period size: 72 Copynumber: 1.9 Consensus size: 72
45532 ATATAATAGT
*
45542 ATAACAAGCTAGCTGAATATTATCCATAATGCCGGGGTGATTAACCAATTGCTTTAGGGGGACAA
1 ATAACAAGCTAGCTGAATATTATCCATAAAGCCGGGGTGATTAACCAATTGCTTTAGGGGGACAA
45607 CTCAAGC
66 CTCAAGC
* * *
45614 ATAACAGGCTAGCTGAATATTATCCATAAAGCTGGGGCT-ATTAACCAATTGCTTTAGGGGGATA
1 ATAACAAGCTAGCTGAATATTATCCATAAAGCCGGGG-TGATTAACCAATTGCTTTAGGGGGACA
45678 ACT
65 ACT
45681 TAACCTTTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 61 0.98
73 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (72 bp):
ATAACAAGCTAGCTGAATATTATCCATAAAGCCGGGGTGATTAACCAATTGCTTTAGGGGGACAA
CTCAAGC
Found at i:50382 original size:12 final size:12
Alignment explanation
Indices: 50339--50388 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
50329 CAAAGCATTT
50339 TTATTTTACTTG
1 TTATTTTACTTG
50351 TTCATTTT--TTG
1 TT-ATTTTACTTG
50362 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
50376 TTATTTTCCTTG
1 TTATTTTACTTG
50388 T
1 T
50389 CTTTTCAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:50798 original size:2 final size:2
Alignment explanation
Indices: 50791--50834 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
50781 ACGCCAGGGC
50791 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
50833 AT
1 AT
50835 TATTAGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51941 original size:3 final size:3
Alignment explanation
Indices: 51935--51983 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
51925 ATTTATTTAT
* * *
51935 TAA TAA TAA TAA -AA -AA TAA TAT TAA TAT TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51981 TAA
1 TAA
51984 AAGAGATCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:51968 original size:12 final size:12
Alignment explanation
Indices: 51932--51979 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
51922 ATTATTTATT
51932 TATTAATAATAA
1 TATTAATAATAA
*
51944 TA--AAAAATAA
1 TATTAATAATAA
*
51954 TATTAATATTAA
1 TATTAATAATAA
51966 TATTAATAATAA
1 TATTAATAATAA
51978 TA
1 TA
51980 ATAAAAGAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 9 0.30
12 21 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATTAATAATAA
Found at i:53854 original size:23 final size:23
Alignment explanation
Indices: 53765--53861 Score: 61
Period size: 23 Copynumber: 4.2 Consensus size: 23
53755 TGGTAAATAC
* * * **
53765 TAAACAAACATGTTCGTGATCGC
1 TAAACAAACATATTCATGAACAT
*
53788 TAAATAAACA-AGTTCATGAACAT
1 TAAACAAACATA-TTCATGAACAT
* * **
53811 ATAAACGAATACGTTCATGAACAT
1 -TAAACAAACATATTCATGAACAT
* *
53835 TAAACAAACATATTCGTGAACAA
1 TAAACAAACATATTCATGAACAT
53858 TAAA
1 TAAA
53862 TAAATGAACG
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
23 37 0.67
24 18 0.33
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
TAAACAAACATATTCATGAACAT
Found at i:57419 original size:2 final size:2
Alignment explanation
Indices: 57414--57467 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
57404 AGGAAAAAGA
57414 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
57456 AT AT AT AT AT AT
1 AT AT AT AT AT AT
57468 CAAAGTATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57688 original size:16 final size:16
Alignment explanation
Indices: 57623--57697 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
57613 ACACAAGGTT
57623 TAAAT-AATATAATAA
1 TAAATAAATATAATAA
* *
57638 TAAATAAAGAAAATAA
1 TAAATAAATATAATAA
* *
57654 TAAATAAAAATAATTA
1 TAAATAAATATAATAA
* *
57670 TAAATATATATATTAA
1 TAAATAAATATAATAA
*
57686 T-AATATATATAA
1 TAAATAAATATAA
57698 ATAAACTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
15 15 0.31
16 34 0.69
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (16 bp):
TAAATAAATATAATAA
Found at i:57693 original size:13 final size:13
Alignment explanation
Indices: 57623--57701 Score: 57
Period size: 13 Copynumber: 6.5 Consensus size: 13
57613 ACACAAGGTT
57623 TAAATAATATA-A
1 TAAATAATATATA
*
57635 T-AATAA-ATAAA
1 TAAATAATATATA
*
57646 GAAAATAATA-A-A
1 -TAAATAATATATA
57658 TAAA-AATA-ATTA
1 TAAATAATATA-TA
57670 TAAAT-ATATATA
1 TAAATAATATATA
*
57682 TTAATAATATATA
1 TAAATAATATATA
57695 TAAATAA
1 TAAATAA
57702 ACTATTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
10 8 0.15
11 9 0.17
12 16 0.30
13 20 0.37
14 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (13 bp):
TAAATAATATATA
Found at i:57892 original size:15 final size:15
Alignment explanation
Indices: 57862--57896 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57852 ATATACATAT
* *
57862 AATAATAATAACATG
1 AATAATAAAAAAATG
57877 AATAATAAAAAAATG
1 AATAATAAAAAAATG
57892 AATAA
1 AATAA
57897 AATATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAATAAAAAAATG
Found at i:58355 original size:35 final size:35
Alignment explanation
Indices: 58313--58382 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
58303 GAATCATAGC
58313 AAAATTCTATCATATCTTTAGGAGTTTGAATCCTA
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCTA
* *
58348 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCTA
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCTA
58383 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (35 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCTA
Found at i:59566 original size:106 final size:105
Alignment explanation
Indices: 58931--59924 Score: 1347
Period size: 105 Copynumber: 9.5 Consensus size: 105
58921 CATTGTTCCA
* * * ** * *
58931 AGTCCAATATCCTCCG-TCGTGAAGCTGAAATTGGCTCTGGAACCGGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAA
* * *
58995 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * *
59037 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-T--GAA-ATTTTGTTGACAAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
* *
59097 AGCGGTCCATTCGTCGTGAAGTTAAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
59137 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
* *
59202 AGCGGTCCCTTCTTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
59242 ATTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
* *
59307 AGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
59347 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTAACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
59412 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
59452 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAAC
59517 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
59558 AGTCCAATATCCTTCGCTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAATTGTTGTTGACAACT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
* * * *
59623 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
59663 AGTCTAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAAC
59728 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
59769 AGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAAC
* * *
59834 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
59875 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG
59925 CCCCTTCATC
Statistics
Matches: 799, Mismatches: 79, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
99 1 0.00
100 81 0.10
101 2 0.00
102 3 0.00
104 3 0.00
105 388 0.49
106 319 0.40
107 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:59614 original size:211 final size:209
Alignment explanation
Indices: 58931--59924 Score: 1399
Period size: 211 Copynumber: 4.7 Consensus size: 209
58921 CATTGTTCCA
* * * ** *
58931 AGTCCAATATCCTCCG-TCGTGAAGCTGAAATTGGCTCTGGAACCGGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAA
* *
58995 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAG-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
** * * *
59060 GTTGAAATTGAATCTG-AA-T--GAA-ATTTTGTTGACAAACAGCGGTCCATTCGTCGTGAAGTT
128 GTTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
59120 AAACTTGCGTTGTCTGG
193 GAACTTGCGTTGTCTGG
* * * * *
59137 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
** * *
59202 AGCGGTCCCTTC-TTCGTGAAGTTGAACTTGCATTGTCTGGATTCCAATATCCTTCGTTGTGAAG
66 AGC-GTCCCTTCGTT-GTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
* * * * *
59266 TTGAAATTGACTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTTGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
59331 AACTTGCGTTGTCTGA
194 AACTTGCGTTGTCTGG
* * * * *
59347 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTAACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* *
59412 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
*
59477 TGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
59542 AACTTGCGTTGTCTGG
194 AACTTGCGTTGTCTGG
* *
59558 AGTCCAATATCCTTCGCTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAATTGTTGTTGACAACT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* * * *
59623 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCTAATATCATTCGATGTGAAGT
66 AG-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
*
59688 TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
59753 AACTTGCGTTGTCTGG
194 AACTTGCGTTGTCTGG
* * *
59769 AGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
* *
59834 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCATTCGCTGTGAAG
65 CAG-CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
59899 TTGAAATTGGCTCTGAAATTGGGAAG
129 TTGAAATTGGCTCTGAAATTGGGAAG
59925 CCCCTTCATC
Statistics
Matches: 713, Mismatches: 63, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
204 3 0.00
205 80 0.11
206 43 0.06
207 2 0.00
209 3 0.00
210 193 0.27
211 291 0.41
212 98 0.14
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (209 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
AGCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTT
GAAATTGGCTCTGAAATTGGGAAGTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGG
Found at i:61102 original size:18 final size:18
Alignment explanation
Indices: 61075--61110 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61065 TGTTGAATCC
*
61075 CCAAATATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
61093 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
61111 TTGATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:61551 original size:22 final size:22
Alignment explanation
Indices: 61525--61579 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
61515 TTGTGTTTGG
61525 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
*
61547 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
61569 TCAAAGGTTTG
1 TCAAAGGTTTG
61580 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:62250 original size:32 final size:32
Alignment explanation
Indices: 62214--62290 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
62204 TTGTCCCTTT
* *
62214 TTCTTTTTGATTTTTTTCTTTTTT-TTGTTTTC
1 TTCTTTTTGATTCTTTTCTTTTTTGTT-TTTGC
*
62246 TTCTTTTTTGCTTCTTTTCTTTTTTGTTTTTGC
1 TTC-TTTTTGATTCTTTTCTTTTTTGTTTTTGC
62279 -TCTTTTTG-TTCT
1 TTCTTTTTGATTCT
62291 GATTGAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.10
31 6 0.15
32 5 0.12
33 23 0.57
34 2 0.05
ACGTcount: A:0.01, C:0.13, G:0.08, T:0.78
Consensus pattern (32 bp):
TTCTTTTTGATTCTTTTCTTTTTTGTTTTTGC
Found at i:62282 original size:16 final size:15
Alignment explanation
Indices: 62226--62285 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
62216 CTTTTTGATT
*
62226 TTTTTCTTTTTTTTG
1 TTTTTCTCTTTTTTG
62241 -TTTTCTTCTTTTTTG
1 TTTTTC-TCTTTTTTG
62256 CTTCTTT-TCTTTTTTG
1 -TT-TTTCTCTTTTTTG
62272 TTTTTGCTCTTTTT
1 TTTTT-CTCTTTTT
62286 GTTCTGATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 8 0.21
15 10 0.26
16 16 0.42
17 1 0.03
18 3 0.08
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTCTCTTTTTTG
Found at i:62284 original size:15 final size:14
Alignment explanation
Indices: 62211--62288 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 14
62201 TTTTTGTCCC
62211 TTTTTC-TTTTTGATT
1 TTTTTCTTTTTTG--T
62226 TTTTTCTTTTTTTTGT
1 TTTTTC--TTTTTTGT
62242 TTTCTTCTTTTTTGCT
1 TTT-TTCTTTTTTG-T
62258 TCTTTTCTTTTTTGT
1 T-TTTTCTTTTTTGT
*
62273 TTTTGCTCTTTTTGT
1 TTTTTCT-TTTTTGT
62288 T
1 T
62289 CTGATTGAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
14 5 0.09
15 23 0.42
16 16 0.29
17 5 0.09
18 6 0.11
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTTTGT
Found at i:66920 original size:2 final size:2
Alignment explanation
Indices: 66907--66938 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
66897 GGAAAAAGAA
*
66907 AT AT AA 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
66939 CAAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:67422 original size:2 final size:2
Alignment explanation
Indices: 67415--67439 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67405 AAATAATTTA
67415 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
67440 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67462 original size:15 final size:15
Alignment explanation
Indices: 67442--67480 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
67432 TATATATAAT
*
67442 AATAATAATAACATG
1 AATAATAATAAAATG
*
67457 AATAATAAAAAAATG
1 AATAATAATAAAATG
67472 AATAA-AATA
1 AATAATAATA
67481 TCCATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (15 bp):
AATAATAATAAAATG
Found at i:67919 original size:36 final size:33
Alignment explanation
Indices: 67878--67954 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 33
67868 CTATCATATT
67878 TTTGAATCATAGCAAATTCTATCATATCTTTAGGAG
1 TTTGAATCATA--AAATTCTATCATAT-TTTAGGAG
* *
67914 TTTGAATCCTAAAATTCTATCCTATTTTAGGAG
1 TTTGAATCATAAAATTCTATCATATTTTAGGAG
67947 TTTGAATC
1 TTTGAATC
67955 CTAGTAGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 16 0.41
34 13 0.33
36 10 0.26
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (33 bp):
TTTGAATCATAAAATTCTATCATATTTTAGGAG
Found at i:67948 original size:33 final size:34
Alignment explanation
Indices: 67891--67957 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
67881 GAATCATAGC
67891 AAATTCTATCATATCTTTAGGAGTTTGAATCCTA
1 AAATTCTATCATATCTTTAGGAGTTTGAATCCTA
*
67925 AAATTCTATCCTAT-TTTAGGAGTTTGAATCCTA
1 AAATTCTATCATATCTTTAGGAGTTTGAATCCTA
67958 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (34 bp):
AAATTCTATCATATCTTTAGGAGTTTGAATCCTA
Found at i:77312 original size:6 final size:6
Alignment explanation
Indices: 77301--77332 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
77291 TGATAAAGAA
77301 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GA
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GA
77333 GGAGAGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAAGG
Done.