Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000949.1 Hibiscus syriacus cultivar Beakdansim tig00001899_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: 58881
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:3070 original size:29 final size:29
Alignment explanation
Indices: 2998--3085 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
2988 ATCATATATG
* *
2998 ATTTAAAGGACTAAATAGTAAAAACATA-AT
1 ATTTAAGGGACTAAATAG-AAAAA-ATAGAA
* * * *
3028 CTTGAAGGG-TTAAATAGCAAAAATAGAA
1 ATTTAAGGGACTAAATAGAAAAAATAGAA
3056 ATTTAAGGGACTAAAATAGAAAAAATAGAA
1 ATTTAAGGGACT-AAATAGAAAAAATAGAA
3086 CTTAAAAGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
27 3 0.07
28 12 0.27
29 8 0.18
30 22 0.49
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.23
Consensus pattern (29 bp):
ATTTAAGGGACTAAATAGAAAAAATAGAA
Found at i:3147 original size:29 final size:29
Alignment explanation
Indices: 3046--3242 Score: 81
Period size: 27 Copynumber: 6.9 Consensus size: 29
3036 GTTAAATAGC
* * *
3046 AAAAATAGAAATTTAAGGGACTAAAATAGA
1 AAAAATAGAAACTTAAAGGAATAAAAT-GA
* * * *
3076 AAAAATAG-AACTTAAAAGATTAACA-CA
1 AAAAATAGAAACTTAAAGGAATAAAATGA
* *
3103 ACAAAA-A-AAATTTAAAGGAATAAAATGG
1 A-AAAATAGAAACTTAAAGGAATAAAATGA
**
3131 AAAAATAGAAACTTAAAGGTCT-AAAT-A
1 AAAAATAGAAACTTAAAGGAATAAAATGA
** * * **
3158 GTAAATTGAAACTTAAGGGTCT-AAAT-A
1 AAAAATAGAAACTTAAAGGAATAAAATGA
* * *
3185 ACAAATACAAACATTAAAGGACTAAAAT-A
1 AAAAATAGAAAC-TTAAAGGAATAAAATGA
*
3214 ACAAAA-ACAAACATTTAAAGGAATAAAAT
1 A-AAAATAGAAAC--TTAAAGGAATAAAAT
3243 AACAAAACAC
Statistics
Matches: 129, Mismatches: 29, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
27 51 0.40
28 18 0.14
29 35 0.27
30 25 0.19
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAAATAGAAACTTAAAGGAATAAAATGA
Found at i:3171 original size:27 final size:27
Alignment explanation
Indices: 3133--3210 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
3123 TAAAATGGAA
3133 AAATAGAAACTTAAAGGTCTAAATAGT
1 AAATAGAAACTTAAAGGTCTAAATAGT
* * **
3160 AAATTGAAACTTAAGGGTCTAAATAAC
1 AAATAGAAACTTAAAGGTCTAAATAGT
* *
3187 AAATACAAACATTAAAGGACTAAA
1 AAATAGAAAC-TTAAAGGTCTAAA
3211 ATAACAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 31 0.74
28 11 0.26
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (27 bp):
AAATAGAAACTTAAAGGTCTAAATAGT
Found at i:3234 original size:30 final size:29
Alignment explanation
Indices: 3180--3270 Score: 123
Period size: 29 Copynumber: 3.1 Consensus size: 29
3170 TTAAGGGTCT
*
3180 AAATAACAAATACAAACATTAAAGGACTA
1 AAATAACAAAAACAAACATTAAAGGACTA
*
3209 AAATAACAAAAACAAACATTTAAAGGAATA
1 AAATAACAAAAACAAACA-TTAAAGGACTA
*
3239 AAATAAC-AAAACACAAC-TTAAGGGACTA
1 AAATAACAAAAACA-AACATTAAAGGACTA
3267 AAAT
1 AAAT
3271 GGTATTAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
28 13 0.23
29 23 0.41
30 20 0.36
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (29 bp):
AAATAACAAAAACAAACATTAAAGGACTA
Found at i:3249 original size:29 final size:28
Alignment explanation
Indices: 3180--3270 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 28
3170 TTAAGGGTCT
*
3180 AAATAACAAATACAAACATTAAAGGACTA
1 AAATAACAAA-ACAAACATTAAAGGAATA
3209 AAATAACAAAAACAAACATTTAAAGGAATA
1 AAATAAC-AAAACAAACA-TTAAAGGAATA
* *
3239 AAATAACAAAACACAAC-TTAAGGGACTA
1 AAATAACAAAACA-AACATTAAAGGAATA
3267 AAAT
1 AAAT
3271 GGTATTAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
28 13 0.23
29 20 0.36
30 23 0.41
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (28 bp):
AAATAACAAAACAAACATTAAAGGAATA
Found at i:4636 original size:3 final size:3
Alignment explanation
Indices: 4628--4673 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
4618 AATGTAATTT
4628 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA TATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
4673 A
1 A
4674 GATAATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4678 original size:21 final size:21
Alignment explanation
Indices: 4634--4683 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4624 ATTTATAATA
*
4634 ATAATA-ATAATAATAATAAT
1 ATAATATATAATAATAATAAG
4654 ATAATATATAATAATAATAAG
1 ATAATATATAATAATAATAAG
4675 ATAATATAT
1 ATAATATAT
4684 TGTGACCCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATATATAATAATAATAAG
Found at i:5240 original size:92 final size:91
Alignment explanation
Indices: 5076--5256 Score: 242
Period size: 92 Copynumber: 2.0 Consensus size: 91
5066 CATGCCATCT
*
5076 TTAGGAAAGGTGATAACACGGTTCCTACACTGAGGACGATTGGTTATCTAGGGGTGACACTGCTC
1 TTAGGAAAGGTGATAACACGGTTCCTACACTGAGGACGACTGGTTATCTAGGGGTGACACTGCTC
*
5141 CTACGTGATTAGGAGGTATGGTCGTC
66 CTACGTGATGAGGAGGTATGGTCGTC
* * * *
5167 TTAGG-AAGAGTGATAACATGGTTCCTACGCGATGAGGATGACTGG-TGTCTAGGGGTGACA-TG
1 TTAGGAAAG-GTGATAACACGGTTCCTACAC--TGAGGACGACTGGTTATCTAGGGGTGACACT-
*
5229 GCTCCTACGTGATGAGGAGGTTTGGTCG
62 GCTCCTACGTGATGAGGAGGTATGGTCG
5257 GGGGATGACA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
90 3 0.04
91 25 0.32
92 40 0.51
93 11 0.14
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (91 bp):
TTAGGAAAGGTGATAACACGGTTCCTACACTGAGGACGACTGGTTATCTAGGGGTGACACTGCTC
CTACGTGATGAGGAGGTATGGTCGTC
Found at i:5692 original size:35 final size:35
Alignment explanation
Indices: 5623--5705 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
5613 AGAAAATATC
* * * *
5623 CAAGTAAGACAAATTTGTTTTGAGAGAAATTGTCT
1 CAAGCAAGACAAATTCGTTTTAAGAGAAACTGTCT
*
5658 CAAGCGAGACACAATTCGTTTTAAGA-AAACTGTCT
1 CAAGCAAGACA-AATTCGTTTTAAGAGAAACTGTCT
5693 CAAGCAAGACAAA
1 CAAGCAAGACAAA
5706 ATTTGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.05
35 27 0.66
36 12 0.29
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (35 bp):
CAAGCAAGACAAATTCGTTTTAAGAGAAACTGTCT
Found at i:5732 original size:39 final size:36
Alignment explanation
Indices: 5623--5734 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 36
5613 AGAAAATATC
* * * *
5623 CAAGTAAGAC-AAATTTGTTTTGAGAGAAATTGTCT
1 CAAGCAAGACAAAATTCGTTTTAAAAGAAATTGTCT
* * * *
5658 CAAGCGAGACACAATTCGTTTTAAGA-AAACTGTCT
1 CAAGCAAGACAAAATTCGTTTTAAAAGAAATTGTCT
*
5693 CAAGCAAGACAAAATTTGATTTTTTAAAAGAAATTGTCT
1 CAAGCAAGACAAAATTCG---TTTTAAAAGAAATTGTCT
5732 CAA
1 CAA
5735 AGGTGACAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
35 31 0.51
36 12 0.20
38 7 0.11
39 11 0.18
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (36 bp):
CAAGCAAGACAAAATTCGTTTTAAAAGAAATTGTCT
Found at i:7816 original size:81 final size:81
Alignment explanation
Indices: 7391--8027 Score: 864
Period size: 81 Copynumber: 8.0 Consensus size: 81
7381 TTCATTTATG
* * * *
7391 TCAAAGGTA--TAGCCTTTCATCTAACTTGCATGATTGACACC-TTCTTGTCCAATACACAGCTA
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC-TGTCAAATGCACAGCTA
7453 GGCCATTAATCTTTTAC
65 GGCCATTAATCTTTTAC
* * *
7470 TCAAAGGTATTTAACCTTTCATCT-ACTGGCATAATTGACA-CTTTCTATCAAAAGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
7533 GCTATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * **
7549 TCAAAGGTATTTAACCTTTTATCTAACTGGCATAATTGGTACCTTTCTGTCAAATGCACAG--AG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
7612 GCTATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * * *
7628 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
**
7693 GCTTTTAA---TTTAC
66 GCCATTAATCTTTTAC
* ** *
7706 TCAAAGGTATTTAACCTTTCACCTAACTGGCATGATTGGGATCTTTCTGTCAAATGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
* *
7771 GCTATTAGTCTTTTAC
66 GCCATTAATCTTTTAC
* * * * *
7787 TGAAAGGTATTTAACCTTTCATCTAACTGGAATGATTGACACCTTTCTGTCAAATACAAAGTTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
7852 GCCATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* *
7868 TCAAAGGTATTTAACCTTTTATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
7933 GCCATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * * *
7949 TCAAAGGTATTTAACCTTTTATATAACTGGCATGATTGACACCTTTATGTCAAATGCACAACTA-
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
8013 GCCATTAATCTTTTA
66 GCCATTAATCTTTTA
8028 TTTAGAACAA
Statistics
Matches: 498, Mismatches: 50, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
78 68 0.14
79 135 0.27
80 46 0.09
81 249 0.50
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (81 bp):
TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
GCCATTAATCTTTTAC
Found at i:8231 original size:54 final size:54
Alignment explanation
Indices: 8165--8290 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 54
8155 TTTATCAAGA
* * * *
8165 TGCACACGTAGTGCCTATACGGTCGTTCATCAACACATGAT-ACATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGA-ATTCCGTGGAT
* * * *
8219 TGCACACATAGTGCATGTACGGTTGTCCATCAACTCATGATGAATTCCGTGGAT
1 TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGAATTCCGTGGAT
*
8273 TGAACACATAGTGCCTAT
1 TGCACACATAGTGCCTAT
8291 TTGGTAATCA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 59 0.98
55 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGAATTCCGTGGAT
Found at i:8743 original size:18 final size:19
Alignment explanation
Indices: 8703--8770 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
8693 TTATCAATGC
8703 TATCGATACCATCCTCATAG
1 TATCGATACCA-CCTCATAG
* *
8723 TATCGATACC-CCTCTTGG
1 TATCGATACCACCTCATAG
* *
8741 TATCGATACTACTTGCATTAG
1 TATCGATACCACCT-CA-TAG
8762 TATCGATAC
1 TATCGATAC
8771 TACTCGCTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 15 0.38
19 2 0.05
20 11 0.28
21 11 0.28
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (19 bp):
TATCGATACCACCTCATAG
Found at i:10857 original size:2 final size:2
Alignment explanation
Indices: 10852--10889 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
10842 CCAAAAAAGC
*
10852 TA TA TA TA TA TT TA T- 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 TA TA TA TA T
10890 GTTTTGACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:16113 original size:55 final size:54
Alignment explanation
Indices: 16019--16176 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 54
16009 ATATTCGGAA
*
16019 AACGAGTTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCGCTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
16072 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* * * * *
16128 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
16177 ATCAATCGTG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
53 18 0.20
54 25 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (54 bp):
AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:16231 original size:55 final size:55
Alignment explanation
Indices: 16083--16671 Score: 760
Period size: 55 Copynumber: 10.7 Consensus size: 55
16073 AACGAGTTCA
* * * * *
16083 CTCCCTCTTTCTTCGGGGAGTAT-AGAACTCGAACAATCTTCTGTCAA-CGGGT-TCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGTGTCT-G
* * * ** * *
16138 TTCCCTCTTTCTT-AGGGAGTAGGA-ACTTGAAGAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * * *
16191 CTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCTTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AATCGTGTCTG
* *
16247 CTCCCTATTTCTTCAGAGAGTATAAGACCCAAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
16302 CTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
**
16357 CTCCCTATTTCCGCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
16412 CTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
16467 CTCCCTATTTCTTCAGAGAGTACAAGACTCGAACAATCTTCATCCATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
16522 CTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
16577 CTCCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
*
16632 CT-CCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
16672 GATTATCGTT
Statistics
Matches: 475, Mismatches: 51, Indels: 17
0.87 0.09 0.03
Matches are distributed among these distances:
52 4 0.01
53 28 0.06
54 55 0.12
55 333 0.70
56 55 0.12
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
Found at i:17688 original size:8 final size:8
Alignment explanation
Indices: 17671--17722 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
17661 GAACCCTTCC
*
17671 TTTTTCCA
1 TTTTTTCA
17679 TTTTTTCA
1 TTTTTTCA
*
17687 TTTTTTTA
1 TTTTTTCA
*
17695 TTTTTTTA
1 TTTTTTCA
17703 TTTTTTTC-
1 -TTTTTTCA
17711 TTTTTTCA
1 TTTTTTCA
17719 TTTT
1 TTTT
17723 CACTCATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
7 7 0.18
8 26 0.67
9 6 0.15
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:17697 original size:16 final size:16
Alignment explanation
Indices: 17678--17722 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
17668 TCCTTTTTCC
17678 ATTTTTTCATTTTTTT
1 ATTTTTTCATTTTTTT
*
17694 ATTTTTTTATTTTTTT
1 ATTTTTTCATTTTTTT
*
17710 CTTTTTTCATTTT
1 ATTTTTTCATTTT
17723 CACTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTTCATTTTTTT
Found at i:31663 original size:81 final size:81
Alignment explanation
Indices: 31537--31944 Score: 573
Period size: 81 Copynumber: 5.0 Consensus size: 81
31527 GGCATATAGT
* * * * * * *
31537 CTTTCATCTAACTTGCATGATAGATACCTTTCTGTCTAATACACAACTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
31602 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
31618 CTTTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGCACAACTGGGCTATTAATATTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
31683 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
31699 CTGTCATATAACTGACGTAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
31764 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
31780 CTTTCATCTAACTGGCATAATTAACACCTTTTTTGTTAAATGCACAACTAGGCTATTAATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACC-TTTCTGTCAAATGCACAACTAGGCTATTAATCTTTT
*
31845 ATTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * * * ** * *
31862 CTTTCATCTAACTGGCATGATTGAAACCCTTATGTCAAATGCACAGTTAGACCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
31927 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
31943 CT
1 CT
31945 GTAACATCTC
Statistics
Matches: 290, Mismatches: 36, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 215 0.74
82 75 0.26
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:31921 original size:163 final size:162
Alignment explanation
Indices: 31537--31944 Score: 591
Period size: 163 Copynumber: 2.5 Consensus size: 162
31527 GGCATATAGT
* * * * *
31537 CTTTCATCTAACTTGCATGATAGATACCTTTCTGTCTAATACACAACTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATGATTGAAACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
* * *
31602 CTCAAAGGTATTTAACCTTTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGCACAACTG
66 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACAACTA
31667 GGCTATTAATATTTTACTCAAAGGTATTTAAC
131 GGCTATTAATATTTTACTCAAAGGTATTTAAC
* * * * * * *
31699 CTGTCATATAACTGACGTAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATGATTGAAACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
* *
31764 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACCTTTTTTGTTAAATGCACAACT
66 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACC-TTTCTGTCAAATGCACAACT
* *
31829 AGGCTATTAATCTTTTATTCAAAGGTATTTAAC
130 AGGCTATTAATATTTTACTCAAAGGTATTTAAC
* * ** *
31862 CTTTCATCTAACTGGCATGATTGAAACCCTTATGTCAAATGCACAGTTAGACCATTAATCTTTTA
1 CTTTCATCTAACTGGCATGATTGAAACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
31927 CTCAAAGGTATTTAACCT
66 CTCAAAGGTATTTAACCT
31945 GTAACATCTC
Statistics
Matches: 215, Mismatches: 30, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
162 96 0.45
163 119 0.55
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (162 bp):
CTTTCATCTAACTGGCATGATTGAAACCTTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTA
CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACAACTA
GGCTATTAATATTTTACTCAAAGGTATTTAAC
Found at i:32636 original size:45 final size:46
Alignment explanation
Indices: 32583--32826 Score: 347
Period size: 45 Copynumber: 5.4 Consensus size: 46
32573 TTTTTAACAT
* * *
32583 CTTTCATA-CTGATAATGCACCTATATGTATTTCAATTATGGCATC
1 CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
* * *
32628 ATTTCATA-CCTATAATGCACCCATATGCATTTCAATTATGGCATA
1 CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
*
32673 CTTTCAT-GCCGATAATGCACCCATATGCATTTCAATTATGGCATC
1 CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
*
32718 CTTTCA-AGCCGATAATGCACCCATATGCATTTCAATTATGGCATC
1 CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
* *
32763 CTTTCAT-GCCGATAATGCACCCATATGCATTTCAATTATGACATC
1 CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
*
32808 CTTTCATA-CCTATAATGCA
1 CTTTCATACCCGATAATGCA
32827 TTGTTGTATA
Statistics
Matches: 184, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
45 184 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (46 bp):
CTTTCATACCCGATAATGCACCCATATGCATTTCAATTATGGCATC
Found at i:32689 original size:90 final size:90
Alignment explanation
Indices: 32583--32826 Score: 400
Period size: 90 Copynumber: 2.7 Consensus size: 90
32573 TTTTTAACAT
* * * * *
32583 CTTTCATACTGATAATGCACCTATATGTATTTCAATTATGGCATCATTTCATACCTATAATGCAC
1 CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAATGCAC
32648 CCATATGCATTTCAATTATGGCATA
66 CCATATGCATTTCAATTATGGCATA
*
32673 CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCA-AGCCGATAATGCA
1 CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATA-CCTATAATGCA
*
32737 CCCATATGCATTTCAATTATGGCATC
65 CCCATATGCATTTCAATTATGGCATA
*
32763 CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATACCTATAATGCA
1 CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAATGCA
32827 TTGTTGTATA
Statistics
Matches: 143, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
89 1 0.01
90 141 0.99
91 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (90 bp):
CTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAATGCAC
CCATATGCATTTCAATTATGGCATA
Found at i:33297 original size:67 final size:67
Alignment explanation
Indices: 33086--33675 Score: 857
Period size: 67 Copynumber: 8.8 Consensus size: 67
33076 TCTTTAACCG
* *
33086 TTCATCTAACTGGCATAATTGACACATTTCT-TCCAAATGCACA-TCTAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCACAATTGACACCTTTCTGT-C-AATGCACAGT-TAGGCCTCAAAGGCACTT
33149 AGCCT
63 AGCCT
* * **
33154 TTCATCTAACAGGCACAATTAACACCTTTCT-TCCAAATGCACAACTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCACAATTGACACCTTTCTGT-C-AATGCACAGTTAGGCCTCAAAGGCACTTA
33218 GCCT
64 GCCT
* *
33222 TTCATCTAACTGGCACAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTTAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
33287 CT
66 CT
* * *
33289 TTCATCTAACTGGAACAATTGACACCATTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
33354 CT
66 CT
* * *
33356 TTCATCTAACTGGCACAATTGACACATTTCTGCCAAATGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACTTAG
*
33421 ACT
65 CCT
*
33424 TTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
33489 C-
66 CT
* * * * * *
33490 TTCATCTAACT-GCATAACTAACATCTTTTTGTCAATGCACAGTTAGGCCTCAAAGGAACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
33554 CT
66 CT
* * *
33556 TTCATCTTACTGGCACAATTGACACCTTTATGTCAATGCACAATTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
33621 CT
66 CT
*
33623 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
33676 TAATTTTTTA
Statistics
Matches: 473, Mismatches: 44, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
65 48 0.10
66 21 0.04
67 248 0.52
68 155 0.33
69 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (67 bp):
TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:33433 original size:202 final size:199
Alignment explanation
Indices: 33086--33675 Score: 880
Period size: 202 Copynumber: 2.9 Consensus size: 199
33076 TCTTTAACCG
33086 TTCATCTAACTGGCATAATTGACACATTTCTTCCAAATGCACA-TCTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACACA-TTCTT-C-AATGCACAGT-TAGGCCTCAAAGGCACTTA
* * * *
33150 GCCTTTCATCTAACAGGCACAATTAACACCTTTCTTCCAAATGCACAACTAGGCCTCAAAGGCAC
62 GCCTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAATTAGGCCTCAAAGGCAC
* *
33215 TTAGCCTTTCATCTAACTGGCACAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTTAAAGGC
127 TTAGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGC
33280 ACTTAGCC
192 ACTTAGCC
* *
33288 TTTCATCTAACTGGAACAATTGACACCATTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 -TTCATCTAACTGGCATAATTGACA-CATTCT-TCAATGCACAGTTAGGCCTCAAAGGCACTTAG
* * *
33353 CCTTTCATCTAACTGGCACAATTGACACATTTCTGCCAAATGCACAGTTAGGCCCCAAAGGCACT
63 CCTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAATTAGGCCTCAAAGGCACT
* *
33418 TAGACTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCA
128 TAGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCA
33483 CTTAGCC
193 CTTAGCC
* * * * *
33490 TTCATCTAACT-GCATAACTAACATCTTTTTGTCAATGCACAGTTAGGCCTCAAAGGAACTTAGC
1 TTCATCTAACTGGCATAATTGACA-CATTCT-TCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * *
33554 CTTTCATCTTACTGGCACAATTGACACCTTTATGTC-AATGCACAATTAGGCCTCAAAGGCACTT
64 CTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAATTAGGCCTCAAAGGCACTT
*
33618 AGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
129 AGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
33676 TAATTTTTTA
Statistics
Matches: 353, Mismatches: 31, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
199 81 0.23
200 76 0.22
201 11 0.03
202 154 0.44
203 28 0.08
204 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (199 bp):
TTCATCTAACTGGCATAATTGACACATTCTTCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
TTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAATTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
AGCC
Found at i:34054 original size:55 final size:55
Alignment explanation
Indices: 33876--34188 Score: 438
Period size: 54 Copynumber: 5.7 Consensus size: 55
33866 GATAATTTCA
* *
33876 CATATAGAAATTCATACACTTAGTATGGATTTCTTA-TTTCGTACACATAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
33930 CATAC-GAAAATTCATACACTTAGTATGGATTTCTTAG-TTCGCACACATAGTGCC
1 CATACAG-AAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
* ** * *
33984 CATA-TGAAAATTCATACACTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCC
1 CATACAG-AAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
*
34039 CATACAGAAATTCATACACTTAGTATGGATTTCTTAG-TTCGCACACTTAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
* * * *
34093 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
* *
34148 CATACATAAATTCATACACCTAGTATGGATTTCTTAAGTTT
1 CATACAGAAATTCATACACTTAGTATGGATTTCTT-AGTTT
34189 TTGCACACTC
Statistics
Matches: 232, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
53 1 0.00
54 133 0.57
55 92 0.40
56 6 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (55 bp):
CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
Found at i:34066 original size:109 final size:109
Alignment explanation
Indices: 33876--34183 Score: 478
Period size: 109 Copynumber: 2.8 Consensus size: 109
33866 GATAATTTCA
* * * * *
33876 CATATAGAAATTCATACACTTAGTATGGATTTCTTA-TTTCGTACACATAGTGCCCATAC-GAAA
1 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG-AA
33939 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
65 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
* *
33984 CATA-TGAAAATTCATACACTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAA
1 CATACAG-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAA
*
34048 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACTTAGTGCC
65 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
* *
34093 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTGCCCATACATAAA
1 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAA
*
34158 TTCATACACCTAGTATGGATTTCTTA
66 TTCATACACTTAGTATGGATTTCTTA
34184 AGTTTTTGCA
Statistics
Matches: 184, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
107 1 0.01
108 31 0.17
109 150 0.82
110 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (109 bp):
CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAA
TTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
Found at i:36231 original size:20 final size:22
Alignment explanation
Indices: 36201--36257 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
36191 ATTTCTGGCT
36201 CATGAGTATCGATACCA-T-TAC
1 CATG-GTATCGATACCACTATAC
*
36222 CATGGTATCGATACTACTATAC
1 CATGGTATCGATACCACTATAC
*
36244 CATGGTACCGATAC
1 CATGGTATCGATAC
36258 TTTATTACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 16 0.50
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (22 bp):
CATGGTATCGATACCACTATAC
Found at i:37440 original size:2 final size:2
Alignment explanation
Indices: 37433--37457 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37423 AGCTTTATTG
37433 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 T
37458 TTGTTTACAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39321 original size:28 final size:29
Alignment explanation
Indices: 39259--39499 Score: 209
Period size: 29 Copynumber: 8.3 Consensus size: 29
39249 ATAAATTTAT
* * *
39259 TTACGAAACTATCACCCTTTTAAAAATAT
1 TTACGAAAATAGCACCCTTTTAAAAATAA
* *
39288 TTACGAAAATAACACCATTTT-AAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
*
39316 TTACGAAAATAGCA-TCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
** *
39344 TTACGAAAAATAAAACCCTTTCAAAAATAA
1 TTACG-AAAATAGCACCCTTTTAAAAATAA
39374 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAGCACCCTTTTAAAAATAA
* * *** *
39403 TTACAAAAATAGCACCGTTACCGAAATTAA
1 TTACGAAAATAGCACCCTT-TTAAAAATAA
* * * * *
39433 TTAC-AAAACTAACATCATTTTAAACATAT
1 TTACGAAAA-TAGCACCCTTTTAAAAATAA
* * * *
39462 TTATGAAACTAGCACACTTTTAAAAATAT
1 TTACGAAAATAGCACCCTTTTAAAAATAA
*
39491 TTACAAAAA
1 TTACGAAAA
39500 CAACATCAAA
Statistics
Matches: 167, Mismatches: 39, Indels: 12
0.77 0.18 0.06
Matches are distributed among these distances:
27 4 0.02
28 31 0.19
29 95 0.57
30 37 0.22
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.29
Consensus pattern (29 bp):
TTACGAAAATAGCACCCTTTTAAAAATAA
Found at i:39578 original size:58 final size:58
Alignment explanation
Indices: 39473--39586 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
39463 TATGAAACTA
* *
39473 GCACACTTTTAAAAATATTTACAAAAACAACATCAAACAGAATTTAATTACGTATTAG
1 GCACACTTTTAAAAATATTCACAAAAACAACATCAAACAGAAATTAATTACGTATTAG
* * * *
39531 GCACTCTTTTAAAAATATTCCCAGAATAACACCAT-AACCA-AAATTAATTACGTATT
1 GCACACTTTTAAAAATATTCACA-AA-AACAACATCAAACAGAAATTAATTACGTATT
39587 TATCACCCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 35 0.73
59 6 0.12
60 7 0.15
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (58 bp):
GCACACTTTTAAAAATATTCACAAAAACAACATCAAACAGAAATTAATTACGTATTAG
Found at i:40093 original size:20 final size:20
Alignment explanation
Indices: 40068--40105 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40058 CACTTCATTT
40068 TTTTATTCT-TAGTGCTATTA
1 TTTTATT-TATAGTGCTATTA
40088 TTTTATTTATAGTGCTAT
1 TTTTATTTATAGTGCTAT
40106 AGGATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAGTGCTATTA
Found at i:46772 original size:28 final size:29
Alignment explanation
Indices: 46690--46922 Score: 220
Period size: 29 Copynumber: 8.1 Consensus size: 29
46680 ATGAAACTAT
* *
46690 CACCCTTTTAAAAATATTTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
*
46719 CACCTTTTTTAAAATAATTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
** * *
46748 CATTTTTTTAAAAATAATTACAAAAATAA
1 CACCTTTTTAAAAATAATTACGAAAATAG
*
46777 AACCTTTTTAAAAATAATTAC-AAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
* *
46805 TACCCTTTTAAAAATAATTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
*** * *
46834 CACCTTACCAAAATTAATTAC-AAAACTAA
1 CACCTTTTTAAAAATAATTACGAAAA-TAG
* * * * *
46863 CATCATTTTAAACATATTTACGAAACTAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
* * *
46892 TACAC-TTTTAAAAATATTTACAAAAATAG
1 CAC-CTTTTTAAAAATAATTACGAAAATAG
46921 CA
1 CA
46923 TCGAACAGAA
Statistics
Matches: 163, Mismatches: 37, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
28 29 0.18
29 130 0.80
30 4 0.02
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (29 bp):
CACCTTTTTAAAAATAATTACGAAAATAG
Found at i:46872 original size:115 final size:115
Alignment explanation
Indices: 46691--46916 Score: 278
Period size: 115 Copynumber: 2.0 Consensus size: 115
46681 TGAAACTATC
* *** * **
46691 ACCCTTTTAAAAATATTTACGAAAATAGCACCTTTTTTAAAATAATTACGAAAATAGCATTTTTT
1 ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAATAATTACGAAAATAACATCATTT
46756 TAAAAATAATTACAAAAATAAAAC-CTTTTTAAAAATAATTACAAAATAGT
66 TAAAAATAATTACAAAAATAAAACAC-TTTTAAAAATAATTACAAAATAGT
46806 ACCCTTTTAAAAATAATTACGAAAATAGCACC-TTACCAAAATTAATTAC-AAAACTAACATCAT
1 ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAA-TAATTACGAAAA-TAACATCAT
* * * * ** *
46869 TTTAAACATATTTACGAAACTAGTACACTTTTAAAAATATTTACAAAA
64 TTTAAAAATAATTACAAAAATAAAACACTTTTAAAAATAATTACAAAA
46917 ATAGCATCGA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
114 10 0.11
115 83 0.88
116 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (115 bp):
ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAATAATTACGAAAATAACATCATTT
TAAAAATAATTACAAAAATAAAACACTTTTAAAAATAATTACAAAATAGT
Found at i:46935 original size:87 final size:86
Alignment explanation
Indices: 46695--46941 Score: 228
Period size: 86 Copynumber: 2.8 Consensus size: 86
46685 ACTATCACCC
* * * * ** ****
46695 TTTTAAAAATATTTACGAAAATAGCAC-CTTTTTTAAAATAATTACGAAAATAGCATTTTTTTAA
1 TTTTAAAAATAATTAC-AAAATAGTACAC-TTTTAAAAATAATTACAAAAATAGCACCTGAACAA
* *
46759 AAATAATTACAAAAATAAAACCT
64 AATTAATTACAAAAATAAAACCA
* * * *
46782 TTTTAAAAATAATTACAAAATAGTACCCTTTTAAAAATAATTACGAAAATAGCACCTTACCAAAA
1 TTTTAAAAATAATTACAAAATAGTACACTTTTAAAAATAATTACAAAAATAGCACCTGAACAAAA
* * *
46847 TTAATTACAAAACTAACATCA
66 TTAATTACAAAAATAAAACCA
* * * * *
46868 TTTTAAACATATTTACGAAACTAGTACACTTTTAAAAATATTTACAAAAATAGCATC-GAACAGA
1 TTTTAAAAATAATTAC-AAAATAGTACACTTTTAAAAATAATTACAAAAATAGCACCTGAACA-A
46932 AATTAATTAC
64 AATTAATTAC
46942 GTGTTACTCT
Statistics
Matches: 135, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
86 73 0.54
87 62 0.46
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (86 bp):
TTTTAAAAATAATTACAAAATAGTACACTTTTAAAAATAATTACAAAAATAGCACCTGAACAAAA
TTAATTACAAAAATAAAACCA
Found at i:51467 original size:30 final size:28
Alignment explanation
Indices: 51433--51700 Score: 135
Period size: 30 Copynumber: 9.1 Consensus size: 28
51423 CATATTAGAT
*
51433 TTAAAGGACTTAAATAGTAATAACATAAAC
1 TTAAAGGACTAAAATAGTAA-AA-ATAAAC
* *
51463 TTAAAGGGCTAAAATAGTAAAAATAGCAAT
1 TTAAAGGACTAAAATAGTAAAAATA--AAC
* *
51493 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAAT--AAAC
* * * ** * *
51523 TTAAAGGATTAACACAACAAAATAGAAAT
1 TTAAAGGACTAAAATAGTAAAA-ATAAAC
* * * *
51552 TTAAAGGAATAAAATGGCAAAAACAAAAAC
1 TTAAAGGACTAAAATAG-TAAAA-ATAAAC
* *
51582 TTAAAGGTCTAAAATAGTAAAAACCAAAC
1 TTAAAGGACTAAAATAGTAAAAA-TAAAC
* * * * *
51611 TTAAGGGTCT-AAATAGCAATACAA-ATAT
1 TTAAAGGACTAAAATAGTAA-A-AATAAAC
** *
51639 TTAAAGGACTAAAATAACAAAAATAGACAT
1 TTAAAGGACTAAAATAGTAAAAATA-A-AC
* * *
51669 TTAAAGGACTAAAATAGCAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAATAAAC
51697 TTAA
1 TTAA
51701 GCAACTAAAT
Statistics
Matches: 185, Mismatches: 40, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.01
28 29 0.16
29 44 0.24
30 108 0.58
31 1 0.01
32 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (28 bp):
TTAAAGGACTAAAATAGTAAAAATAAAC
Found at i:51722 original size:87 final size:87
Alignment explanation
Indices: 51550--51710 Score: 189
Period size: 87 Copynumber: 1.9 Consensus size: 87
51540 CAAAATAGAA
** * *
51550 ATTTAAAGGAATAAAATGGCAAAAACAAAAACTTAAAGGTCTAAAATAGTAAAAACCAAACTTAA
1 ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGCAAAAACCAAACTTAA
***
51615 GGGTCTAAATAGCAATACAAAT
66 GCAACTAAATAGCAATACAAAT
* * * * * * *
51637 ATTTAAAGGACTAAAATAACAAAAATAGACATTTAAAGGACTAAAATAGCAAATA-GAAACTTAA
1 ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGCAAAAACCAAACTTAA
51701 GCAACTAAAT
66 GCAACTAAAT
51711 GGTAATAACA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
86 15 0.25
87 45 0.75
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (87 bp):
ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGCAAAAACCAAACTTAA
GCAACTAAATAGCAATACAAAT
Found at i:52600 original size:15 final size:14
Alignment explanation
Indices: 52574--52613 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
52564 TTGAATGGGT
*
52574 TTTTGGTTTTTTTTG
1 TTTT-GTTTTTTTTC
*
52589 TTATGTTTTTTTTC
1 TTTTGTTTTTTTTC
52603 TTTTGTTTTTT
1 TTTTGTTTTTT
52614 CTCTGGGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTGTTTTTTTTC
Found at i:53051 original size:3 final size:3
Alignment explanation
Indices: 53043--53078 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53033 AAATGTAATT
53043 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53079 GATAATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55930 original size:19 final size:19
Alignment explanation
Indices: 55906--55952 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
55896 CCAGCCTATA
55906 ACTCGATTCGAGACTCGTG
1 ACTCGATTCGAGACTCGTG
* *
55925 ACTCGATTCGAGATTTGTG
1 ACTCGATTCGAGACTCGTG
*
55944 ACCCGATTC
1 ACTCGATTC
55953 AAGATTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (19 bp):
ACTCGATTCGAGACTCGTG
Found at i:55957 original size:19 final size:19
Alignment explanation
Indices: 55922--55970 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
55912 TTCGAGACTC
* *
55922 GTGACTCGATTCGAGATTT
1 GTGACCCGATTCAAGATTT
55941 GTGACCCGATTCAAGATTT
1 GTGACCCGATTCAAGATTT
*
55960 GTGACCTGATT
1 GTGACCCGATT
55971 TATTACTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (19 bp):
GTGACCCGATTCAAGATTT
Found at i:56967 original size:29 final size:29
Alignment explanation
Indices: 56934--57004 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
56924 TTGGTTCGTG
56934 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
*
56963 AGTTTGAGTCGAGTTGAGCTTATTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
56992 AGTTTGAGTCGAG
1 AGTTTGAGTCGAG
57005 CTCAGCAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (29 bp):
AGTTTGAGTCGAGTTGAGCTTACTTTTAA
Found at i:58578 original size:28 final size:28
Alignment explanation
Indices: 58546--58601 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
58536 GATCAATGTA
58546 ACCTTATAGATTTGGCTATAACATTTAG
1 ACCTTATAGATTTGGCTATAACATTTAG
*
58574 ACCTTCTAGATTTGGCTATAACATTTAG
1 ACCTTATAGATTTGGCTATAACATTTAG
58602 GTCAGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (28 bp):
ACCTTATAGATTTGGCTATAACATTTAG
Done.