Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009747.1 Corchorus capsularis cultivar CVL-1 contig09768, 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: 45753
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:859 original size:20 final size:21
Alignment explanation
Indices: 834--875 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
824 TCTTGGGTTC
*
834 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGCAATTGTGAGT
*
854 TACTCTCATGCAATTGTGAGT
1 TACTCTCACGCAATTGTGAGT
875 T
1 T
876 TTCTTTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (21 bp):
TACTCTCACGCAATTGTGAGT
Found at i:8162 original size:7 final size:7
Alignment explanation
Indices: 8150--8216 Score: 113
Period size: 7 Copynumber: 10.0 Consensus size: 7
8140 AATTAATCTC
8150 GGTTTAG
1 GGTTTAG
8157 GGTTTAG
1 GGTTTAG
8164 GG-TTAG
1 GGTTTAG
8170 GGTTTAG
1 GGTTTAG
8177 GGTTTAG
1 GGTTTAG
8184 GG-TTAG
1 GGTTTAG
8190 GG-TTAG
1 GGTTTAG
8196 GGTTTAG
1 GGTTTAG
8203 GGTTTAG
1 GGTTTAG
8210 GGTTTAG
1 GGTTTAG
8217 CGCTAAAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.31
7 40 0.69
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:8171 original size:13 final size:14
Alignment explanation
Indices: 8150--8216 Score: 113
Period size: 13 Copynumber: 5.0 Consensus size: 14
8140 AATTAATCTC
8150 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAG
8164 GG-TTAGGGTTTAG
1 GGTTTAGGGTTTAG
8177 GGTTTAGGG-TTAG
1 GGTTTAGGGTTTAG
8190 GG-TTAGGGTTTAG
1 GGTTTAGGGTTTAG
8203 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAG
8217 CGCTAAAATG
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.12
13 25 0.50
14 19 0.38
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:8175 original size:20 final size:20
Alignment explanation
Indices: 8150--8216 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
8140 AATTAATCTC
8150 GGTTTAGGGTTTAGGGTTAG
1 GGTTTAGGGTTTAGGGTTAG
8170 GGTTTAGGGTTTAGGGTTAG
1 GGTTTAGGGTTTAGGGTTAG
8190 GG-TTAGGGTTTAGGGTTTAG
1 GGTTTAGGGTTTAGGG-TTAG
8210 GGTTTAG
1 GGTTTAG
8217 CGCTAAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.29
20 28 0.62
21 4 0.09
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (20 bp):
GGTTTAGGGTTTAGGGTTAG
Found at i:8681 original size:27 final size:27
Alignment explanation
Indices: 8651--8707 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
8641 CGCCTCGGGC
8651 ATTCCCGTTTTGGGCTTAATTTGTTTT
1 ATTCCCGTTTTGGGCTTAATTTGTTTT
8678 ATTCCCGTTTTGGGCTTAATTTGTTTT
1 ATTCCCGTTTTGGGCTTAATTTGTTTT
8705 ATT
1 ATT
8708 TGATTATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.56
Consensus pattern (27 bp):
ATTCCCGTTTTGGGCTTAATTTGTTTT
Found at i:19056 original size:14 final size:14
Alignment explanation
Indices: 19037--19065 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19027 ATTAGTGATC
19037 GTACCCTATTCACG
1 GTACCCTATTCACG
19051 GTACCCTATTCACG
1 GTACCCTATTCACG
19065 G
1 G
19066 AACTGAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (14 bp):
GTACCCTATTCACG
Found at i:19330 original size:2 final size:2
Alignment explanation
Indices: 19325--19359 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19315 TGGTGAAAAT
*
19325 TA TA TA TA TA TA TA CA 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 T
19360 TAGATACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21024 original size:156 final size:155
Alignment explanation
Indices: 20580--21053 Score: 618
Period size: 156 Copynumber: 3.0 Consensus size: 155
20570 ATCTCAAACA
* * * *
20580 GACTTA-AGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGTGAGAAACCAACTT
1 GACTTAGA-ATGAAAAACTTATACAAGTTTTTCACTTAAGGACAATTTGGGTGTGAAACCAACTT
* * *
20644 CACTATGATAGGGAGTTGGGTTTTACTTAGAATTTTTTTCATAG-TCTTAT-GGAGATAGTCTAA
65 CACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGAT-TTATGGGA-ATAATCTAA
* * ** ** * * *
20707 GTCTAATGG-CCAAGTTTCATCTTAAGTG
128 GCCTACTGGTGGAA-AATCAACTTCATTG
* * * *
20735 GACTTAGTATGAAAAGCTTATACATGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCAACTT
1 GACTTAGAATGAAAAACTTATACAAGTTTTTCACTTAAGGACAATTT-GGGTGTGAAACCAACTT
*
20800 CACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATA-ACTTTATGGAAATAATCTAAG
65 CACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGA-TTTATGGGAATAATCTAAG
20864 CCTACTGGTGGAAAATCAACTTCATTG
129 CCTACTGGTGGAAAATCAACTTCATTG
20891 GACTTAGAATGAAAAACTTATACAAGTTTTTCACTTAAGGACAATTTGGGATGTGAAACCAACTT
1 GACTTAGAATGAAAAACTTATACAAGTTTTTCACTTAAGGACAATTTGGG-TGTGAAACCAACTT
*
20956 CACTATGATAGGTAGTTCGGTTTTACTTAG-ATTTTTTCCCATAGATTTATGGGAATAATCTAAG
65 CACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTT-CCATAGATTTATGGGAATAATCTAAG
* *
21020 CCTACTGGTGGATAATCAGCTTCATTG
129 CCTACTGGTGGAAAATCAACTTCATTG
21047 GACTTAG
1 GACTTAG
21054 GGAGACAAAC
Statistics
Matches: 282, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
155 50 0.18
156 226 0.80
157 6 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (155 bp):
GACTTAGAATGAAAAACTTATACAAGTTTTTCACTTAAGGACAATTTGGGTGTGAAACCAACTTC
ACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTCCATAGATTTATGGGAATAATCTAAGCC
TACTGGTGGAAAATCAACTTCATTG
Found at i:23038 original size:22 final size:22
Alignment explanation
Indices: 23008--23066 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
22998 TAATAGTGCA
* *
23008 GTTACCAAAATTTCACAGGGGG
1 GTTATCAAAATTTCACAGGGAG
**
23030 GTTATCAAAATTTCATTGGGAG
1 GTTATCAAAATTTCACAGGGAG
*
23052 GTTATCAAAGTTTCA
1 GTTATCAAAATTTCA
23067 TAGTGTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (22 bp):
GTTATCAAAATTTCACAGGGAG
Found at i:23651 original size:60 final size:63
Alignment explanation
Indices: 23555--23673 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 63
23545 CATAAGGAGG
*
23555 TTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATGTGA
1 TTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTGTGGTTACCAAAATTTTATGTGA
*
23618 TTATCAAAATTT-A-ACAGG-G-TTATCAACATTTCATAGTGTGGTTACCAAAATTTTAT
1 TTATCAAAATTTCATA-AGGAGATTATCAAAATTTCATAGTGTGGTTACCAAAATTTTAT
23674 AAGAATGTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
60 35 0.66
61 2 0.04
62 4 0.08
63 12 0.23
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (63 bp):
TTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTGTGGTTACCAAAATTTTATGTGA
Found at i:23670 original size:22 final size:22
Alignment explanation
Indices: 23531--23670 Score: 116
Period size: 22 Copynumber: 6.6 Consensus size: 22
23521 AGTACCTAAA
* * *
23531 GGTTAACAAAATGTCATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
*
23553 GGTTATCAAAATTTCATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
*
23575 GATTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
23597 GGTTATCAAAATTT--TA-TGT
1 GGTTATCAAAATTTCATAGTGT
* **
23616 GATTATCAAAATTT-A-ACAG-
1 GGTTATCAAAATTTCATAGTGT
*
23635 GGTTATCAACATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
23657 GGTTACCAAAATTT
1 GGTTATCAAAATTT
23671 TATAAGAATG
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
19 29 0.29
20 4 0.04
21 4 0.04
22 62 0.63
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:23718 original size:22 final size:22
Alignment explanation
Indices: 23687--23765 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
23677 AATGTTGTGT
* *
23687 GGTTATCAAAATTTCATAGGAA
1 GGTTAACAAAATTTCATTGGAA
*
23709 GGTTAACAAAATTTCATTGGCA
1 GGTTAACAAAATTTCATTGGAA
* *
23731 GGTTATCAAAATTTCATTGGGA
1 GGTTAACAAAATTTCATTGGAA
*
23753 GATTAACAAAATT
1 GGTTAACAAAATT
23766 ACAAATGGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (22 bp):
GGTTAACAAAATTTCATTGGAA
Found at i:23778 original size:44 final size:44
Alignment explanation
Indices: 23687--23793 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
23677 AATGTTGTGT
* * *
23687 GGTTATCAAAATTTCATAGGAAGGTTAACAAAATTTCATTGGCA
1 GGTTATCAAAATTTCATAGGAAGATTAACAAAATTACAATGGCA
* *
23731 GGTTATCAAAATTTCATTGGGAGATTAACAAAATTACAAATGG-A
1 GGTTATCAAAATTTCATAGGAAGATTAACAAAATTAC-AATGGCA
**
23775 GGTTAT-AAAAAATCATAGG
1 GGTTATCAAAATTTCATAGG
23794 GAGACTAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 10 0.19
44 40 0.74
45 4 0.07
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGGAAGATTAACAAAATTACAATGGCA
Found at i:23845 original size:22 final size:22
Alignment explanation
Indices: 23819--23909 Score: 110
Period size: 22 Copynumber: 4.1 Consensus size: 22
23809 TTAAGGGCAT
* *
23819 TTATCTAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAATGAGG
* *
23841 TTATCAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
23863 TTATCACAATTTCATAATGTGA
1 TTATCAAAATTTCATAATGAGG
*
23885 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAATGAGG
23907 TTA
1 TTA
23910 AAAAATTCTG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:24024 original size:22 final size:22
Alignment explanation
Indices: 23996--24084 Score: 101
Period size: 22 Copynumber: 4.0 Consensus size: 22
23986 TTATTAAAAA
*
23996 TTATAGTGTGGTTATCAAAATT
1 TTATAGTGAGGTTATCAAAATT
24018 TTATAGTGAGGTTATCAAAATT
1 TTATAGTGAGGTTATCAAAATT
* * *
24040 TT-TCTGTGTA-GTTATCGAAACT
1 TTAT-AGTG-AGGTTATCAAAATT
*
24062 GTATAGTGAGGTTATCAAAATT
1 TTATAGTGAGGTTATCAAAATT
24084 T
1 T
24085 CATAATTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.04
22 50 0.93
23 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (22 bp):
TTATAGTGAGGTTATCAAAATT
Found at i:24055 original size:44 final size:44
Alignment explanation
Indices: 24001--24084 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
23991 AAAAATTATA
* * *
24001 GTGTGGTTATCAAAATTTTATAGTGAGGTTATCAAAATTTTTCT
1 GTGTAGTTATCAAAACTGTATAGTGAGGTTATCAAAATTTTTCT
*
24045 GTGTAGTTATCGAAACTGTATAGTGAGGTTATCAAAATTT
1 GTGTAGTTATCAAAACTGTATAGTGAGGTTATCAAAATTT
24085 CATAATTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (44 bp):
GTGTAGTTATCAAAACTGTATAGTGAGGTTATCAAAATTTTTCT
Found at i:27367 original size:23 final size:23
Alignment explanation
Indices: 27335--27383 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
27325 CATTTTGGTC
*
27335 AATTCGTAGTTCATTTTTAAGTA
1 AATTCATAGTTCATTTTTAAGTA
*
27358 AATTCATAGTTTATTTTTAAGTA
1 AATTCATAGTTCATTTTTAAGTA
27381 AAT
1 AAT
27384 ATGTTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (23 bp):
AATTCATAGTTCATTTTTAAGTA
Found at i:30909 original size:99 final size:96
Alignment explanation
Indices: 30475--31330 Score: 664
Period size: 99 Copynumber: 8.8 Consensus size: 96
30465 CCTACTTTTT
* * * ** * *
30475 CCCAAAGCGCCCTTCCCGGACGGAAGGCACTCAATTTTTATTTGCTTTTTCCCTAAA-CGCCCTT
1 CCCAAAACGCCCTTCCCAGACGGAAGCCA-TTTA-TTTTACTTGCTATTTCCC-AAAGCGCCCTT
** * * * * * *
30539 CCTGGACGGAAGGCACTTCTTTTATTTGCTTTTT
63 CCCAGACGGAAGCCATTTATTTTACTTGCTATTC
* * * * *
30573 CCTAAAATGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTACCT-TTCCCCAAAGCGCCCTTC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTAT-TTTACTT-GCTATTTCCCAAAGCGCCCTTC
* *
30637 CCAGACGGAAGCCATTCATCTTTACTTGCTATTT
64 CCAGACGGAAGCCATTTAT-TTTACTTGCTATTC
* * *
30671 CCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTTCTATTTCCCAAAGCGCCCTTCA
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTTGCTATTTCCCAAAGCGCCCTTCC
* *
30736 CAGACGGAAGCCACTTATTTTACTTGCTATTT
65 CAGACGGAAGCCATTTATTTTACTTGCTATTC
* * *
30768 CCCAAAGCGCCCTTCTCAGACGGAAGCCATTTATTTTCGCTTGCTATTTCCCAAAGCGCCCTTCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTT-ACTTGCTATTTCCCAAAGCGCCCTTCC
* *
30833 CAGACGGAAGCCATTTATTTTCGCTAGCTATCTC
65 CAGACGGAAGCCATTTATTTT-ACTTGCTAT-TC
*
30867 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTATTTCCCAAAGCGCCCTTCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTT-ACTTGCTATTTCCCAAAGCGCCCTTCC
*
30932 CAGACGGAAGCCATTTATTTTTGCTTGCTATCTC
65 CAGACGGAAGCCATTTA-TTTTACTTGCTAT-TC
** * *
30966 CCCAAAACGCCCTTCCTGGACGGAAGCCGTTTATCTTTACTTGCTATTTCCCAAAACGCCCTTCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTAT-TTTACTTGCTATTTCCCAAAGCGCCCTTCC
* * * * * * *
31031 CGGACGGAAGGCATTGATTACTACCTG-TTTTT
65 CAGACGGAAGCCATTTATT-TTACTTGCTATTC
* * * * * * * ** *
31063 CCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTACTACCTG-TTTTTCCCAAAATGCCCTTAC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT-TTACTTGCTATTTCCCAAAGCGCCCTTCC
* * * * * * *
31127 CGGATGGAAGGCACTAACCTTTACCTT--T-TTT
65 CAGACGGAAGCCATTTA-TTTTA-CTTGCTATTC
* *** * * * * **
31158 CCCAAAATGCCCTTCTTGGACGGAAGGCACTTATCTTACTTGCTATTTTCCAAAAATGCCCTTCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTA-TTTCCCAAAGCGCCCTTCC
* * * * *** *
31223 CGGATGGAAGACACTTATTTTTACCCACTTTTC
65 CAGACGGAAGCCATTTA-TTTTACTTGCTATTC
** * * * * * * *
31256 CCCAAAGTGCCCTTCCCTGACGGAAGGCACTGACTTTTACTTGCTTTTTCCTAAAACGCCCTTCC
1 CCCAAAACGCCCTTCCCAGACGGAAGCCATTTA-TTTTACTTGCTATTTCCCAAAGCGCCCTTCC
*
31321 CGGACGGAAG
65 CAGACGGAAG
31331 GCGTTAGTTT
Statistics
Matches: 643, Mismatches: 94, Indels: 42
0.83 0.12 0.05
Matches are distributed among these distances:
94 5 0.01
95 35 0.05
96 80 0.12
97 165 0.26
98 174 0.27
99 177 0.28
100 7 0.01
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (96 bp):
CCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTACTTGCTATTTCCCAAAGCGCCCTTCCC
AGACGGAAGCCATTTATTTTACTTGCTATTC
Found at i:31332 original size:49 final size:48
Alignment explanation
Indices: 30469--31330 Score: 706
Period size: 49 Copynumber: 17.7 Consensus size: 48
30459 TCTTTACCTA
* * ** *
30469 CTTTTTCCCAAAGCGCCCTTCCCGGACGGAAGGCACTCAATTTTTATTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCA-TTTA-TTTTACTTG
* * * * * *
30519 CTTTTTCCCTAAACGCCCTTCCTGGACGGAAGGCACTTCTTTTATTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTTACTTG
* * * * *
30567 CTTTTTCCTAAAATGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTA
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTAT-TTTACTTG
* * * * *
30616 CCTTTCCCCAAAGCGCCCTTCCCAGACGGAAGCCATTCATCTTTACTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTAT-TTTACTTG
* * * *
30665 CTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTT
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTA-TTTTACTTG
* * * * *
30714 CTATTTCCCAAAGCGCCCTTCACAGACGGAAGCCACTTATTTTACTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTTACTTG
* * * * *
30762 CTATTTCCCAAAGCGCCCTTCTCAGACGGAAGCCATTTATTTTCGCTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTT-ACTTG
* * * * *
30811 CTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTAG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTT-ACTTG
* * * *
30860 CTATCTCCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTG
1 CT-TTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTT-ACTTG
* * * *
30910 CTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTGCTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTA-TTTTACTTG
* * * *
30959 CTATCTCCCCAAAACGCCCTTCCTGGACGGAAGCCGTTTATCTTTACTTG
1 CT-TTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTAT-TTTACTTG
* * * * *
31009 CTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCATTGATTACTACCTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATT-TTACTTG
* * * * *
31058 -TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTACTACCTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATT-TTACTTG
* * * * * * * *
31106 -TTTTTCCCAAAATGCCCTTACCGGATGGAAGGCACTAACCTTTACCT-
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTA-TTTTACTTG
* ** * * *
31153 -TTTTTCCCAAAATGCCCTTCTTGGACGGAAGGCACTTATCTTACTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTTACTTG
* * * * * ***
31200 CTATTTTCCAAAAATGCCCTTCCCGGATGGAAGACACTTATTTTTACCCA
1 CT-TTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTA-TTTTACTTG
* ** * * * *
31250 CTTTTCCCCAAAGTGCCCTTCCCTGACGGAAGGCACTGACTTTTACTTG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTA-TTTTACTTG
*
31299 CTTTTTCCTAAAACGCCCTTCCCGGACGGAAG
1 CTTTTTCCCAAAACGCCCTTCCCGGACGGAAG
31331 GCGTTAGTTT
Statistics
Matches: 695, Mismatches: 104, Indels: 27
0.84 0.13 0.03
Matches are distributed among these distances:
46 5 0.01
47 33 0.05
48 176 0.25
49 354 0.51
50 127 0.18
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.31
Consensus pattern (48 bp):
CTTTTTCCCAAAACGCCCTTCCCGGACGGAAGCCATTTATTTTACTTG
Found at i:32870 original size:14 final size:13
Alignment explanation
Indices: 32851--33057 Score: 75
Period size: 14 Copynumber: 16.4 Consensus size: 13
32841 CAATTTGCTC
32851 AAAAACAGGAACCT
1 AAAAACAGGAA-CT
32865 AAAAACAGGAACT
1 AAAAACAGGAACT
*
32878 AAAAA-A--CACT
1 AAAAACAGGAACT
32888 -AAAACAGGAACT
1 AAAAACAGGAACT
*
32900 AAAAAACAGGAAGT
1 -AAAAACAGGAACT
* *
32914 CAAAAATA-GAAAT
1 -AAAAACAGGAACT
*
32927 AAAAAACA-GAAAT
1 -AAAAACAGGAACT
*
32940 AAAAAACAGCAACT
1 -AAAAACAGGAACT
*
32954 CAAAAACAGTAA--
1 -AAAAACAGGAACT
* ***
32966 AACAATTTG--CT
1 AAAAACAGGAACT
* *
32977 CAAAAACATGAACC
1 -AAAAACAGGAACT
*
32991 CAAAACAGGAACT
1 AAAAACAGGAACT
*
33004 AAAAA-A--CACT
1 AAAAACAGGAACT
33014 -AAAACAGGAACT
1 AAAAACAGGAACT
*
33026 AAAAAACAGGAAGT
1 -AAAAACAGGAACT
*
33040 CAAAAACA-GAAAT
1 -AAAAACAGGAACT
33053 AAAAA
1 AAAAA
33058 ACTGCACTTA
Statistics
Matches: 147, Mismatches: 30, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
9 8 0.05
10 8 0.05
11 4 0.03
12 19 0.13
13 48 0.33
14 60 0.41
ACGTcount: A:0.63, C:0.16, G:0.11, T:0.10
Consensus pattern (13 bp):
AAAAACAGGAACT
Found at i:32893 original size:22 final size:22
Alignment explanation
Indices: 32866--32907 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
32856 CAGGAACCTA
32866 AAAACAGGAACTAAAAAACACT
1 AAAACAGGAACTAAAAAACACT
32888 AAAACAGGAACTAAAAAACA
1 AAAACAGGAACTAAAAAACA
32908 GGAAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAACAGGAACTAAAAAACACT
Found at i:33017 original size:22 final size:22
Alignment explanation
Indices: 32992--33033 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
32982 ACATGAACCC
32992 AAAACAGGAACTAAAAAACACT
1 AAAACAGGAACTAAAAAACACT
33014 AAAACAGGAACTAAAAAACA
1 AAAACAGGAACTAAAAAACA
33034 GGAAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAACAGGAACTAAAAAACACT
Found at i:33051 original size:126 final size:127
Alignment explanation
Indices: 32822--33059 Score: 424
Period size: 126 Copynumber: 1.9 Consensus size: 127
32812 AAACAGCCAT
* *
32822 CAACTCAAAAACAGTTAACCAATTTGCTCAAAAACAGGAACCTAAAAACAGGAACTAAAAAACAC
1 CAACTCAAAAACAGTAAAACAATTTGCTCAAAAACAGGAACCTAAAAACAGGAACTAAAAAACAC
*
32887 TAAAACAGGAACTAAAAAACAGGAAGTCAAAAATAGAAATAAAAAACAGAAATAAAAAACAG
66 TAAAACAGGAACTAAAAAACAGGAAGTCAAAAACAGAAATAAAAAACAGAAATAAAAAACAG
* *
32949 CAACTCAAAAACAGTAAAACAATTTGCTCAAAAACATGAACC-CAAAACAGGAACTAAAAAACAC
1 CAACTCAAAAACAGTAAAACAATTTGCTCAAAAACAGGAACCTAAAAACAGGAACTAAAAAACAC
33013 TAAAACAGGAACTAAAAAACAGGAAGTCAAAAACAGAAATAAAAAAC
66 TAAAACAGGAACTAAAAAACAGGAAGTCAAAAACAGAAATAAAAAAC
33060 TGCACTTAAG
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
126 67 0.63
127 39 0.37
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.11
Consensus pattern (127 bp):
CAACTCAAAAACAGTAAAACAATTTGCTCAAAAACAGGAACCTAAAAACAGGAACTAAAAAACAC
TAAAACAGGAACTAAAAAACAGGAAGTCAAAAACAGAAATAAAAAACAGAAATAAAAAACAG
Found at i:35479 original size:11 final size:11
Alignment explanation
Indices: 35460--35521 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
35450 AACAAAAGAA
35460 AACAGAATTAT
1 AACAGAATTAT
* *
35471 AACATAATTAG
1 AACAGAATTAT
*
35482 AACAAAATTAT
1 AACAGAATTAT
* *
35493 AACATAATTAA
1 AACAGAATTAT
35504 AACAGAATTAT
1 AACAGAATTAT
*
35515 AATAGAA
1 AACAGAA
35522 CATAATTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (11 bp):
AACAGAATTAT
Found at i:35490 original size:22 final size:22
Alignment explanation
Indices: 35458--35516 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
35448 ACAACAAAAG
35458 AAAACAGAATTATAACATAATT
1 AAAACAGAATTATAACATAATT
* *
35480 AGAACAAAATTATAACATAATT
1 AAAACAGAATTATAACATAATT
35502 AAAACAGAATTATAA
1 AAAACAGAATTATAA
35517 TAGAACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAACAGAATTATAACATAATT
Found at i:35539 original size:23 final size:23
Alignment explanation
Indices: 35509--35553 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35499 ATTAAAACAG
* * *
35509 AATTATAATAGAACATAATTATT
1 AATTATAACAGAAAAAAATTATT
35532 AATTATAACAGAAAAAAATTAT
1 AATTATAACAGAAAAAAATTAT
35554 AAACAGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTATAACAGAAAAAAATTATT
Found at i:35568 original size:17 final size:16
Alignment explanation
Indices: 35531--35570 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35521 ACATAATTAT
35531 TAATTATAACAGAAAA
1 TAATTATAACAGAAAA
* *
35547 AAATTATAAACAGAACA
1 TAATTAT-AACAGAAAA
35564 TAATTAT
1 TAATTAT
35571 CCAAGAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (16 bp):
TAATTATAACAGAAAA
Found at i:44138 original size:29 final size:29
Alignment explanation
Indices: 44072--44141 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
44062 GTTTTTTACT
*
44072 AAACTATAACAGTTTAGAAACTTATTTCAT
1 AAACTATAACAGTTTA-AAACTTATTTCAC
* * *
44102 AAAATATAATAGATTT-AAACTTATTTCCC
1 AAACTATAACAG-TTTAAAACTTATTTCAC
44131 AAACTATAACA
1 AAACTATAACA
44142 ATTTTTGCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 20 0.61
30 10 0.30
31 3 0.09
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTATAACAGTTTAAAACTTATTTCAC
Found at i:44602 original size:25 final size:25
Alignment explanation
Indices: 44568--44618 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
44558 GACTTCTTCT
44568 ATGGAACAATCATGGTTGCAAAGCC
1 ATGGAACAATCATGGTTGCAAAGCC
44593 ATGGAACAATCATGGTTGCAAAGCC
1 ATGGAACAATCATGGTTGCAAAGCC
44618 A
1 A
44619 GGTGTAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
ATGGAACAATCATGGTTGCAAAGCC
Found at i:45028 original size:80 final size:79
Alignment explanation
Indices: 44918--45073 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 79
44908 TAAAAAACTC
* **
44918 ATCAAAATCCTATGCCCCATTTTTGGTGTCCCATTGTG-CCTCAACGATTAAATTACGCCACGTG
1 ATCAAAATCCTATGCCCCATTTTTGGTGTCCCATTGTGTCC-CAACCACCAAATTACGCCACGTG
44982 TCCCTAGTATTATGG
65 TCCCTAGTATTATGG
* *
44997 ATCAAAATCCTCTGTCCCTATTTTTGGTGTCCCATTGTGTCCCAACCACCAAATTACGCCACGTG
1 ATCAAAATCCTATG-CCCCATTTTTGGTGTCCCATTGTGTCCCAACCACCAAATTACGCCACGTG
*
45062 TCCTTAGTATTA
65 TCCCTAGTATTA
45074 CACCTTATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.19
80 54 0.78
81 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (79 bp):
ATCAAAATCCTATGCCCCATTTTTGGTGTCCCATTGTGTCCCAACCACCAAATTACGCCACGTGT
CCCTAGTATTATGG
Done.