Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006693.1 Corchorus capsularis cultivar CVL-1 contig06714, 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: 68515
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:904 original size:45 final size:45
Alignment explanation
Indices: 848--961 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
838 TTCAGGAGCA
848 GCTAGCTGAACTGGAGAAAATGATACTTAAATCATTTGAGCAGCG
1 GCTAGCTGAACTGGAGAAAATGATACTTAAATCATTTGAGCAGCG
* **
893 GCTAGCTGAACTAGAGAAAATGATACTTAAATTGTTTGAGCAGCG
1 GCTAGCTGAACTGGAGAAAATGATACTTAAATCATTTGAGCAGCG
* *
938 GCTAGCTGAAATGAAGAAAATGAT
1 GCTAGCTGAACTGGAGAAAATGAT
962 TTTAGATCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (45 bp):
GCTAGCTGAACTGGAGAAAATGATACTTAAATCATTTGAGCAGCG
Found at i:3533 original size:22 final size:21
Alignment explanation
Indices: 3491--3999 Score: 101
Period size: 22 Copynumber: 23.0 Consensus size: 21
3481 GACAATCAAA
* *
3491 CAAAATTGCATAGGAAAGTTAT
1 CAAAATTTCATA-GTAAGTTAT
* *
3513 CAAAATTTCATAGTATTGTTAC
1 CAAAATTTCATAGTA-AGTTAT
* *
3535 CAAAACTTT-TTA-TGGAGATTAT
1 CAAAA-TTTCATAGT-AAG-TTAT
* * * *
3557 CAAAACTTCATATTCTAGTCAT
1 CAAAATTTCATAGT-AAGTTAT
* *
3579 CAAAATTTCATA-CAGAGATTAC
1 CAAAATTTCATAGTA-AG-TTAT
*
3601 CAAAATTTCATA-AAACGGTTAT
1 CAAAATTTCATAGTAA--GTTAT
* * *
3623 CAAAATTTCTTAGTGATGTTAA
1 CAAAATTTCATAGT-AAGTTAT
*
3645 CAAAATTTCATATGAAAGGTTAT
1 CAAAATTTCATA-GTAA-GTTAT
* * *
3668 CAAAATTTTATGAGGAGGTTAT
1 CAAAATTTCAT-AGTAAGTTAT
* ** *
3690 CAAATTTTTCATAGTGCGGTTAC
1 CAAA-ATTTCATAGT-AAGTTAT
*
3713 CAAAACTTT-ATA-TGGAGATTAT
1 CAAAA-TTTCATAGT-AAG-TTAT
* * *
3735 CAAAACTTT-GTATTCTAGTTAT
1 CAAAA-TTTCATAGT-AAGTTAT
*
3757 CAAAATTTCATA-TAGAGATTAC
1 CAAAATTTCATAGTA-AG-TTAT
* *
3779 CAGAATTTCATA-AAACGATTAT
1 CAAAATTTCATAGTAA-G-TTAT
* * *
3801 CAAAATTTCTTAGTGATGTTAA
1 CAAAATTTCATAGT-AAGTTAT
* *
3823 CAAAATTTTATATGAAAGGTTAT
1 CAAAATTTCATA-GTAA-GTTAT
* * *
3846 CAAAATTTTATGAGGAGGTTAT
1 CAAAATTTCAT-AGTAAGTTAT
* *
3868 CAAATTTTTCATAGTGCAGTTA-
1 CAAA-ATTTCATAGT-AAGTTAT
* * *
3890 C-CAATTTTATAATGT-ATTTAT
1 CAAAATTTCAT-A-GTAAGTTAT
*
3911 CGAAAA-TTCATA-TGGAGATTAT
1 C-AAAATTTCATAGT-AAG-TTAT
* * *
3933 CAAAATTTCACACTGAGGTTAT
1 CAAAATTTCATAGT-AAGTTAT
**
3955 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGT-AAGTTAT
* *
3977 CAAATTTTCATAGGGAAGTTAT
1 CAAAATTTCATA-GTAAGTTAT
3999 C
1 C
4000 GGAATTCCAT
Statistics
Matches: 362, Mismatches: 83, Indels: 84
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.00
20 9 0.02
21 28 0.08
22 242 0.67
23 78 0.22
24 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (21 bp):
CAAAATTTCATAGTAAGTTAT
Found at i:3559 original size:44 final size:43
Alignment explanation
Indices: 3509--3882 Score: 163
Period size: 44 Copynumber: 8.4 Consensus size: 43
3499 CATAGGAAAG
** *
3509 TTATCAAAATTTCATAGTATTGTTACCAAAACTTTTTATGGAGA
1 TTATCAAAATTTCATAGTACGGTTATCAAAA-TTTTTATGGAGA
* * * * * **
3553 TTATCAAAACTTCATA-TTCTAGTCATCAAAATTTCATACAGAGA
1 TTATCAAAATTTCATAGTAC-GGTTATCAAAATTT-TTATGGAGA
* **
3597 TTACCAAAATTTCATAAAACGGTTATCAAAATTTCTTA-GTGATG-
1 TTATCAAAATTTCATAGTACGGTTATCAAAATTT-TTATG-GA-GA
* * * *
3641 TTAACAAAATTTCATATGAAAGGTTATCAAAA-TTTTATGAGGAGG
1 TTATCAAAATTTCATA-GTACGGTTATCAAAATTTTTAT--GGAGA
* * * *
3686 TTATCAAATTTTTCATAGTGCGGTTACCAAAACTTTATATGGAGA
1 TTATCAAA-ATTTCATAGTACGGTTATCAAAA-TTTTTATGGAGA
* * * * *
3731 TTATCAAAACTTT-GTA-TTCTAGTTATCAAAATTTCATATAGAGA
1 TTATCAAAA-TTTCATAGTAC-GGTTATCAAAATTT-TTATGGAGA
* * ** *
3775 TTACCAGAATTTCATAAAACGATTATCAAAATTTCTTA-GTGATG-
1 TTATCAAAATTTCATAGTACGGTTATCAAAATTT-TTATG-GA-GA
* * * * *
3819 TTAACAAAATTTTATATGAAAGGTTATCAAAA-TTTTATGAGGAGG
1 TTATCAAAATTTCATA-GTACGGTTATCAAAATTTTTAT--GGAGA
*
3864 TTATCAAATTTTTCATAGT
1 TTATCAAA-ATTTCATAGT
3883 GCAGTTACCA
Statistics
Matches: 251, Mismatches: 53, Indels: 51
0.71 0.15 0.14
Matches are distributed among these distances:
43 18 0.07
44 139 0.55
45 74 0.29
46 15 0.06
47 5 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATAGTACGGTTATCAAAATTTTTATGGAGA
Found at i:3817 original size:178 final size:178
Alignment explanation
Indices: 3508--3893 Score: 648
Period size: 178 Copynumber: 2.2 Consensus size: 178
3498 GCATAGGAAA
* *** *
3508 GTTATCAAA-ATTTCATAGTATTGTTACCAAAACTTTTTATGGAGATTATCAAAACTTCATATTC
1 GTTATCAAATTTTTCATAGTGCAGTTACCAAAACTTTATATGGAGATTATCAAAACTTCATATTC
*
3572 TAGTCATCAAAATTTCATACAGAGATTACCAAAATTTCATAAAACGGTTATCAAAATTTCTTAGT
66 TAGTCATCAAAATTTCATACAGAGATTACCAAAATTTCATAAAACGATTATCAAAATTTCTTAGT
3637 GATGTTAACAAAATTTCATATGAAAGGTTATCAAAATTTTATGAGGAG
131 GATGTTAACAAAATTTCATATGAAAGGTTATCAAAATTTTATGAGGAG
* **
3685 GTTATCAAATTTTTCATAGTGCGGTTACCAAAACTTTATATGGAGATTATCAAAACTTTGTATTC
1 GTTATCAAATTTTTCATAGTGCAGTTACCAAAACTTTATATGGAGATTATCAAAACTTCATATTC
* * *
3750 TAGTTATCAAAATTTCATATAGAGATTACCAGAATTTCATAAAACGATTATCAAAATTTCTTAGT
66 TAGTCATCAAAATTTCATACAGAGATTACCAAAATTTCATAAAACGATTATCAAAATTTCTTAGT
*
3815 GATGTTAACAAAATTTTATATGAAAGGTTATCAAAATTTTATGAGGAG
131 GATGTTAACAAAATTTCATATGAAAGGTTATCAAAATTTTATGAGGAG
3863 GTTATCAAATTTTTCATAGTGCAGTTACCAA
1 GTTATCAAATTTTTCATAGTGCAGTTACCAA
3894 TTTTATAATG
Statistics
Matches: 195, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
177 9 0.05
178 186 0.95
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (178 bp):
GTTATCAAATTTTTCATAGTGCAGTTACCAAAACTTTATATGGAGATTATCAAAACTTCATATTC
TAGTCATCAAAATTTCATACAGAGATTACCAAAATTTCATAAAACGATTATCAAAATTTCTTAGT
GATGTTAACAAAATTTCATATGAAAGGTTATCAAAATTTTATGAGGAG
Found at i:5897 original size:23 final size:21
Alignment explanation
Indices: 5869--5913 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
5859 TTTTTAAACG
5869 TTATTTTGTAATAATAATATATA
1 TTATTTTGTAAT-AT-ATATATA
*
5892 TTATTTTTTAATATATATATA
1 TTATTTTGTAATATATATATA
5913 T
1 T
5914 GTGGATTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTTTGTAATATATATATA
Found at i:11803 original size:2 final size:2
Alignment explanation
Indices: 11791--11825 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11781 GTACTGACAT
11791 TA TA T- 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
11826 ATAGATGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14429 original size:16 final size:17
Alignment explanation
Indices: 14403--14435 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
14393 CTTAGGCTTC
14403 TTCTCTTTTTCTTTTTT
1 TTCTCTTTTTCTTTTTT
14420 TTCT-TTTTTCTTTTTT
1 TTCTCTTTTTCTTTTTT
14436 GGTGGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTCTCTTTTTCTTTTTT
Found at i:16373 original size:2 final size:2
Alignment explanation
Indices: 16355--16413 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
16345 ACATACATAA
* *
16355 AT AT ACT AT AT AA AT AT AT AT -T AT AT AT AT -T AT AT AT AT TT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16396 AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT
16414 GCAAATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17087 original size:52 final size:54
Alignment explanation
Indices: 17025--17131 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 54
17015 TAATTATGAG
* * *
17025 CAACACTTTTATGCATAAACCATCATCTCATCCATCA-T-ATCTTATCTAATCC
1 CAACACTTTTATGCACAAACCATCATCCCAGCCATCACTAATCTTATCTAATCC
17077 CAACACTTTTATGCACAAACCATCATCCCAGCCATCATCTAATCTTATCTAATCC
1 CAACACTTTTATGCACAAACCATCATCCCAGCCATCA-CTAATCTTATCTAATCC
17132 TACCCCCATA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 34 0.69
54 1 0.02
55 14 0.29
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.32
Consensus pattern (54 bp):
CAACACTTTTATGCACAAACCATCATCCCAGCCATCACTAATCTTATCTAATCC
Found at i:26816 original size:15 final size:16
Alignment explanation
Indices: 26787--26818 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
26777 CCCACAGAGA
26787 ACAATTAATTTCTATT
1 ACAATTAATTTCTATT
26803 ACAATTAA-TTCTATT
1 ACAATTAATTTCTATT
26818 A
1 A
26819 AGAAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
ACAATTAATTTCTATT
Found at i:30167 original size:21 final size:20
Alignment explanation
Indices: 30128--30172 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30118 ACAGATTAAT
* *
30128 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
30148 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
30169 TAAA
1 TAAA
30173 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:31467 original size:11 final size:11
Alignment explanation
Indices: 31450--31481 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31440 ATTGTCTTCA
31450 AATCTTCAAAT
1 AATCTTCAAAT
*
31461 TATCTTCAAAT
1 AATCTTCAAAT
31472 AATCTTCAAA
1 AATCTTCAAA
31482 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:31478 original size:22 final size:22
Alignment explanation
Indices: 31427--31481 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
31417 TCTGGGCTTG
*
31427 AAATAATTCTTC-AATTGTCTTC
1 AAATAA-TCTTCAAATTATCTTC
31449 --A-AATCTTCAAATTATCTTC
1 AAATAATCTTCAAATTATCTTC
31468 AAATAATCTTCAAA
1 AAATAATCTTCAAA
31482 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 1 0.04
21 1 0.04
22 10 0.36
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATAATCTTCAAATTATCTTC
Found at i:39273 original size:2 final size:2
Alignment explanation
Indices: 39266--39301 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39256 ATGTAGTGTC
39266 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
39302 CTAGGTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43432 original size:6 final size:6
Alignment explanation
Indices: 43421--43458 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
43411 ATTAATTTGC
43421 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
43459 GCTTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:45554 original size:103 final size:103
Alignment explanation
Indices: 45375--45582 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
45365 AGTGCGTTTC
45375 TTTTATTTGGGTTCGACGATCAAATCCCCTGTTTCATCATAGCTCTAATATTTGTAGTTTGGTTA
1 TTTTATTTGGGTTCGACGATCAAATCCCCTGTTTCATCATAGCTCTAATATTTGTAGTTTGGTTA
45440 TTGATAATTGTGGTAGATTAGATGACTTAGACTCAATA
66 TTGATAATTGTGGTAGATTAGATGACTTAGACTCAATA
45478 TTTTATTTGGGTTCGACGATCAAATCCCCTGTTTCATCATAGCTCTAATATTTGTAGTTTGGTTA
1 TTTTATTTGGGTTCGACGATCAAATCCCCTGTTTCATCATAGCTCTAATATTTGTAGTTTGGTTA
45543 TTGATAATTGTGGTAGATTAGATGACTTAGACTCAATA
66 TTGATAATTGTGGTAGATTAGATGACTTAGACTCAATA
45581 TT
1 TT
45583 AGAATTATTG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (103 bp):
TTTTATTTGGGTTCGACGATCAAATCCCCTGTTTCATCATAGCTCTAATATTTGTAGTTTGGTTA
TTGATAATTGTGGTAGATTAGATGACTTAGACTCAATA
Found at i:45650 original size:12 final size:13
Alignment explanation
Indices: 45627--45651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45617 ACAAAACAGA
45627 GGGAATTTTTTTG
1 GGGAATTTTTTTG
45640 GGGAATTTTTTT
1 GGGAATTTTTTT
45652 ATGTTTCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
GGGAATTTTTTTG
Found at i:45885 original size:33 final size:33
Alignment explanation
Indices: 45843--45911 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
45833 GGTGGCTGCA
*
45843 ATGTTTGAATGTTCTTGGTGTTCATAATAGTTC
1 ATGTTTGAATGTTCTTAGTGTTCATAATAGTTC
45876 ATGTTTGAATGTTCTTAGTGTTCATAATAGTTC
1 ATGTTTGAATGTTCTTAGTGTTCATAATAGTTC
45909 ATG
1 ATG
45912 ATAAAATAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (33 bp):
ATGTTTGAATGTTCTTAGTGTTCATAATAGTTC
Found at i:56567 original size:2 final size:2
Alignment explanation
Indices: 56512--56555 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
56502 ATATATTGCA
*
56512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
56554 AT
1 AT
56556 GTAGCTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63792 original size:41 final size:42
Alignment explanation
Indices: 63735--63815 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
63725 TGTGTTTGCT
*
63735 TTATCGTGTCTCGTGTCCGCAA-CGCGTC-AAACACGATTAGA
1 TTATCATGTCTCGTGTCC-CAATCGCGTCAAAACACGATTAGA
* * *
63776 TTATCATGTTTCGTGTCCTAATCGTGTCAAAACACGATTA
1 TTATCATGTCTCGTGTCCCAATCGCGTCAAAACACGATTA
63816 ACATATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.06
41 21 0.62
42 11 0.32
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (42 bp):
TTATCATGTCTCGTGTCCCAATCGCGTCAAAACACGATTAGA
Found at i:66348 original size:20 final size:20
Alignment explanation
Indices: 66307--66349 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
66297 CTCTCACAAG
* *
66307 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
66327 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
66347 TTT
1 TTT
66350 TCAACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:66643 original size:104 final size:105
Alignment explanation
Indices: 66444--66643 Score: 321
Period size: 104 Copynumber: 1.9 Consensus size: 105
66434 TTAATTCCAA
*
66444 TATTAATCGACTAAAACTCCAAGTCTTCTCTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGG
1 TATTAATCGACTAAAACTCCAAGTCTTCACTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGG
* * *
66509 AGGCAGTATTAATCGATGAAAACTCCAGTTTGAGTTTTAG
66 AGCCAGTATTAATCAATGAAAACTCAAGTTTGAGTTTTAG
*
66549 TATTAATCGACTAAAACTCCAAGTCTTCAC-TTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGG
1 TATTAATCGACTAAAACTCCAAGTCTTCACTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGG
* * *
66613 AGCCAGTATTAATTAATGAATACTTAAGTTT
66 AGCCAGTATTAATCAATGAAAACTCAAGTTT
66644 CATGTTTCAA
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 58 0.67
105 29 0.33
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (105 bp):
TATTAATCGACTAAAACTCCAAGTCTTCACTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGG
AGCCAGTATTAATCAATGAAAACTCAAGTTTGAGTTTTAG
Found at i:66669 original size:105 final size:105
Alignment explanation
Indices: 66408--66671 Score: 316
Period size: 105 Copynumber: 2.5 Consensus size: 105
66398 CTGTCAGAAA
* * * * * *
66408 AGTATTAGTCGATGAAAACTTC-AGTTTTAATTCCAATATTAATCGACTAAAACTCCAAGTCTTC
1 AGTATTAATCAATGAAAAC-TCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTC
* *
66472 TCTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGGC
65 ACTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * * **
66513 AGTATTAATCGATGAAAACTCCAGTTTGAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCAATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTCA
*
66578 C-TTTGAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * * *
66617 AGTATTAATTAATGAATACTTAAGTTTCATGTTTCAACATTCATCGATTAAAACT
1 AGTATTAATCAATGAAAACTCAAGTTTCA-GTTTCAACATTAATCGACTAAAACT
66672 TTCTTTAATT
Statistics
Matches: 137, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
104 61 0.45
105 76 0.55
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (105 bp):
AGTATTAATCAATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTTCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Done.