Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021425.1 Corchorus olitorius cultivar O-4 contig21458, 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: 32917
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:17375 original size:22 final size:22
Alignment explanation
Indices: 17350--17516 Score: 81
Period size: 22 Copynumber: 7.6 Consensus size: 22
17340 TCTCCTTATC
17350 AAATTTTGATAACCTTTCTATG
1 AAATTTTGATAACCTTTCTATG
* *** *
17372 AAATTTTAATAATGATACTATCG
1 AAATTTTGATAACCTTTCTAT-G
* * *
17395 -AATTTCGAGAACCTTTTTAT-
1 AAATTTTGATAACCTTTCTATG
* ** *
17415 AATTTTTTTTAACCTTTTTATG
1 AAATTTTGATAACCTTTCTATG
* ** *
17437 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTTCTATG
* **
17459 GAATTTTGA-AGACCTCACTATG
1 AAATTTTGATA-ACCTTTCTATG
* *
17481 AAATTTTGATAA-CTTCCCAATG
1 AAATTTTGATAACCTT-TCTATG
*
17503 AAATTCTGATAACC
1 AAATTTTGATAACC
17517 AACACTATGA
Statistics
Matches: 105, Mismatches: 33, Indels: 13
0.70 0.22 0.09
Matches are distributed among these distances:
21 18 0.17
22 84 0.80
23 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTTCTATG
Found at i:17535 original size:23 final size:22
Alignment explanation
Indices: 17509--17562 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
17499 AATGAAATTC
*
17509 TGATAACCAACACTATGAGATGT
1 TGATAACCAACA-TATGAGATAT
** *
17532 TGATAACCTCCATATGATATAT
1 TGATAACCAACATATGAGATAT
17554 TGATAACCA
1 TGATAACCA
17563 TGTTATGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (22 bp):
TGATAACCAACATATGAGATAT
Found at i:17626 original size:22 final size:22
Alignment explanation
Indices: 17601--17692 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
17591 GAATTGTTAG
* *
17601 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATAAAATTTTGA
* *
17623 TAATCACACTATGAAATTGTGA
1 TAATCACACTATAAAATTTTGA
* * *
17645 TAACCTCGCTATAAAATTTTGA
1 TAATCACACTATAAAATTTTGA
* *
17667 TAAATCTCCCTATAAAATTTTGA
1 T-AATCACACTATAAAATTTTGA
17690 TAA
1 TAA
17693 ACCTCCTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
22 40 0.67
23 20 0.33
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATCACACTATAAAATTTTGA
Found at i:17683 original size:23 final size:23
Alignment explanation
Indices: 17614--17715 Score: 100
Period size: 23 Copynumber: 4.5 Consensus size: 23
17604 TCACACTCTG
* * * *
17614 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* *
17636 AAATTGTGAT-AACCTCGCTATA
1 AAATTTTGATAAACCTCCCTATA
*
17658 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
* *
17681 AAATTTTGATAAACCTCCTTATG
1 AAATTTTGATAAACCTCCCTATA
*
17704 AAATCTTGATAA
1 AAATTTTGATAA
17716 CTACAAATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 26 0.39
23 41 0.61
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:17756 original size:21 final size:22
Alignment explanation
Indices: 17720--17900 Score: 72
Period size: 22 Copynumber: 8.4 Consensus size: 22
17710 TGATAACTAC
* *
17720 AAATTTTGATAGCCTCCCTATG
1 AAATTTTGTTAACCTCCCTATG
* * **
17742 -ATTTTTTTTAACCTCATTATG
1 AAATTTTGTTAACCTCCCTATG
* *
17763 AAATTTTGTTAATCTCCCTATA
1 AAATTTTGTTAACCTCCCTATG
*
17785 AAATTTTGATCTAGA--T-ACTATG
1 AAATTTTG-T-TA-ACCTCCCTATG
* * *
17807 AAATTTTGATAACC-CTCTTATA
1 AAATTTTGTTAACCTC-CCTATG
* * **
17829 AAATTTTG-AAAACTAAACTATG
1 AAATTTTGTTAACCT-CCCTATG
* * *
17851 AAATTTTGATAACCTTCATATG
1 AAATTTTGTTAACCTCCCTATG
* *
17873 AAATTTTGATATCCTCCC--TG
1 AAATTTTGTTAACCTCCCTATG
17893 AAATTTTG
1 AAATTTTG
17901 ATTAGTCCAT
Statistics
Matches: 116, Mismatches: 32, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
19 1 0.01
20 12 0.10
21 18 0.16
22 76 0.66
23 6 0.05
24 2 0.02
25 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTTGTTAACCTCCCTATG
Found at i:17813 original size:44 final size:41
Alignment explanation
Indices: 17759--17882 Score: 124
Period size: 44 Copynumber: 2.9 Consensus size: 41
17749 TTAACCTCAT
*
17759 TATGAAATTTTGTTAATCTCCCTATAAAATTTTGATCTAGATAC
1 TATGAAATTTTGATAA-CTCCCTATAAAATTTTGATCTA-A-AC
*
17803 TATGAAATTTTGATAAC-CCTCTTATAAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACTCC-C-TATAAAATTTTG--ATCTAAAC
* * *
17847 TATGAAATTTTGATAACCTTCATATGAAATTTTGAT
1 TATGAAATTTTGATAA-CTCCCTATAAAATTTTGAT
17883 ATCCTCCCTG
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
42 3 0.04
43 2 0.03
44 56 0.82
45 2 0.03
46 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (41 bp):
TATGAAATTTTGATAACTCCCTATAAAATTTTGATCTAAAC
Found at i:17832 original size:22 final size:21
Alignment explanation
Indices: 17802--17902 Score: 87
Period size: 22 Copynumber: 4.7 Consensus size: 21
17792 GATCTAGATA
*
17802 CTATGAAATTTTGATAACCCT
1 CTATGAAATTTTGATAACCAT
* * * *
17823 CTTATAAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAAC-CAT
*
17846 CTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGATAACCAT
*
17867 CATATGAAATTTTGATATCC-T
1 C-TATGAAATTTTGATAACCAT
**
17888 CCCTGAAATTTTGAT
1 CTATGAAATTTTGAT
17903 TAGTCCATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
20 12 0.19
21 4 0.06
22 47 0.73
23 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCAT
Found at i:18011 original size:22 final size:22
Alignment explanation
Indices: 17983--18193 Score: 137
Period size: 22 Copynumber: 9.5 Consensus size: 22
17973 AGAAATACCA
* *
17983 TTATGAAATTTTGGTAATCTCAT
1 TTATGAAATTTTGATAACCTC-T
*
18006 TT-TGAAAATTTGATAACCTCT
1 TTATGAAATTTTGATAACCTCT
18027 TTATGAAATTTTGATAACCTCT
1 TTATGAAATTTTGATAACCTCT
* * ** *
18049 TTATAAAATTTTGTTGCCCCCT
1 TTATGAAATTTTGATAACCTCT
* * * * *
18071 CTATGAAAGTTTGATAATCACA
1 TTATGAAATTTTGATAACCTCT
*
18093 TTAT-ATAATTTTGATAACCTCGC
1 TTATGA-AATTTTGATAACCTC-T
** *
18116 TT-TGAAATTTTGATAACAACA
1 TTATGAAATTTTGATAACCTCT
*
18137 CTATGAAATTTTGATAA--TCT
1 TTATGAAATTTTGATAACCTCT
18157 TCCTAT-AAATTTTGATAATCCGATCT
1 T--TATGAAATTTTGATAA-CC--TCT
*
18183 CTATGAAATTT
1 TTATGAAATTT
18194 CAATAATCAC
Statistics
Matches: 144, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.01
21 17 0.12
22 109 0.76
23 5 0.03
24 3 0.02
25 6 0.04
26 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTCT
Found at i:18285 original size:22 final size:22
Alignment explanation
Indices: 18270--18417 Score: 140
Period size: 22 Copynumber: 6.7 Consensus size: 22
18260 ATAACCTTCA
18270 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
**
18292 TAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
18314 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
18336 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
18357 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
* * *
18380 TATGAAATTCTT-ATAATCTCGC
1 TATGAAATT-TTGATAACCACAC
*
18402 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
18418 TCTCTTTGAT
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
21 4 0.04
22 96 0.93
23 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:18341 original size:66 final size:66
Alignment explanation
Indices: 18256--18417 Score: 168
Period size: 66 Copynumber: 2.5 Consensus size: 66
18246 AAATTGAGAC
* **
18256 TCTTATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTGATAACCACACTATGAA
1 TCTTATAACCTCCCCATGAAATTTTGATAACCAC-CTTAAAAAATTTTGATAACCACACTATGAA
18320 AT
65 AT
* * ** *
18322 T-TTGATAACCTCCCCATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGA
1 TCTT-ATAACCTCCCCATGAAATTTTGA-TAACCACCTTAAAAAATTTTGATAACCACACTATGA
18385 AAT
64 AAT
* * * *
18388 TCTTATAATCTCGCTATGACATTTTGATAA
1 TCTTATAACCTCCCCATGAAATTTTGATAA
18418 TCTCTTTGAT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
65 4 0.05
66 71 0.91
67 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (66 bp):
TCTTATAACCTCCCCATGAAATTTTGATAACCACCTTAAAAAATTTTGATAACCACACTATGAAA
T
Found at i:18385 original size:44 final size:43
Alignment explanation
Indices: 18260--18588 Score: 155
Period size: 44 Copynumber: 7.7 Consensus size: 43
18250 TGAGACTCTT
* ** *
18260 ATAACCTTCATATGAAATTTTGATAACCACACTAAAAAATTTTG
1 ATAACC-TCCTATGAAATTTTGATAACCACACTATGAAATTTAG
* * * *
18304 ATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAG
1 ATAACCTC-CTATGAAATTTTGATAACCACACTATGAAAT-TTAG
* *
18349 -TAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCT-T
1 ATAACCTCC-TATGAAATTTTGATAACCACACTATGAAATT-TAG
* * * *
18392 ATAATCTCGCTATGACATTTTGAT----A-A-TCT---CTTT-G
1 ATAACCTC-CTATGAAATTTTGATAACCACACTATGAAATTTAG
* * **
18426 ATAACCTTCCTAAGAAATTTTAATAACCTGATC-CTATGAAATTCCG
1 ATAACC-TCCTATGAAATTTTGATAACC--A-CACTATGAAATTTAG
* * * * *
18472 GTAACCACACTATGAAATTTTGATAACCTTC-CCATGAAATTTTG
1 ATAACCTC-CTATGAAATTTTGATAACC-ACACTATGAAATTTAG
* * * * * *
18516 ATAACTTTCATATGAAATTTTGGTAAACACACTATGGAATTTTG
1 ATAAC-CTCCTATGAAATTTTGATAACCACACTATGAAATTTAG
* *
18560 ATAACCTCCTCATGAAATTATAATAACCA
1 ATAACCTCCT-ATGAAATTTTGATAACCA
18589 TCTTATGAGA
Statistics
Matches: 210, Mismatches: 51, Indels: 48
0.68 0.17 0.16
Matches are distributed among these distances:
34 18 0.09
35 4 0.02
38 2 0.01
39 1 0.00
40 2 0.01
42 2 0.01
43 7 0.03
44 143 0.68
45 8 0.04
46 23 0.11
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (43 bp):
ATAACCTCCTATGAAATTTTGATAACCACACTATGAAATTTAG
Found at i:18454 original size:22 final size:22
Alignment explanation
Indices: 18422--18609 Score: 148
Period size: 22 Copynumber: 8.5 Consensus size: 22
18412 TGATAATCTC
*
18422 TTTGATAACCTTCCTAAGAAAT
1 TTTGATAACCTTCCTATGAAAT
*
18444 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
** * *
18468 TCCGGTAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
*
18490 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTCCTATGAAAT
* *
18512 TTTGATAACTTTCATATGAAAT
1 TTTGATAACCTTCCTATGAAAT
* * * *
18534 TTTGGTAAAC-ACACTATGGAAT
1 TTTGATAACCTTC-CTATGAAAT
18556 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * * * *
18578 TATAATAACCATCTTATGAGAT
1 TTTGATAACCTTCCTATGAAAT
18600 TTTGATAACC
1 TTTGATAACC
18610 ACACAAAGAC
Statistics
Matches: 128, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
21 4 0.03
22 104 0.81
23 4 0.03
24 16 0.12
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:18596 original size:66 final size:67
Alignment explanation
Indices: 18422--18613 Score: 228
Period size: 66 Copynumber: 2.9 Consensus size: 67
18412 TGATAATCTC
* * **
18422 TTTGATAACCTTCCT-AAGAAATTTTAATAACCTGATCCTATGAAATTCCGGTAACCACACTATG
1 TTTGATAACCTTCCTCATGAAATTTTAATAACC--ATCATATGAAATTTTGGTAACCACACTATG
18486 AAAT
64 AAAT
* ** * *
18490 TTTGATAACCTTCC-CATGAAATTTTGATAACTTTCATATGAAATTTTGGTAAACACACTATGGA
1 TTTGATAACCTTCCTCATGAAATTTTAATAACCATCATATGAAATTTTGGTAACCACACTATGAA
18554 AT
66 AT
* * * *
18556 TTTGATAACC-TCCTCATGAAATTATAATAACCATCTTATGAGATTTTGATAACCACAC
1 TTTGATAACCTTCCTCATGAAATTTTAATAACCATCATATGAAATTTTGGTAACCACAC
18614 AAAGACCAGA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
65 3 0.03
66 74 0.70
68 28 0.27
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (67 bp):
TTTGATAACCTTCCTCATGAAATTTTAATAACCATCATATGAAATTTTGGTAACCACACTATGAA
AT
Found at i:18902 original size:11 final size:11
Alignment explanation
Indices: 18888--18923 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
18878 TCTAAATTGA
18888 AATTTTTAATT
1 AATTTTTAATT
18899 AATTTTTAATT
1 AATTTTTAATT
*
18910 AATTTTTAAAT
1 AATTTTTAATT
18921 AAT
1 AAT
18924 AAAATTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTTTTAATT
Found at i:20385 original size:31 final size:31
Alignment explanation
Indices: 20347--20426 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
20337 TAAATTGACT
* * *
20347 TTAGGGACTGATTTGAGCTGATTTTACAACA
1 TTAGGGACTGAATTGAACCGATTTTACAACA
* *
20378 TTAGGGACTTAATTGAACCGATTTTACAACG
1 TTAGGGACTGAATTGAACCGATTTTACAACA
* *
20409 TTAAGGACTTAATT-AACC
1 TTAGGGACTGAATTGAACC
20427 AAATTAGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 4 0.09
31 39 0.91
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (31 bp):
TTAGGGACTGAATTGAACCGATTTTACAACA
Found at i:22427 original size:28 final size:28
Alignment explanation
Indices: 22387--22442 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
22377 ATAAATACTC
22387 TTTAAATCATTTATGTTTTGGTGCCAAA
1 TTTAAATCATTTATGTTTTGGTGCCAAA
22415 TTTAAATCATTTATGTTTTGGTGCCAAA
1 TTTAAATCATTTATGTTTTGGTGCCAAA
22443 AAATAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (28 bp):
TTTAAATCATTTATGTTTTGGTGCCAAA
Found at i:22458 original size:30 final size:28
Alignment explanation
Indices: 22394--22461 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
22384 CTCTTTAAAT
* * *
22394 CATTTATGTTTTGGTGCCAAATTTAAAT
1 CATTTATGTTTTGGTGCCAAAATAAAAC
22422 CATTTATGTTTTGGTGCCAAAAAATAAAAC
1 CATTTATGTTTTGGTGCC--AAAATAAAAC
22452 CATTTATGTT
1 CATTTATGTT
22462 CAATTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 18 0.51
30 17 0.49
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (28 bp):
CATTTATGTTTTGGTGCCAAAATAAAAC
Found at i:24251 original size:19 final size:19
Alignment explanation
Indices: 24227--24263 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
24217 TGTATCTGTA
24227 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
24246 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
24264 TGGACCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:29128 original size:32 final size:32
Alignment explanation
Indices: 29092--29159 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
29082 GAGTTTTTTA
** *
29092 AGTTTGAGTTTTT-TGGTGAAATTTTAAGTTTG
1 AGTTT-AGTTTTTATGGCCAAAATTTAAGTTTG
**
29124 AGTTTTTTTTTTATGGCCAAAATTTAAGTTTG
1 AGTTTAGTTTTTATGGCCAAAATTTAAGTTTG
29156 AGTT
1 AGTT
29160 CAAGTTCTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.53
Consensus pattern (32 bp):
AGTTTAGTTTTTATGGCCAAAATTTAAGTTTG
Found at i:29674 original size:17 final size:17
Alignment explanation
Indices: 29652--29691 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
29642 GTCATACTCA
29652 ACATCAAAATCA-TCCCT
1 ACATCAAAAT-ATTCCCT
29669 ACATC-AAATATTCCCT
1 ACATCAAAATATTCCCT
29685 ACATCAA
1 ACATCAA
29692 GCTATTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (17 bp):
ACATCAAAATATTCCCT
Found at i:30696 original size:220 final size:214
Alignment explanation
Indices: 30175--30699 Score: 726
Period size: 214 Copynumber: 2.4 Consensus size: 214
30165 AAAAATGTCG
* * * * *
30175 AAAGAATTTGGAGATGATGCATATGATTATTTGGGGATAATGAGAAATGAGTTGGGTATAAAATA
1 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTA
* * * * *
30240 TGTTAGTTTGAGGATACTGAATTTTGTATTTTGTTTAACTATTAGATGACACTAAATTCATATAG
66 TATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAACTATTAGATGACACTAAATTCATATAG
* *
30305 ACATGGTTTAAATTAATTAGAATGAAAATATGGATTAAAACACGTTTAAACCCAATTTTGGGTAT
131 ACAGGGTTTAAATTAATTAGAATGAAAATATGGATTAAAACACGTTTAAACCCAATTTTGGATAT
30370 TAAAAAAACGCCAATCTCT
196 TAAAAAAACGCCAATCTCT
* * **
30389 AAAGAATTTGGGGATAGTGCATATGATTATGTGGGGATGATGAGAAATGATTTGATTATAAAGTA
1 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTA
*
30454 TATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCATATAG
66 TATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAACTATTAGATGACACTAAATTCATATAG
* * * *
30519 ACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGCCAATTTTGGA
131 ACAGGGTTTA---AATTAATTAGAATGAAAATATGGATTAAAACACGTTTAAACCCAATTTTGGA
* * *
30584 TATATAAGAAAAAATGTCAATCTTT
193 TAT-T-A-AAAAAACGCCAATCTCT
* * * * *
30609 AATGAATTTGGGGATGGTGCTTATGATTATTTGGGAATGATGAGAAATTATTTGGGTATAGAGTA
1 AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTA
*
30674 TATCACTTTGGGGATGCTGAATTTTG
66 TATCACTTTGGGGATACTGAATTTTG
30700 TGTATGCCTC
Statistics
Matches: 271, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
214 123 0.45
217 51 0.19
218 1 0.00
219 1 0.00
220 95 0.35
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (214 bp):
AAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTA
TATCACTTTGGGGATACTGAATTTTGCATTTTGTTTAACTATTAGATGACACTAAATTCATATAG
ACAGGGTTTAAATTAATTAGAATGAAAATATGGATTAAAACACGTTTAAACCCAATTTTGGATAT
TAAAAAAACGCCAATCTCT
Found at i:31959 original size:217 final size:218
Alignment explanation
Indices: 31176--32017 Score: 1274
Period size: 218 Copynumber: 3.9 Consensus size: 218
31166 CTTGATATTA
* * *
31176 CTCATCATTCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGAGATTGACATTTTTTCTTA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACA-TTTTT-TTA
* * *
31241 TATACCCAAAATTGGCTTTAAACGTGCTTTGATCCATATTTTCATCCTAATTAATTGAATAAACC
64 TATACCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
** * * *
31306 TTGTCTATATGAATTTAGTGTCATCTAATAATTACACAAAATGCAAAATTCAGTATCCCCAAACA
129 CCGTCTATATCAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACT
*
31371 GATATACTTTATACCCAACTCATTT
194 GATATACTTTATACCCAAATCATTT
* **
31396 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTCGAGATAAACATTTTTTTATA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
* * * *
31461 TACCCAAAATTGGCTTTAAACGTATTTTAATCCATATTTTCATCATAATTAATTGAATAAACCAC
66 TACCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* * * * *
31526 GTCTATATGAATTTAGAGTCATCTAATAATTAAATAAAATACAAAATTTAGTATCCCCAAACTGA
131 GTCTATATCAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGA
* *
31591 TAGACTTTATACCGAAATCATTT
196 TATACTTTATACCCAAATCATTT
* * * *
31614 CTCATCATCCCCAAATAATCATATGCACCTTCCCCAAATTTTTTAGAGATTTAAATTTTTTTATA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
* * *
31679 TGCCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCTTACTTAATTGAATAAACCCC
66 TACCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
* * *
31744 GTATATATCAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAATTGA
131 GTCTATATCAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGA
*
31809 TATAGTTTATACCCAAATCATTT
196 TATACTTTATACCCAAATCATTT
*
31832 CTCATCATCCCCAAATAATCATATGCATCAT-CCCAAACTT-TTTAGAGATTGACATTTTTTTAT
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAA-TTCTTTAGAGATTGACATTTTTTTAT
* *
31895 ATGCCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTACTTAATTGAATAAACCC
65 ATACCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCC
*
31960 CGTCTATATCAATTTTGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCC
130 CGTCTATATCAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCC
32018 TAAATTGTTT
Statistics
Matches: 571, Mismatches: 50, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
217 148 0.26
218 369 0.65
219 5 0.01
220 49 0.09
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (218 bp):
CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTTATA
TACCCAAAATTGACTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCC
GTCTATATCAATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGA
TATACTTTATACCCAAATCATTT
Done.