Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009662.1 Corchorus olitorius cultivar O-4 contig09694, 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: 11421
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1248 original size:27 final size:27
Alignment explanation
Indices: 1194--1256 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
1184 TACCATTTTT
*
1194 TTAAAT-ATATTTCTAAATTGCCATTA
1 TTAAATAATATTTCTAAATTGCCACTA
1220 TTAAATAATATTT-TAATAATT-CCACTA
1 TTAAATAATATTTCT-A-AATTGCCACTA
1247 TTAAAATAAT
1 TT-AAATAAT
1257 GGAAATTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.22
27 14 0.44
28 11 0.34
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (27 bp):
TTAAATAATATTTCTAAATTGCCACTA
Found at i:1691 original size:565 final size:565
Alignment explanation
Indices: 608--1730 Score: 1601
Period size: 565 Copynumber: 2.0 Consensus size: 565
598 AAACTTTATA
* * *
608 TTTTCCGATTATACCCTTTTTTCTAATATATTTCTAGATTGCCATTATTAAAAAATATTTTAATT
1 TTTTCCGATTATACCATTTTTTCTAATATATTTCTAAATTGCCATTATTAAAAAATATTTTAATA
** * *
673 ATTCCATGATTTTAATAATGGAAATTTAGATTATCCTCAATAATTTGGATCTAACGTGGCCAATA
66 ATTCCATGATTAAAATAATGGAAATTTAGATTATCCTCAATAATTAGGATCCAACGTGGCCAATA
* *
738 GGAATGCTCCACATCATCTTTAACATCTGAATTTTCGTCCAAAACATTCTCCAAGTCGGTTTAGG
131 GGAATACCCCACATCATCTTTAACATCTGAATTTTCGTCCAAAACATTCTCCAAGTCGGTTTAGG
* ** * * * * ** *
803 AGAAGATTAATTTTGTCCAAAACTTTCAAGGGCAAAATCGTCTACCGGAGTAGCAGATTTAGGTC
196 AGAAGATCAATTCAGTCCAAAACTTTCAAGGGCAAAATCATCCACAGAAACAGCAGAATTAGGTC
* *
868 TCGAGGTAAACATAAAAGTGGTAGATCTTAGATTCCTCTTTCCAACGGTACCTCATTTGCATTTT
261 TCGAGATAAACATAAAAGTGGTAGATCTGAGATTCCTCTTTCCAACGGTACCTCATTTGCATTTT
* * * * *** *
933 TCTGAGTTTTGAATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCTTGTGATGTCATACTTCGA
326 CCTGAGTCTAGAATCAAAAGTTATGAATTATCTTCCAAAACTGCTCTTGTGAAACCATACTTCAA
*
998 ATAGGATTTAACAATGCTGCATCAAGATTGAATCATTACTGCATCATAATTACTGATTGGACTTA
391 ATAGGATTTAACAATGCTGCATCAAGACTGAATCATTACTGCATCATAATTACTGATTGGACTTA
* * *
1063 GATTCCTTCTTTGGGCTTCCATATTAACGAATTGCGCCTAAGAATGTCAAATTTAGACTTCAAGA
456 GACTCCTTCTTTGGACTTCCATATTAACGAATTGCGCCTAAGAATATCAAATTTAGACTTCAAGA
* *
1128 CATCTAGTTTGACAATTTGGGCTTCATGGACTCAAACGGGCCATG
521 CATCTAGCTTGACAATTTGGACTTCATGGACTCAAACGGGCCATG
* *
1173 TTTTCCGATTGTACCATTTTTT-TAAATATATTTCTAAATTGCCATTATTAAATAATATTTTAAT
1 TTTTCCGATTATACCATTTTTTCT-AATATATTTCTAAATTGCCATTATTAAAAAATATTTTAAT
*
1237 AATTCCACT-ATTAAAATAATGGAAATTTAGATTATCCTCATTAATTAGGATCCAACGTGGCCAA
65 AATTCCA-TGATTAAAATAATGGAAATTTAGATTATCCTCAATAATTAGGATCCAACGTGGCCAA
* * *
1301 TAGGGATACCCCACATCATCTTTAGCATCTGAATTTTCGTCCAAAGCATTCTCCAAGTCGGTTTA
129 TAGGAATACCCCACATCATCTTTAACATCTGAATTTTCGTCCAAAACATTCTCCAAGTCGGTTTA
** * *
1366 GGAGAAGATCAATTCAGTTTAGAAA-TTTCAAGGGCAAAATTATCCACAGAAACGGCAGAATTAG
194 GGAGAAGATCAATTCAGTCCA-AAACTTTCAAGGGCAAAATCATCCACAGAAACAGCAGAATTAG
*
1430 GTCTCGAGATAAACATAAAAGTTGTAGATCTCGA-ATTCCTCTTTCCAACGGTACCTCATTTGCA
258 GTCTCGAGATAAACATAAAAGTGGTAGATCT-GAGATTCCTCTTTCCAACGGTACCTCATTTGCA
* *
1494 TTTTCCTGAGCTCTAG-ATCAAAAGTTATGAATTATCTTCCAAAACTGGTCTTGTGAAACCCT-C
322 TTTTCCTGAG-TCTAGAATCAAAAGTTATGAATTATCTTCCAAAACTGCTCTTGTGAAACCATAC
* * * * *
1557 ATTTAAATAGGATTTAACAATGTTGCATTAGGGCTGAATCATTACTGCATCATAATTACTGATTG
386 -TTCAAATAGGATTTAACAATGCTGCATCAAGACTGAATCATTACTGCATCATAATTACTGATTG
* * * * * *
1622 GACTTGGACTCCTTCTTTGGACTTCCATATTAACGATTTGGGGCTAAGAATATCAGATTTAGTCT
450 GACTTAGACTCCTTCTTTGGACTTCCATATTAACGAATTGCGCCTAAGAATATCAAATTTAGACT
* *
1687 TCAAGACATCTGGCTTGGCAATTTGGACTTCATGGACTCAAACG
515 TCAAGACATCTAGCTTGACAATTTGGACTTCATGGACTCAAACG
1731 AGCCTAATGG
Statistics
Matches: 491, Mismatches: 61, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
564 2 0.00
565 481 0.98
566 8 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (565 bp):
TTTTCCGATTATACCATTTTTTCTAATATATTTCTAAATTGCCATTATTAAAAAATATTTTAATA
ATTCCATGATTAAAATAATGGAAATTTAGATTATCCTCAATAATTAGGATCCAACGTGGCCAATA
GGAATACCCCACATCATCTTTAACATCTGAATTTTCGTCCAAAACATTCTCCAAGTCGGTTTAGG
AGAAGATCAATTCAGTCCAAAACTTTCAAGGGCAAAATCATCCACAGAAACAGCAGAATTAGGTC
TCGAGATAAACATAAAAGTGGTAGATCTGAGATTCCTCTTTCCAACGGTACCTCATTTGCATTTT
CCTGAGTCTAGAATCAAAAGTTATGAATTATCTTCCAAAACTGCTCTTGTGAAACCATACTTCAA
ATAGGATTTAACAATGCTGCATCAAGACTGAATCATTACTGCATCATAATTACTGATTGGACTTA
GACTCCTTCTTTGGACTTCCATATTAACGAATTGCGCCTAAGAATATCAAATTTAGACTTCAAGA
CATCTAGCTTGACAATTTGGACTTCATGGACTCAAACGGGCCATG
Found at i:2387 original size:22 final size:21
Alignment explanation
Indices: 2331--2540 Score: 125
Period size: 22 Copynumber: 9.5 Consensus size: 21
2321 GTCTTTGTGT
* *
2331 GGTTAACAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
2352 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
2375 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
2397 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
*
2419 AGTTATCAAAATTTCATAGTGTA
1 GGTTATCAAAATTTCATAG-G-A
*
2442 -GTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
2465 AGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
* ** *
2487 GATTATTTAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * * *
2509 GGTTATTACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
2531 GGTTATCAAA
1 GGTTATCAAA
2541 GAGATTATCA
Statistics
Matches: 146, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
21 4 0.03
22 119 0.82
23 7 0.05
24 16 0.11
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:2400 original size:44 final size:44
Alignment explanation
Indices: 2362--2458 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
2352 TGGTTATTAT
*
2362 AATTTCATGA-GGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-ATGGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
* *
2406 AATTTCATATGGAAGTTATCAAAATTTCATAGTGTAGTTACCAA
1 AATTTCATATGGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
2450 AATTTCATA
1 AATTTCATA
2459 GGATCAAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 48 0.98
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (44 bp):
AATTTCATATGGAAGTTATCAAAATTCCATAGTGTGGTTACCAA
Found at i:2451 original size:66 final size:66
Alignment explanation
Indices: 2327--2459 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 66
2317 TCTTGTCTTT
* * * *
2327 GTGTGGTTAACAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTAACAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCAT
2392 A
66 A
* * *
2393 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCAT-AGTGTA-GTTACCAAAATTT
1 GTGTGGTTAACAAAATTTCATA-AGATAGTTATCAAAATTTCATGAG-G-AGGTTACCAAAATTC
2455 CATA
63 CATA
2459 G
1 G
2460 GATCAAGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 2 0.04
66 52 0.91
67 3 0.05
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (66 bp):
GTGTGGTTAACAAAATTTCATAAGATAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCAT
A
Found at i:2584 original size:22 final size:22
Alignment explanation
Indices: 2556--2604 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
2546 TATCATAATG
2556 TCATAGTG-ACGTT-ACAAGAATT
1 TCATAGTGTA-GTTAACAA-AATT
2578 TCATAGTGTAGTTAACAAAATT
1 TCATAGTGTAGTTAACAAAATT
2600 TCATA
1 TCATA
2605 AGGAGGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATAGTGTAGTTAACAAAATT
Found at i:2701 original size:22 final size:22
Alignment explanation
Indices: 2636--2939 Score: 91
Period size: 22 Copynumber: 13.6 Consensus size: 22
2626 GGGGAGAATC
*
2636 ATCAAAATTTCATATTG-TGGTT
1 ATCAAAATTTCATA-TGAAGGTT
** *
2658 ATCAAAATTTTTTAGTG-TGGTT
1 ATCAAAATTTCATA-TGAAGGTT
2680 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
2702 AT-AAAAGTCTCAATTTCAT-AAGGAGT
1 ATCAAAA-TTTC-A--T-ATGAAGG-TT
* *
2728 ACCAAAATTTAAT-TGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
2749 ATC--AATTCTCATA-G-AGTGATT
1 ATCAAAATT-TCATATGAAG-G-TT
*
2770 ATCGAAATTTCATA-GAAATTGGATT
1 ATCAAAATTTCATATG-AA--GG-TT
* *
2795 ATCAAAATTT-ATAGGAAGATT
1 ATCAAAATTTCATATGAAGGTT
* **
2816 ATTAAAATTTCATAGTG-TTGTT
1 ATCAAAATTTCATA-TGAAGGTT
* *
2838 ATCAAAATTTCA-AAGCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * * *
2860 ACCAAAATTACATAATG-TGATT
1 ATCAAAATTTCAT-ATGAAGGTT
* *
2882 ATCAAAATTTCATA-GAGGGGTC
1 ATCAAAATTTCATATGA-AGGTT
* * *
2904 AACAAAATTTTACA-GAGAGGTT
1 ATCAAAATTTCATATGA-AGGTT
2926 ATCAAAATTTCATA
1 ATCAAAATTTCATA
2940 AAGAATTATC
Statistics
Matches: 211, Mismatches: 43, Indels: 56
0.68 0.14 0.18
Matches are distributed among these distances:
19 6 0.03
20 7 0.03
21 28 0.13
22 124 0.59
23 7 0.03
24 8 0.04
25 20 0.09
26 7 0.03
27 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:2815 original size:21 final size:23
Alignment explanation
Indices: 2791--2985 Score: 88
Period size: 22 Copynumber: 8.9 Consensus size: 23
2781 ATAGAAATTG
2791 GATTATCAAAATTT-ATAG-GAA
1 GATTATCAAAATTTCATAGTGAA
* **
2812 GATTATTAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAGTGAA
* *
2835 G-TTATCAAAATTTCAAAGCG-A
1 GATTATCAAAATTTCATAGTGAA
* * * * *
2856 GGTTACCAAAATTACATAATG-T
1 GATTATCAAAATTTCATAGTGAA
* *
2878 GATTATCAAAATTTCATAGAG-G
1 GATTATCAAAATTTCATAGTGAA
* * * * * *
2900 GGTCAACAAAATTTTACAGAG-A
1 GATTATCAAAATTTCATAGTGAA
*
2922 GGTTATCAAAATTTCATA---AA
1 GATTATCAAAATTTCATAGTGAA
* * * *
2942 GAATTATCAAATTTTCAAAATG-T
1 G-ATTATCAAAATTTCATAGTGAA
*
2965 GATTACCAAAATTTCATAGTG
1 GATTATCAAAATTTCATAGTG
2986 GTATTTTTGG
Statistics
Matches: 129, Mismatches: 37, Indels: 15
0.71 0.20 0.08
Matches are distributed among these distances:
20 2 0.02
21 28 0.22
22 96 0.74
23 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGAA
Found at i:2910 original size:44 final size:44
Alignment explanation
Indices: 2819--2912 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
2809 GAAGATTATT
* * * * *
2819 AAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTACC
1 AAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAAC
* *
2863 AAAATTACATAATG-TGATTATCAAAATTTCATAGAGGGGTCAAC
1 AAAATTACATAATGTTG-TTATCAAAATTTCAAAGAGAGGTCAAC
2907 AAAATT
1 AAAATT
2913 TTACAGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (44 bp):
AAAATTACATAATGTTGTTATCAAAATTTCAAAGAGAGGTCAAC
Found at i:2910 original size:66 final size:65
Alignment explanation
Indices: 2812--2958 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 65
2802 TTTATAGGAA
* * ** * * * *
2812 GATTATTAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTACCAAAATTACATAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTACCAAAATTACATAAAG
* * * *
2877 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTACAGAGAGGTTATCAAAATTTCATAAA
1 -GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTACCAAAATTACATAAA
2942 G
65 G
* *
2943 AATTATCAAATTTTCA
1 GATTATCAAAATTTCA
2959 AAATGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
65 14 0.21
66 53 0.79
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (65 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTACCAAAATTACATAAAG
Found at i:3110 original size:22 final size:22
Alignment explanation
Indices: 3083--3556 Score: 185
Period size: 22 Copynumber: 21.7 Consensus size: 22
3073 TCAGGGAGAA
*
3083 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGGAGGT
* **
3105 TATCAAAATTTCGTAGTTTA-GT
1 TATCAAAATTTCATA-TGGAGGT
* * *
3127 TTTCAAATTTTCATA-AGAGAGT
1 TATCAAAATTTCATATGGAG-GT
* * * *
3149 TACCCAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGGAGGT
* * *
3170 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGGAGGT
*
3193 TAACAAAATTTCATGAT-GAGGT
1 TATCAAAATTTCAT-ATGGAGGT
** *
3215 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGGAGGT
*
3237 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGGAGGT
* * *
3253 TAGCAAGATTTCATACGGAGGT
1 TATCAAAATTTCATATGGAGGT
* *
3275 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGGAGG-T
* *
3298 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGGAGG-T
*
3321 TATCAAAATTTCATA-GCATGGT
1 TATCAAAATTTCATATGGA-GGT
* *
3343 TATCACAA-TTCATAGTGTGA-AT
1 TATCAAAATTTCATA-TG-GAGGT
*
3365 TATCAAAATTTCAGAGTGTGA--T
1 TATCAAAATTTCATA-TG-GAGGT
*
3387 TATTAACAA-TTCATATGGAGGT
1 TATCAA-AATTTCATATGGAGGT
* * * ** *
3409 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATATGGAGGT
* ** *
3431 TATCAATATAACGTATGGAGGT
1 TATCAAAATTTCATATGGAGGT
* *** * **
3453 TGTCGGCATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGGAGGT
**
3476 TATCAAAATTTCAT-TGGGAACT
1 TATCAAAATTTCATAT-GGAGGT
3498 TATCAAAATTTCATA-GTGAGGT
1 TATCAAAATTTCATATG-GAGGT
* * *
3520 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGGAGGT
*
3542 TAACAAAATTTCATA
1 TATCAAAATTTCATA
3557 AGAATGTTAA
Statistics
Matches: 334, Mismatches: 88, Indels: 60
0.69 0.18 0.12
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 5 0.01
21 17 0.05
22 223 0.67
23 76 0.23
24 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGGAGGT
Found at i:3343 original size:23 final size:23
Alignment explanation
Indices: 3260--3336 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
3250 AGTTAGCAAG
*
3260 ATTTCATACGGAGG-TTATCAAA
1 ATTTCATAGGGAGGTTTATCAAA
*
3282 ATTTTATAGGGAGGTTTATCAAA
1 ATTTCATAGGGAGGTTTATCAAA
*
3305 ATTTTATAGGGAGGTTTATCAAA
1 ATTTCATAGGGAGGTTTATCAAA
3328 ATTTCATAG
1 ATTTCATAG
3337 CATGGTTATC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 12 0.24
23 39 0.76
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATTTCATAGGGAGGTTTATCAAA
Found at i:3397 original size:23 final size:24
Alignment explanation
Indices: 3342--3397 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
3332 CATAGCATGG
*
3342 TTATC-ACAA-TTCATAGTGTGAA
1 TTATCAACAATTTCAGAGTGTGAA
3364 TTATCAA-AATTTCAGAGTGTG-A
1 TTATCAACAATTTCAGAGTGTGAA
*
3386 TTATTAACAATT
1 TTATCAACAATT
3398 CATATGGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (24 bp):
TTATCAACAATTTCAGAGTGTGAA
Found at i:3661 original size:23 final size:22
Alignment explanation
Indices: 3613--3659 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3603 ATCGTTATTG
* *
3613 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGATCATCA
3635 AAATTTCATAAGG-AGATCATCA
1 AAATTTCAT-AGGAAGATCATCA
3657 AAA
1 AAA
3660 ATAGTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.28
Consensus pattern (22 bp):
AAATTTCATAGGAAGATCATCA
Found at i:4960 original size:173 final size:175
Alignment explanation
Indices: 4669--5022 Score: 631
Period size: 173 Copynumber: 2.0 Consensus size: 175
4659 TTCGAAAATG
* **
4669 CCCTTGGTTGTCAGCCTAAATAACTGAAAAACCAACCATGGAATTAGTCAAAATCATGCTAAACC
1 CCCTTGGTTGTCACCCTAAATAACTGAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
4734 CTAGGAGAGACAGACCCAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAAAAACATGC
66 CTAGGAGAGACAGACCCAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAAAAACATGC
4799 TAAACCCTAGGTGAGATAAAAAAAATTAATGGAAAACCATATTTA
131 TAAACCCTAGGTGAGATAAAAAAAATTAATGGAAAACCATATTTA
4844 CCCTTGGTTGTCACCCTAAATAACT-AAAAACCAACCATGGAATT-CCCAAAATCATGCTAAACC
1 CCCTTGGTTGTCACCCTAAATAACTGAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
**
4907 CTAGGAGAGAGGGACCCAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAAAAACATGC
66 CTAGGAGAGACAGACCCAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAAAAACATGC
* *
4972 TAAACCTTAGGTGAGATAAAAAAAATTAATGGAACACCATATTTA
131 TAAACCCTAGGTGAGATAAAAAAAATTAATGGAAAACCATATTTA
5017 CCCTTG
1 CCCTTG
5023 CCAATTTACA
Statistics
Matches: 172, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
173 129 0.75
174 19 0.11
175 24 0.14
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (175 bp):
CCCTTGGTTGTCACCCTAAATAACTGAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
CTAGGAGAGACAGACCCAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAAAAACATGC
TAAACCCTAGGTGAGATAAAAAAAATTAATGGAAAACCATATTTA
Found at i:5066 original size:30 final size:32
Alignment explanation
Indices: 5004--5067 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
4994 AAATTAATGG
*
5004 AACACCATATTTACCCTTGCCAATTTACATGA
1 AACACCATATTTACCCTTGCCAATTCACATGA
**
5036 AACACCATATTTGTCCTTG-CAA-TCACATGA
1 AACACCATATTTACCCTTGCCAATTCACATGA
5066 AA
1 AA
5068 TTACATCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.31
31 3 0.10
32 17 0.59
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.30
Consensus pattern (32 bp):
AACACCATATTTACCCTTGCCAATTCACATGA
Found at i:6051 original size:173 final size:175
Alignment explanation
Indices: 5761--6114 Score: 561
Period size: 173 Copynumber: 2.0 Consensus size: 175
5751 TACGAAAATG
* * *
5761 CCCTTGGTTGTCACCCTAGATAACTAAAAAACCAACCATGGAATTAGCCACAATCATGCTAAACC
1 CCCTTGGTTGTCACCCTAAATAACTAAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
* ** * *
5826 CTAGGAGAGAGAGGGCGAAACCCTATACATATAAGCTAAACCCTAAAATGACCCCAGAAACATGC
66 CTAAGAGAGAGAGCCCGAAACCCTATACATATAAGCTAAACCCTAAAATGACCCAAAAAACATGC
* *
5891 TAAACCCTAGGTGAGATAAAAAAA-TTAATGGAACACCATATTTA
131 CAAACCCTAGGTGAGAAAAAAAAATTTAATGGAACACCATATTTA
5935 CCCTTGGTTGTCACCCTAAATAACTAAAAAACCAACCATGGAATT-CCCAAAATCATGCTAAACC
1 CCCTTGGTTGTCACCCTAAATAACTAAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
*
5999 CTAAGAGAGAGAGACCCG-AACCCTATACATATAAGCTAAACCCTAAAATGACCTAAAAAACATG
66 CTAAGAGAGAGAG-CCCGAAACCCTATACATATAAGCTAAACCCTAAAATGACCCAAAAAACATG
* *
6063 CCAAACCCTAGGTGAGAAAAAAAAATTTAATGGAATACCATATTTG
130 CCAAACCCTAGGTGAGAAAAAAAAATTTAATGGAACACCATATTTA
6109 CCCTTG
1 CCCTTG
6115 CCAATTTTAC
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
173 95 0.58
174 70 0.42
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (175 bp):
CCCTTGGTTGTCACCCTAAATAACTAAAAAACCAACCATGGAATTACCCAAAATCATGCTAAACC
CTAAGAGAGAGAGCCCGAAACCCTATACATATAAGCTAAACCCTAAAATGACCCAAAAAACATGC
CAAACCCTAGGTGAGAAAAAAAAATTTAATGGAACACCATATTTA
Found at i:6159 original size:30 final size:32
Alignment explanation
Indices: 6099--6160 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
6089 TTAATGGAAT
* *
6099 ACCATATTTGCCCTTGCCAATTTTACATGAAAC
1 ACCATATTTACCCTTGCCAA-TTCACATGAAAC
6132 ACCATATTTACCCTTG-CAA-TCACATGAAA
1 ACCATATTTACCCTTGCCAATTCACATGAAA
6161 TTACATCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
32 3 0.11
33 15 0.56
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (32 bp):
ACCATATTTACCCTTGCCAATTCACATGAAAC
Found at i:8841 original size:45 final size:45
Alignment explanation
Indices: 8764--8860 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
8754 AGTACATTAC
** *
8764 CTAA-ATTCAACTCCTCCATCTCTAGGTGATTCATCAAAATAAAG
1 CTAATATTCAACTCCTCCATCTCTAGGCAATTCATCAAAATAAAA
* *
8808 CTAATATTCTACTCCTTCATCTCTAGGCAATTCATCAAAATAAAA
1 CTAATATTCAACTCCTCCATCTCTAGGCAATTCATCAAAATAAAA
8853 CTAATATT
1 CTAATATT
8861 AAATGTTGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (45 bp):
CTAATATTCAACTCCTCCATCTCTAGGCAATTCATCAAAATAAAA
Done.