Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012518.1 Corchorus capsularis cultivar CVL-1 contig12539, 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: 68162
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1737 original size:431 final size:431
Alignment explanation
Indices: 937--2234 Score: 1607
Period size: 431 Copynumber: 3.0 Consensus size: 431
927 TTGGCTTTTT
*
937 TGTAATTAGAGTTGATGGCCAAGGGTATTTTGGGAACTTTGAGAATAAGATACCCTTGGTGGGTC
1 TGTAATTAGAGTTGATGACCAAGGGTATTTTGGGAACTTTGAGAATAAGATACCCTTGGTGGGTC
* *
1002 CCATCTCCACCAACACAATTTTTTTTTGGCTTATTTAAGAAATGACCCCCATACTTTTCTACTTG
66 CCATCTCCACCAACACAA-ATTTTTTTGGCTTATTTATGAAATGACCCCCATACTTTTCTACTTG
1067 ATGCTATTTAGTCCTTTACAAATC----AATTTAACGCTTTCGGTCATTTTTTTTTCTATTTTTC
130 ATGCTATTTAGTCCTTTACAAATCATTTAATTTAACGCTTTCGGT-ATTTTTTTTTCTATTTTTC
*
1128 CGATTAAGGTGATTCAGATGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATAAGGACTC
194 CGATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATAAGGACTC
*
1193 AAAAGTCAATTTTTATGTTTCAATTCAAAAAACTGCTTCCGAAATTTGGTGATTTTGATTGCCGG
259 AAAAGCCAATTTTTATGTTTCAATTCAAAAAACTGCTTCCGAAATTTGGTGATTTTGATTGCCGG
* * *
1258 TCTATTAAATATCTTATAATTTTCGAT-TTACAAGTCCGATTAATGTTATTCAAGTTTCGATTAA
324 TCTATTAAATATCATATAATTTTCGATCAT-CAAGTCCGATTAATGTTATTCAAGTGTCGATTAA
** ** *
1322 AAGGTTATTGCATGATCTATGACTTTTA-GAGTTGATGGCCAAG
388 AAGGTTATTGCATGATCTATGACTTTTAGGAGCCGAAAGCCAAA
*
1365 TGTAATTAGAGTTGATGACCAATGGTATTTTGGGAACTTTGAGAATAAGATACCCTTGGTGGGTC
1 TGTAATTAGAGTTGATGACCAAGGGTATTTTGGGAACTTTGAGAATAAGATACCCTTGGTGGGTC
1430 CCATCTCCACCAACACAAATTTTTTTGGCTTATTTATGAAATGACCCCCATACTTTTCTACTTGA
66 CCATCTCCACCAACACAAATTTTTTTGGCTTATTTATGAAATGACCCCCATACTTTTCTACTTGA
*
1495 TGCTATTTAGTCCTTTACAAATCGATTTAATTTAACGCTTTCGGTAATTTTTTTTCTATTTTTCC
131 TGCTATTTAGTCCTTTACAAATC-ATTTAATTTAACGCTTTCGGTATTTTTTTTTCTATTTTTCC
*
1560 GATTAAGGTGATTCAGGTGTGTATTAAAAGGTAATTTCATGATTTACAACTTTCATAAGGACTCA
195 GATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATAAGGACTCA
* *
1625 AAAGCCAATTTTTATATTTCAATTCAAAAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGGT
260 AAAGCCAATTTTTATGTTTCAATTCAAAAAACTGCTTCCGAAATTTGGTGATTTTGATTGCCGGT
* * *
1690 CTATTAAATATCATATGATTTTCGATCATCAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAAT
325 CTATTAAATATCATATAATTTTCGATCATCAAGTCCGATTAATGTTATTCAAGTGTCGATTAAAA
* * *
1755 GGTTATTGCATGATCTACGAATTTTATGAAGGAGCCGAAAGCTAAA
390 GGTTATTGCATGATCTATG-ACTTT-T--AGGAGCCGAAAGCCAAA
* * * * * ** * **
1801 TTTGATCTACGAGTTTCAT-A--AAGGGTTTTTTTTTTGGTCAAACATAAGGGTTCAA-AAGGGA
1 TGTAAT-TA-GAG-TTGATGACCAAGGG----TATTTTGG--GAAC-TTTGAG---AATAAGATA
* ** ** ** ** ** * * * *
1862 --ATTTTTATGTTTCAAATCCATTAACAAATAATTTCTTATTTGGATTATTTATCAAATGACCCT
53 CCCTTGGTGGGTCCCATCTCCACCAACACA-AA-TT-TT-TTTGGCTTATTTATGAAATGACCCC
* * * * * * * *
1925 CATATTTTTCTACTTTATACTACTTAGTCCTTTACTAATTTTATCTTAATCGATTTAATGCTTTA
114 CATACTTTTCTACTTGATGCTATTTAGTCCTTTAC-AA-ATCAT-TT-A---ATTTAACGCTTTC
*
1990 GGTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAGGTGTCTATTAAAAGATAATTTCATGA
172 GGTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGA
* * *
2055 TTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTATGTTTCAGTTCGAAAAACTGCTTCCGA
237 TTTACAACTTTCAT-AAGGACTCAAAAGCCAATTTTTATGTTTCAATTCAAAAAACTGCTTCCGA
* *
2120 AATTTGGTGATTTTGATTGGCGGTCTATTAAATATCATATAATTTTTGATCCA-CAAGTCCGATT
301 AATTTGGTGATTTTGATTGCCGGTCTATTAAATATCATATAATTTTCGAT-CATCAAGTCCGATT
*
2184 AATGTCATTCAAGTGTC-AGTTAAAAGGTTATTGCATGATCTATGACTTTTA
365 AATGTTATTCAAGTGTCGA-TTAAAAGGTTATTGCATGATCTATGACTTTTA
2235 TGAAGGACCT
Statistics
Matches: 758, Mismatches: 74, Indels: 54
0.86 0.08 0.06
Matches are distributed among these distances:
427 68 0.09
428 81 0.11
431 219 0.29
432 22 0.03
433 1 0.00
435 1 0.00
436 17 0.02
437 2 0.00
438 4 0.01
439 4 0.01
440 7 0.01
442 3 0.00
443 19 0.03
444 2 0.00
445 6 0.01
446 4 0.01
447 53 0.07
448 4 0.01
449 3 0.00
450 2 0.00
452 1 0.00
453 91 0.12
454 142 0.19
455 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (431 bp):
TGTAATTAGAGTTGATGACCAAGGGTATTTTGGGAACTTTGAGAATAAGATACCCTTGGTGGGTC
CCATCTCCACCAACACAAATTTTTTTGGCTTATTTATGAAATGACCCCCATACTTTTCTACTTGA
TGCTATTTAGTCCTTTACAAATCATTTAATTTAACGCTTTCGGTATTTTTTTTTCTATTTTTCCG
ATTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATAAGGACTCAA
AAGCCAATTTTTATGTTTCAATTCAAAAAACTGCTTCCGAAATTTGGTGATTTTGATTGCCGGTC
TATTAAATATCATATAATTTTCGATCATCAAGTCCGATTAATGTTATTCAAGTGTCGATTAAAAG
GTTATTGCATGATCTATGACTTTTAGGAGCCGAAAGCCAAA
Found at i:2454 original size:454 final size:455
Alignment explanation
Indices: 1453--2729 Score: 1713
Period size: 454 Copynumber: 2.8 Consensus size: 455
1443 CACAAATTTT
* * * * * * * * *
1453 TTTGGCTTATTTATGAAATGACCCCCATACTTTTCTACTTGATGCTATTTAGTCCTTTAC-AAAT
1 TTTGGATTATTTATCAAATGACCCTCACATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
** * * *
1517 CGAT-TT-A---ATTTAACGCTTT-CGGTAATTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
66 TTATCTTAATCGATTTAACGCTTTAAGTTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
* *
1576 GTGTGTATTAAAAGGTAATTTCATGATTTACAACTTTCAT-AAGGACTCAAAAGCCAATTTTTAT
131 GTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTAT
* *
1640 ATTTCAATTCAAAAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGGTCTATTAAATATCATA
196 GTTTCAATTCGAAAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGGTCTATTAAATATCATA
* *
1705 TGATTTTCGAT-CATCAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAATGGTTATTGCATGAT
261 TAATTTTCGATCCA-CAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATGAT
* * *
1769 CTACGAATTTTATGAAGGAGCCGAAAGCTAAATTTGATCTACGAGTTTCATAAAGGGTTTTTTTT
325 CTACGACTTTTATGAAGGAGCCGAAAACTAAATTTGATCTACGAGTTTCATAAAGGGGTTTTTTT
*
1834 TTGGTCAAACATAAGGGTTCAAAAGGGAATTTTTATGTTTCAAATCCATTAACAAATAATTTCTT
390 TTGGCCAAACATAAGGGTTCAAAAGGGAATTTTTATGTTTCAAATCCATTAACAAATAATTTCTT
1899 A
455 A
*
1900 TTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
1 TTTGGATTATTTATCAAATGACCCTCACATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
* *
1965 TTATCTTAATCGATTTAATGCTTT-AGGTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
66 TTATCTTAATCGATTTAACGCTTTAAGTTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
*
2029 GTGTCTATTAAAAGATAATTTCATGATTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTAT
131 GTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTAT
* * *
2094 GTTTCAGTTCGAAAAACTGCTTCCGAAATTTGGTGATTTTGATTGGCGGTCTATTAAATATCATA
196 GTTTCAATTCGAAAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGGTCTATTAAATATCATA
* * *
2159 TAATTTTTGATCCACAAGTCCGATTAATGTCATTCAAGTGTCAGTTAAAAGGTTATTGCATGATC
261 TAATTTTCGATCCACAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATGATC
* * *
2224 TATGACTTTTATGAAGGA-CCTGAAAACTAAATTTTATCTACGAGTTTCATTAAGGGGGGTTTTT
326 TACGACTTTTATGAAGGAGCC-GAAAACTAAATTTGATCTACGAGTTTCA-TAA-AGGGGTTTTT
* *
2288 TTTT-GCCAAACATTAAGGGTTCAAAAGGGAATTTTTATGTTTCGAATCCATTAACAAATATTTT
388 TTTTGGCCAAACA-TAAGGGTTCAAAAGGGAATTTTTATGTTTCAAATCCATTAACAAATAATTT
2352 CTTA
452 CTTA
2356 TTTGGATTATTTATCAAATGACCCTCACATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
1 TTTGGATTATTTATCAAATGACCCTCACATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
* * *
2421 TTATCTTAATCGATTTAACGC-TTAAGTT-TTTTTTTTTCTATTTGTCCGAGTAAGGT-ATTCGG
66 TTATCTTAATCGATTTAACGCTTTAAGTTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
*
2483 GTGTCTATTAAAAGGTAATTTTATGA--T----CTTTCATGAAGGACTCAAAAGCCCATTTTTAT
131 GTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTAT
* **
2542 GTTTCAATT-GAAAAAAAAATGCTTCCCAAATTTGGT-AGTTTCT-ATTGCCGGTCTATTTTATA
196 GTTTCAATTCG---AAAAAATGCTTCCGAAATTTGGTGA-TTT-TGATTGCCGGTCTATTAAATA
* * * * ** * *
2604 ACATATAATTTTGGATCCACATGTCCAATTAAAATTATTTAAGTGTCGGTTAAAAGGTTATTGCG
256 TCATATAATTTTCGATCCACAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAAAGGTTATTGCA
* * * ** * * * *
2669 TGATATACGACTTTCATGGA-GTCCACGAAAGCTAAATTTGATCTACAAGATTCATGAAGGG
321 TGATCTACGACTTTTATGAAGGAGC-CGAAAACTAAATTTGATCTACGAGTTTCATAAAGGG
2730 TTCAAAAAGA
Statistics
Matches: 740, Mismatches: 70, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
447 54 0.07
448 48 0.06
449 6 0.01
450 137 0.19
451 2 0.00
452 1 0.00
453 89 0.12
454 211 0.29
455 40 0.05
456 152 0.21
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (455 bp):
TTTGGATTATTTATCAAATGACCCTCACATTTTTCTACTTTATACTACTTAGTCCTTTACTAATT
TTATCTTAATCGATTTAACGCTTTAAGTTATTTTTTTTTCTATTTTTCCGATTAAGGTGATTCAG
GTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAGGACTCAAAAGCCCATTTTTAT
GTTTCAATTCGAAAAAATGCTTCCGAAATTTGGTGATTTTGATTGCCGGTCTATTAAATATCATA
TAATTTTCGATCCACAAGTCCGATTAATGTTATTCAAGTGTCGGTTAAAAGGTTATTGCATGATC
TACGACTTTTATGAAGGAGCCGAAAACTAAATTTGATCTACGAGTTTCATAAAGGGGTTTTTTTT
TGGCCAAACATAAGGGTTCAAAAGGGAATTTTTATGTTTCAAATCCATTAACAAATAATTTCTTA
Found at i:8783 original size:12 final size:13
Alignment explanation
Indices: 8758--8791 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
8748 ATAATTATTG
8758 TTTGCTTTATTAA
1 TTTGCTTTATTAA
8771 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
8783 TCTGCTTTA
1 TTTGCTTTA
8792 GATTTAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:8799 original size:6 final size:6
Alignment explanation
Indices: 8788--8814 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8778 TATAATCTGC
8788 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
8815 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:14971 original size:3 final size:3
Alignment explanation
Indices: 14963--15017 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
14953 AGTTAATTTG
14963 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15011 ATA ATA A
1 ATA ATA A
15018 ACTGCCAGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16872 original size:10 final size:10
Alignment explanation
Indices: 16859--16894 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
16849 AAATCTCGAT
16859 ATATCCGTAA
1 ATATCCGTAA
16869 ATATCCGTAA
1 ATATCCGTAA
*
16879 ATATCCATAA
1 ATATCCGTAA
16889 ATATCC
1 ATATCC
16895 ATATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:18594 original size:12 final size:12
Alignment explanation
Indices: 18577--18632 Score: 103
Period size: 12 Copynumber: 4.6 Consensus size: 12
18567 CATCGATACC
18577 TCGATATATCCG
1 TCGATATATCCG
18589 TCGATATATCCG
1 TCGATATATCCG
18601 TCGATATATCCG
1 TCGATATATCCG
18613 TTCGATATATCCG
1 -TCGATATATCCG
18626 TCGATAT
1 TCGATAT
18633 CTGTATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
12 31 0.72
13 12 0.28
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:18623 original size:25 final size:24
Alignment explanation
Indices: 18577--18632 Score: 103
Period size: 25 Copynumber: 2.3 Consensus size: 24
18567 CATCGATACC
18577 TCGATATATCCGTCGATATATCCG
1 TCGATATATCCGTCGATATATCCG
18601 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCG-TCGATATATCCG
18626 TCGATAT
1 TCGATAT
18633 CTGTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (24 bp):
TCGATATATCCGTCGATATATCCG
Found at i:19631 original size:27 final size:27
Alignment explanation
Indices: 19558--19633 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 27
19548 CCAAACCGAA
*
19558 CCAAAAACAGAAGCAAGTAATATATTC
1 CCAAAAACAGCAGCAAGTAATATATTC
*
19585 ACAAAAACAGAAACTCAGCAAGTAATATATTC
1 CCAAAAACAG-----CAGCAAGTAATATATTC
*
19617 CCAAGAACAGCAGCAAG
1 CCAAAAACAGCAGCAAG
19634 AACTCATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
27 16 0.40
32 24 0.60
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.14
Consensus pattern (27 bp):
CCAAAAACAGCAGCAAGTAATATATTC
Found at i:22711 original size:18 final size:17
Alignment explanation
Indices: 22684--22721 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
22674 GTAAAAATTT
22684 TATTTTAATATATAATA
1 TATTTTAATATATAATA
*
22701 TATTATTAATATGTAATA
1 TATT-TTAATATATAATA
22719 TAT
1 TAT
22722 ATGCAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTAATATATAATA
Found at i:22713 original size:39 final size:38
Alignment explanation
Indices: 22628--22721 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 38
22618 AAATCATTTT
22628 TATT-TTAATATGTAAAATATTTTATTAAATAAGAATA
1 TATTATTAATATGTAAAATATTTTATTAAATAAGAATA
* *
22665 TA-TA-T-ATATGTAAAA-ATTTTATTTTAATATATAATA
1 TATTATTAATATGTAAAATATTTTA-TTAAATA-AGAATA
*
22701 TATTATTAATATGTAATATAT
1 TATTATTAATATGTAAAATAT
22722 ATGCAATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
34 6 0.13
35 16 0.34
36 9 0.19
37 4 0.09
38 1 0.02
39 9 0.19
40 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (38 bp):
TATTATTAATATGTAAAATATTTTATTAAATAAGAATA
Found at i:22729 original size:18 final size:18
Alignment explanation
Indices: 22690--22732 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
22680 ATTTTATTTT
*
22690 AATATATAATATATTATT
1 AATATATAATATATTATC
*
22708 AATATGTAATATA-TATGC
1 AATATATAATATATTAT-C
22726 AATATAT
1 AATATAT
22733 TCAAACCGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (18 bp):
AATATATAATATATTATC
Found at i:26679 original size:79 final size:79
Alignment explanation
Indices: 26563--26732 Score: 322
Period size: 79 Copynumber: 2.1 Consensus size: 79
26553 AATTATAAAA
26563 TAGGGAAAATTGGGGGGTAAAATCATTAAATAAAGTTTTCCCTCATTTTCCCCTAAAAACTCACG
1 TAGGGAAAATTGGGGGGTAAAATCATTAAATAAAGTTTTCCCTCATTTTCCCCTAAAAACTCACG
26628 GGAAATTGAGAGAG
66 GGAAATTGAGAGAG
26642 TAGGGAAAATTGGGGGGTAAAATCATTAAATAAAGTTTTCCCTCATTTTCCCCTAAAAACTCACG
1 TAGGGAAAATTGGGGGGTAAAATCATTAAATAAAGTTTTCCCTCATTTTCCCCTAAAAACTCACG
26707 GGAAATTGAGAGAG
66 GGAAATTGAGAGAG
*
26721 TTGGAGAAAATT
1 TAGG-GAAAATT
26733 TTATCGGGCC
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 82 0.92
80 7 0.08
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
TAGGGAAAATTGGGGGGTAAAATCATTAAATAAAGTTTTCCCTCATTTTCCCCTAAAAACTCACG
GGAAATTGAGAGAG
Found at i:26937 original size:19 final size:19
Alignment explanation
Indices: 26913--26950 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
26903 CAAGGTCAAT
*
26913 CGGTTGAGAATTTGTTCTC
1 CGGTTGAGAATTTCTTCTC
26932 CGGTTGAGAATTTCTTCTC
1 CGGTTGAGAATTTCTTCTC
26951 GAATAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (19 bp):
CGGTTGAGAATTTCTTCTC
Found at i:35611 original size:13 final size:13
Alignment explanation
Indices: 35589--35628 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
35579 CAGAGAATAT
35589 TATCAACAGAAGA
1 TATCAACAGAAGA
*
35602 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
35615 TTTCAACTGAAGA
1 TATCAACAGAAGA
35628 T
1 T
35629 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:36074 original size:41 final size:41
Alignment explanation
Indices: 36017--36124 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
36007 AATAATATTG
* **
36017 AAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTCCGGTAAATT
*
36058 AAAATTACCTTTGACACAAGAAG-TGTCACTCCGGTAAATT
1 AAAATTACCTTTGACACCAGAAGTTGTCACTCCGGTAAATT
* *
36098 ATAATTA---TTGATACCAGAAGTTGTCAC
1 AAAATTACCTTTGACACCAGAAGTTGTCAC
36125 CTTGAATTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
37 11 0.19
38 6 0.10
40 20 0.34
41 22 0.37
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAGAAGTTGTCACTCCGGTAAATT
Found at i:41775 original size:13 final size:13
Alignment explanation
Indices: 41753--41792 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
41743 CAGAGAATAT
41753 TATCAACAGAAGA
1 TATCAACAGAAGA
*
41766 TATCACCAGAAGA
1 TATCAACAGAAGA
* *
41779 TTTCAACTGAAGA
1 TATCAACAGAAGA
41792 T
1 T
41793 TATATGAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:43004 original size:18 final size:18
Alignment explanation
Indices: 42981--43017 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
42971 TACTCAAATT
42981 AACTGACTCAAAAAACTG
1 AACTGACTCAAAAAACTG
42999 AACTGACTCAAAAAACTG
1 AACTGACTCAAAAAACTG
43017 A
1 A
43018 CTAAACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (18 bp):
AACTGACTCAAAAAACTG
Found at i:44616 original size:175 final size:175
Alignment explanation
Indices: 44322--44652 Score: 563
Period size: 175 Copynumber: 1.9 Consensus size: 175
44312 ATTATACCCC
*
44322 TGACCTTCTAGTATTCTCATCTTCTCTTCCTGCTAGCATTTCTGAGGAGATATGCAATACTGCTT
1 TGACCTTCTAGTATTCTCATCTTCTCTTCCTGCTAGCATTTCTGAGGAGATATGCAATACTACTT
*
44387 CCAGAATGGGTGAGTGAACTTTTCTGTTTTTACTTTTGTAAAATCTACTGAATTGGAGATCATTT
66 CCAGAATGGGTGAGTGAACATTTCTGTTTTTACTTTTGTAAAATCTACTGAATTGGAGATCATTT
*
44452 TATCTTAATTCTCTATATGAACAAGTTGTGCATATCGTATACCAT
131 TATCTTAATTCTCTATAGGAACAAGTTGTGCATATCGTATACCAT
* * *
44497 TGACCTTTTAGTATTCTCATCTTTTCTTCTTGCTAGCATTTCTGAGGAGATATGCAATACTACTT
1 TGACCTTCTAGTATTCTCATCTTCTCTTCCTGCTAGCATTTCTGAGGAGATATGCAATACTACTT
* * *
44562 CCAGAATGGGTGAGTGGACATTTCTGTTTTTACTTTTGTTAAATCTATTGAATTGGAGATCATTT
66 CCAGAATGGGTGAGTGAACATTTCTGTTTTTACTTTTGTAAAATCTACTGAATTGGAGATCATTT
* *
44627 TATCTTAGTTTTCTATAGGAACAAGT
131 TATCTTAATTCTCTATAGGAACAAGT
44653 CGTAAATCTA
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 145 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (175 bp):
TGACCTTCTAGTATTCTCATCTTCTCTTCCTGCTAGCATTTCTGAGGAGATATGCAATACTACTT
CCAGAATGGGTGAGTGAACATTTCTGTTTTTACTTTTGTAAAATCTACTGAATTGGAGATCATTT
TATCTTAATTCTCTATAGGAACAAGTTGTGCATATCGTATACCAT
Found at i:44668 original size:54 final size:54
Alignment explanation
Indices: 44601--44709 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
44591 TTACTTTTGT
* * *
44601 TAAATCTATTGAATTGGAGATCATTTTATCTTAGTTTTCTATAGGAACAAGTCG
1 TAAATCTACTGAATTGGAGATAATTTTATCTTAGTTCTCTATAGGAACAAGTCG
*
44655 TAAATCTACTGAATTGGAGATAATTTTATCTTAGTTCTCTATATGAACAAGTCG
1 TAAATCTACTGAATTGGAGATAATTTTATCTTAGTTCTCTATAGGAACAAGTCG
44709 T
1 T
44710 GCATATCATA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (54 bp):
TAAATCTACTGAATTGGAGATAATTTTATCTTAGTTCTCTATAGGAACAAGTCG
Found at i:45349 original size:18 final size:18
Alignment explanation
Indices: 45326--45361 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
45316 AAGGAAGCTT
*
45326 AGCCAAATTTGATTCCTC
1 AGCCAAATCTGATTCCTC
45344 AGCCAAATCTGATTCCTC
1 AGCCAAATCTGATTCCTC
45362 CATTAGCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
AGCCAAATCTGATTCCTC
Found at i:45579 original size:41 final size:39
Alignment explanation
Indices: 45500--45580 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 39
45490 TTTAGTCTTG
* * *
45500 GTTCGTTCAATTTGAACATTCAAAAAAACATCAGTAATT
1 GTTCGTCCAATTTGAACATTCAAAAAAAAATCAATAATT
45539 GTTCGTCCAATTTGAACATTCCAAAAAAAAAATCAATAATT
1 GTTCGTCCAATTTGAACATT-C-AAAAAAAAATCAATAATT
45580 G
1 G
45581 ATCAATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 19 0.51
40 1 0.03
41 17 0.46
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (39 bp):
GTTCGTCCAATTTGAACATTCAAAAAAAAATCAATAATT
Found at i:45593 original size:113 final size:111
Alignment explanation
Indices: 45428--45652 Score: 369
Period size: 113 Copynumber: 2.0 Consensus size: 111
45418 TGAAGTCTCG
* * *
45428 GTTCGTCCAATTTGAACATTAAAAAAAACATCAGTAATTGATTAATTATACCCAAGTCAATTTTT
1 GTTCGTCCAATTTGAACATTAAAAAAAAAATCAATAATTGATCAATTATACCCAAGTCAATTTTT
* * *
45493 AGTCTTGGTTCGTTCAATTTGAACATTCAAAAAAACATCAGTAATT
66 AGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAACATAAGTAATT
45539 GTTCGTCCAATTTGAACATTCCAAAAAAAAAATCAATAATTGATCAATTATACCCAAGTCAATTT
1 GTTCGTCCAATTTGAACATT--AAAAAAAAAATCAATAATTGATCAATTATACCCAAGTCAATTT
*
45604 TTAGTCTCGGTTTGTCCAATTTGAACATTCAAAAAAACATAAGTAATT
64 TTAGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAACATAAGTAATT
45652 G
1 G
45653 ATCAATTATA
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 20 0.19
113 85 0.81
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.34
Consensus pattern (111 bp):
GTTCGTCCAATTTGAACATTAAAAAAAAAATCAATAATTGATCAATTATACCCAAGTCAATTTTT
AGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAACATAAGTAATT
Found at i:45662 original size:72 final size:71
Alignment explanation
Indices: 45539--45749 Score: 309
Period size: 72 Copynumber: 2.9 Consensus size: 71
45529 ATCAGTAATT
45539 GTTCGTCCAATTTGAACATTCCAAAAAAAAAATCAA-TAATTGATCAATTATACCCAAGTCAATT
1 GTTCGTCCAATTTGAACATT-C--AAAAAAAAT-AAGTAATTGATCAATTATACCCAAGTCAATT
45603 TTTAGTCTCG
62 TTTAGTCTCG
* *
45613 GTTTGTCCAATTTGAACATTCAAAAAAACATAAGTAATTGATCAATTATATCCAAGTCAATATTT
1 GTTCGTCCAATTTGAACATTCAAAAAAA-ATAAGTAATTGATCAATTATACCCAAGTC-A-ATTT
45678 TTAGTCTCG
63 TTAGTCTCG
* *
45687 GTTCGTCCAATTTGAACATT-AAAAAAAATCAGTAATTGATCAATTATACCAAAGTCAATTTTT
1 GTTCGTCCAATTTGAACATTCAAAAAAAATAAGTAATTGATCAATTATACCCAAGTCAATTTTT
45750 GCAGAGATAA
Statistics
Matches: 127, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
70 6 0.05
71 10 0.08
72 51 0.40
73 9 0.07
74 51 0.40
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (71 bp):
GTTCGTCCAATTTGAACATTCAAAAAAAATAAGTAATTGATCAATTATACCCAAGTCAATTTTTA
GTCTCG
Found at i:48650 original size:24 final size:24
Alignment explanation
Indices: 48594--48670 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
48584 ATCACATTTA
** * **
48594 ATGGTGGGCACACTGCCACTTTGG
1 ATGGTGGGTGCACTCCCACTTCCG
** *
48618 ATGG-GGGTGTGCTCCCGCTTCCG
1 ATGGTGGGTGCACTCCCACTTCCG
*
48641 ATGGTGGGTGCACTCCCACTTCTG
1 ATGGTGGGTGCACTCCCACTTCCG
48665 ATGGTG
1 ATGGTG
48671 AGCATTCTAC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
23 15 0.38
24 25 0.62
ACGTcount: A:0.12, C:0.26, G:0.35, T:0.27
Consensus pattern (24 bp):
ATGGTGGGTGCACTCCCACTTCCG
Found at i:48690 original size:24 final size:22
Alignment explanation
Indices: 48653--48709 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 22
48643 GGTGGGTGCA
48653 CTCCCACTTCTGATGGTGAGCATT
1 CTCCCA-TT-TGATGGTGAGCATT
48677 CTACCTCATTTGATGGTGAGCATT
1 CT-CC-CATTTGATGGTGAGCATT
48701 CTCCCATTT
1 CTCCCATTT
48710 TTTATGGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.16
23 2 0.06
24 18 0.58
25 4 0.13
26 2 0.06
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (22 bp):
CTCCCATTTGATGGTGAGCATT
Found at i:48719 original size:24 final size:24
Alignment explanation
Indices: 48663--48709 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
48653 CTCCCACTTC
48663 TGATGGTGAGCATTCTACCTCATT
1 TGATGGTGAGCATTCTACCTCATT
48687 TGATGGTGAGCATTCT-CC-CATT
1 TGATGGTGAGCATTCTACCTCATT
48709 T
1 T
48710 TTTATGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 16 0.70
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATGGTGAGCATTCTACCTCATT
Found at i:50885 original size:58 final size:58
Alignment explanation
Indices: 50791--50956 Score: 181
Period size: 58 Copynumber: 2.9 Consensus size: 58
50781 AAGCAATAAC
* * * **
50791 GACCGAGCATCCCTCGGTCGCACGGCCAAGCAGGCATCCCCCACTCATTTAATAAGTAA
1 GACCGAGCATCCCTCGGTCACACGGCCCAGTAGGCATCCCCCACTCATGCAATAAG-AA
* * * *
50850 -ATCGAGCATCCCTCGGTCACATGGCCCAGTGGGCATCCCCCAATCATGCAATAAGAA
1 GACCGAGCATCCCTCGGTCACACGGCCCAGTAGGCATCCCCCACTCATGCAATAAGAA
* * * * * *
50907 GACCGAGCAACCCTCTGTCACACGACCCAATTGGCATCCCCCACACATGC
1 GACCGAGCATCCCTCGGTCACACGGCCCAGTAGGCATCCCCCACTCATGC
50957 GAGAAGAAAA
Statistics
Matches: 88, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
57 2 0.02
58 86 0.98
ACGTcount: A:0.27, C:0.37, G:0.19, T:0.16
Consensus pattern (58 bp):
GACCGAGCATCCCTCGGTCACACGGCCCAGTAGGCATCCCCCACTCATGCAATAAGAA
Found at i:51079 original size:48 final size:48
Alignment explanation
Indices: 51008--51111 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 48
50998 GAGCACCCCC
* * *
51008 CAAAGGCATACAGCCTACCCCAAAGGCATACAGTCTAGATAAAATTTA
1 CAAAGGCAGACAACCTACCCCAAAGGCATACAGCCTAGATAAAATTTA
* *
51056 CAAAGGCAGACAATCTACCCCAAAGGCATACAGCCTAGATAAAATTTC
1 CAAAGGCAGACAACCTACCCCAAAGGCATACAGCCTAGATAAAATTTA
51104 CAAAGGCA
1 CAAAGGCA
51112 TGCAGCAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.16
Consensus pattern (48 bp):
CAAAGGCAGACAACCTACCCCAAAGGCATACAGCCTAGATAAAATTTA
Found at i:51117 original size:28 final size:28
Alignment explanation
Indices: 51075--51201 Score: 127
Period size: 28 Copynumber: 4.6 Consensus size: 28
51065 ACAATCTACC
51075 CCAAAGGCATACAGCCTAGATAAAATTT
1 CCAAAGGCATACAGCCTAGATAAAATTT
* * *
51103 CCAAAGGCATGCAG-C-AGATAGAATCT
1 CCAAAGGCATACAGCCTAGATAAAATTT
* *
51129 CTAAAGGCATACAGTCTTA-ATAAAA-TT
1 CCAAAGGCATACAG-CCTAGATAAAATTT
* * *
51156 CCTAAAGGCATACGGCCTATACAAAAATTT
1 CC-AAAGGCATACAGCCTAGA-TAAAATTT
51186 CCAAAGGCATACAGCC
1 CCAAAGGCATACAGCC
51202 AAAATAGAGT
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
26 21 0.27
27 6 0.08
28 30 0.38
29 18 0.23
30 4 0.05
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (28 bp):
CCAAAGGCATACAGCCTAGATAAAATTT
Found at i:51891 original size:29 final size:29
Alignment explanation
Indices: 51859--52278 Score: 211
Period size: 29 Copynumber: 14.4 Consensus size: 29
51849 TAAAGAGCAA
*
51859 GAAGCGGTAGTACGGCCC-CCAAAGTTCGG
1 GAAGTGGTAGTAC-GCCCTCCAAAGTTCGG
*
51888 GAAGTGGTAGTACGCCCTCCAAAGTTCGT
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* * **
51917 GAAGTGGTAGTACTCCCTCTAAAGTTCCC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
** **
51946 GAAGTGGTAGTATTCCCTCCAAAGTTCCC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* *****
51975 GAAGTGGTAGTACTCCCTCCAAAGGAAAA
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* * *** * **** *****
52004 AAAATACCAAGTCATGGGAAACCAAA-AAAAA
1 GAAGT-GGTAGT-A-CGCCCTCCAAAGTTCGG
* * * * * **
52035 AAAGGTGATATTACGCCC-CCAAGGCTCAC
1 GAA-GTGGTAGTACGCCCTCCAAAGTTCGG
** *
52064 GAAGTGGTAGTATTCCCTCCAAAGTTCGC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* **
52093 GAAGTGGTAGTACTCCCTCCAAAGTTCAC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
*
52122 G-AGTGGTAGTACTCCCTCCAAAGATTCGG
1 GAAGTGGTAGTACGCCCTCCAAAG-TTCGG
* **
52151 GAAGTGGTAGTACTCCCTCCAAAGTTCAC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* ** **
52180 GAAGTGGTAGTACACCCTCCAAAACTCAA
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* **
52209 GAAGTGGTAGTACGCCCTCCAAAGCTCAC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
* * **
52238 GAAGTGGTAGTATGCCCTCC-AAGCTCAC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCGG
52266 GAAGTGGTAGTAC
1 GAAGTGGTAGTAC
52279 ACCCCCTAGA
Statistics
Matches: 319, Mismatches: 63, Indels: 19
0.80 0.16 0.05
Matches are distributed among these distances:
28 60 0.19
29 217 0.68
30 26 0.08
31 10 0.03
32 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (29 bp):
GAAGTGGTAGTACGCCCTCCAAAGTTCGG
Found at i:51926 original size:58 final size:58
Alignment explanation
Indices: 51859--52278 Score: 247
Period size: 58 Copynumber: 7.2 Consensus size: 58
51849 TAAAGAGCAA
* ** **
51859 GAAGCGGTAGTACGGCCC-CCAAAGTTCGGGAAGTGGTAGTACGCCCTCCAAAGTTCGT
1 GAAGTGGTAGTAC-GCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
* * **
51917 GAAGTGGTAGTACTCCCTCTAAAGTTCCCGAAGTGGTAGTATTCCCTCCAAAGTTCCC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
* ****** * *** * **** *****
51975 GAAGTGGTAGTACTCCCTCCAAAGGAAAAAAAATACCAAGTCATGGGAAACCAAA-AAAAA
1 GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGT-GGTAGT-A-CGCCCTCCAAAGTTCCC
* * * * * * ** *
52035 AAAGGTGATATTACGCCC-CCAAGGCTCACGAAGTGGTAGTATTCCCTCCAAAGTTCGC
1 GAA-GTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
* * * **
52093 GAAGTGGTAGTACTCCCTCCAAAGTTCACG-AGTGGTAGTACTCCCTCCAAAGATTCGG
1 GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAG-TTCCC
* * * ** **
52151 GAAGTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTACACCCTCCAAAACTCAA
1 GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
* * * * *
52209 GAAGTGGTAGTACGCCCTCCAAAGCTCACGAAGTGGTAGTATGCCCTCC-AAGCTCAC
1 GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
52266 GAAGTGGTAGTAC
1 GAAGTGGTAGTAC
52279 ACCCCCTAGA
Statistics
Matches: 278, Mismatches: 75, Indels: 19
0.75 0.20 0.05
Matches are distributed among these distances:
57 59 0.21
58 165 0.59
59 26 0.09
60 12 0.04
61 16 0.06
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (58 bp):
GAAGTGGTAGTACGCCCTCCAAAGTTCCCGAAGTGGTAGTACGCCCTCCAAAGTTCCC
Found at i:52168 original size:87 final size:86
Alignment explanation
Indices: 52046--52282 Score: 318
Period size: 87 Copynumber: 2.7 Consensus size: 86
52036 AAGGTGATAT
* * *
52046 TACGCCC-CCAAGGCTCACGAAGTGGTAGTATTCCCTCCAAAGTTCGCGAAGTGGTAGTACTCCC
1 TACGCCCTCCAAAGCTCACGAAGTGGTAGTA-TCCCTCCAAAGTTCACGAAGTGGTAGTACACCC
** *
52110 TCCAAAGTTCACG-AGTGGTAG
65 TCCAAAACTCAAGAAGTGGTAG
* * **
52131 TACTCCCTCCAAAGATTCGGGAAGTGGTAGTACTCCCTCCAAAGTTCACGAAGTGGTAGTACACC
1 TACGCCCTCCAAAG-CTCACGAAGTGGTAGTA-TCCCTCCAAAGTTCACGAAGTGGTAGTACACC
52196 CTCCAAAACTCAAGAAGTGGTAG
64 CTCCAAAACTCAAGAAGTGGTAG
*
52219 TACGCCCTCCAAAGCTCACGAAGTGGTAGTATGCCCTCC-AAGCTCACGAAGTGGTAGTACACCC
1 TACGCCCTCCAAAGCTCACGAAGTGGTAGTAT-CCCTCCAAAGTTCACGAAGTGGTAGTACACCC
52283 CCTAGATGGC
Statistics
Matches: 132, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
85 6 0.05
86 30 0.23
87 75 0.57
88 21 0.16
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (86 bp):
TACGCCCTCCAAAGCTCACGAAGTGGTAGTATCCCTCCAAAGTTCACGAAGTGGTAGTACACCCT
CCAAAACTCAAGAAGTGGTAG
Found at i:52437 original size:29 final size:29
Alignment explanation
Indices: 52405--52819 Score: 371
Period size: 29 Copynumber: 14.7 Consensus size: 29
52395 ATATCAAAAG
*
52405 AGAGAGCGACGTACATCCACCATTTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
*
52434 AGAGAGCGCCGTACA---ACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
52460 AGAGAGCGCCGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATTTTGGA
* **
52488 A-CGAGCGTTGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACATCCACCATTTTGGA
* * *
52515 A-TGAGCGCTGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
* * ** *
52543 CGAGAGTGTTGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
52572 AGAGAGCGCCGTACATCCACCATTTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
**
52601 CA-AGAGCATCGTACATCCACCATTTTGGA
1 -AGAGAGCGCCGTACATCCACCATTTTGGA
*
52630 CA-AGAGCGCCGTACA-CCACCATTTCGGTA
1 -AGAGAGCGCCGTACATCCACCATTTTGG-A
* * * *
52659 CGTAAAGCGTTCGTACACTCGACCA-TTTGGA
1 AG-AGAGCG-CCGTACA-TCCACCATTTTGGA
*
52690 CGTA-AGCGCCGTACATCCACCATTTTGG-
1 AG-AGAGCGCCGTACATCCACCATTTTGGA
* * * *
52718 A-CGAGCGCTGTACATCCACTATCTTGGCA
1 AGAGAGCGCCGTACATCCACCATTTTGG-A
* *
52747 A-AGAGCGCCGTACA---ATCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
* *
52772 AGAGAGCACCGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACATCCACCATTTTGGA
52801 AGAGAGCGCCGTACATCCA
1 AGAGAGCGCCGTACATCCA
52820 TCTTGGAAAA
Statistics
Matches: 324, Mismatches: 42, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.01
26 45 0.14
27 68 0.21
28 18 0.06
29 161 0.50
30 10 0.03
31 11 0.03
32 4 0.01
33 5 0.02
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (29 bp):
AGAGAGCGCCGTACATCCACCATTTTGGA
Found at i:52822 original size:55 final size:56
Alignment explanation
Indices: 52405--52827 Score: 297
Period size: 55 Copynumber: 7.5 Consensus size: 56
52395 ATATCAAAAG
* * *
52405 AGAGAGCGACGTACATCCACCATTTTGGAAGAGAGCGCCGTACA---ACCATCTTGGA
1 AGAGAGCGCCGTACAT-C-CCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGGA
* * * *
52460 AGAGAGCGCCGTACATCCACCATTTTGG-A-CGAGCGTTGTACATCCACCATTTTGG-
1 AGAGAGCGCCGTACAT-C-CCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGGA
* * * * *
52515 A-TGAGCGCTGTACATCCACCATCTTGGACGAGAGTGTTGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTACAT-C-CCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGGA
* * *
52572 AGAGAGCGCCGTACATCCACCATTTTGGACA-AGAGCATCGTACATCCACCATTTTGGA
1 AGAGAGCGCCGTACAT-C-CCATCTTGGA-AGAGAGCGTCGTACATCCACCATCTTGGA
* * * *
52630 CA-AGAGCGCCGTACACCACCAT-TTCGGTACGTAAAGCGTTCGTACACTCGACCAT-TTGGA
1 -AGAGAGCGCCGTACATC-CCATCTT-GG-AAG-AGAGCG-TCGTACA-TCCACCATCTTGGA
* * * * *
52690 CGTA-AGCGCCGTACATCCACCATTTTGGACGAGCGC-T-GTACATCCACTATCTTGGCA
1 AG-AGAGCGCCGTACAT-C-CCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGG-A
**
52747 A-AGAGCGCCGTACAAT--CATCTTGGAAGAGAGCACCGTACATCCACCATCTTGGA
1 AGAGAGCGCCGTAC-ATCCCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGGA
52801 AGAGAGCGCCGTACAT-CCATCTTGGAA
1 AGAGAGCGCCGTACATCCCATCTTGGAA
52828 AAGGGCGCCG
Statistics
Matches: 304, Mismatches: 37, Indels: 54
0.77 0.09 0.14
Matches are distributed among these distances:
53 23 0.08
54 28 0.09
55 74 0.24
56 53 0.17
57 13 0.04
58 61 0.20
59 8 0.03
60 26 0.09
61 16 0.05
62 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (56 bp):
AGAGAGCGCCGTACATCCCATCTTGGAAGAGAGCGTCGTACATCCACCATCTTGGA
Found at i:52847 original size:55 final size:55
Alignment explanation
Indices: 52733--52849 Score: 132
Period size: 55 Copynumber: 2.1 Consensus size: 55
52723 CGCTGTACAT
* * * *
52733 CCACTATCTTGGCAAAGAGCGCCGTACAATCATCTTGGAAGAGAGCACCGTACAT
1 CCACCATCTTGGCAAAGAGCGCCGTACAATCATCTTGGAAAAGAGCACCGCACAC
* *
52788 CCACCATCTTGG-AAGAGAGCGCCGTAC-ATCCATCTTGGAAAAGGGCGCCGCA-AGC
1 CCACCATCTTGGCAA-AGAGCGCCGTACAAT-CATCTTGGAAAAGAGCACCGCACA-C
52843 CCACCAT
1 CCACCAT
52850 AGCAATAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 5 0.09
55 48 0.91
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (55 bp):
CCACCATCTTGGCAAAGAGCGCCGTACAATCATCTTGGAAAAGAGCACCGCACAC
Found at i:52973 original size:28 final size:28
Alignment explanation
Indices: 52941--53021 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
52931 AGGGAGTGTG
52941 CCCAATGACCGCGAAGCGGTAGTACGCT
1 CCCAATGACCGCGAAGCGGTAGTACGCT
52969 CCCAATGACCGCGAAGCGGTAGTACGCT
1 CCCAATGACCGCGAAGCGGTAGTACGCT
* * * *
52997 CCTAATGATCGCGAAGAGCTAGTAC
1 CCCAATGACCGCGAAGCGGTAGTAC
53022 ACTCTCAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (28 bp):
CCCAATGACCGCGAAGCGGTAGTACGCT
Found at i:53202 original size:24 final size:24
Alignment explanation
Indices: 53174--53230 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
53164 AGAAGACAAG
53174 TCACCAT-AAAAAATGGGAGAATGC
1 TCACCATCAAAAAA-GGGAGAATGC
* *
53198 TCACCATCAAATAAGGTAGAATGC
1 TCACCATCAAAAAAGGGAGAATGC
53222 TCACCATCA
1 TCACCATCA
53231 GAAGTGGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (24 bp):
TCACCATCAAAAAAGGGAGAATGC
Found at i:53263 original size:24 final size:23
Alignment explanation
Indices: 53223--53282 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
53213 GTAGAATGCT
* **
53223 CACCATCAGAAGTGGGAGTGCACC
1 CACCATCA-AAGCGGGAGCACACC
53247 CACCATCTAAAGCGGGAGCACACC
1 CACCATC-AAAGCGGGAGCACACC
*
53271 CCCCATCCAAAG
1 CACCAT-CAAAG
53283 TAGCAGTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.32, C:0.37, G:0.22, T:0.10
Consensus pattern (23 bp):
CACCATCAAAGCGGGAGCACACC
Found at i:53938 original size:16 final size:16
Alignment explanation
Indices: 53916--53961 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
53906 AATAAGTACT
*
53916 ATAACCCGAAACCGAT
1 ATAACCCGAAACCGAG
* *
53932 TTAACCCG-AATCGAG
1 ATAACCCGAAACCGAG
53947 ATAACCCGAAACCGA
1 ATAACCCGAAACCGA
53962 CAAAATCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (16 bp):
ATAACCCGAAACCGAG
Found at i:55880 original size:192 final size:184
Alignment explanation
Indices: 55553--55932 Score: 591
Period size: 192 Copynumber: 2.0 Consensus size: 184
55543 TGATCCGATA
55553 TATATAGTGACCCGAATCCGATTTTATCCGATTTAAAATAACCCGAAACCCGATAAACAAAATGA
1 TATATAGTGACCCGAATCCGATTTTATCCGATTTAAAATAACCCGAAACCCGATAAACAAAATGA
* * *
55618 CCCGAACCCGATTATATCCGATCTGATAAGACCCGTGATCCATTAAGACCCGGGACTTATTAAGA
66 CCCGAACCCGATTATATCCAATCTGATAAGACCCGTGATCCATTAAGACCCGGAACTTATTAACA
55683 CCCGAACCCGACTAGACTCGACCCGAAACCGACTTAACCCGCAAAATTGCCACC
131 CCCGAACCCGACTAGACTCGACCCGAAACCGACTTAACCCGCAAAATTGCCACC
* *
55737 TATA-AGTGACCCGAATCCGATTTTATCTGATTTAAAATAACCCGAAACCCGTTAAACCCGACAA
1 TATATAGTGACCCGAATCCGATTTTATCCGATTTAAAATAACCCGAAACCCGAT-AA----AC--
* *
55801 ACATAATGACCCGAACCCGATTCTATCCAATCTGCTAAGACCCGTGATCCATTAAGACCCGGAAC
59 A-A-AATGACCCGAACCCGATTATATCCAATCTGATAAGACCCGTGATCCATTAAGACCCGGAAC
* *
55866 TTGTTAACACCCGAACCCGACTAGACTCGACCCGAAACCGACTTAACCCGTAAAATTGCCACC
122 TTATTAACACCCGAACCCGACTAGACTCGACCCGAAACCGACTTAACCCGCAAAATTGCCACC
55929 TATA
1 TATA
55933 CCGGGGACCC
Statistics
Matches: 178, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
183 47 0.26
184 6 0.03
188 2 0.01
190 1 0.01
191 1 0.01
192 121 0.68
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.21
Consensus pattern (184 bp):
TATATAGTGACCCGAATCCGATTTTATCCGATTTAAAATAACCCGAAACCCGATAAACAAAATGA
CCCGAACCCGATTATATCCAATCTGATAAGACCCGTGATCCATTAAGACCCGGAACTTATTAACA
CCCGAACCCGACTAGACTCGACCCGAAACCGACTTAACCCGCAAAATTGCCACC
Found at i:59360 original size:3 final size:3
Alignment explanation
Indices: 59352--59392 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
59342 TAGTACTAGT
59352 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
59393 GTTATGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.