Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000707.1 Hibiscus syriacus cultivar Beakdansim tig00001375_pilon, 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: 67584
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1015 original size:2 final size:2
Alignment explanation
Indices: 1008--1035 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
998 TAATGTTTAT
1008 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
1036 CCTGTTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5905 original size:22 final size:23
Alignment explanation
Indices: 5880--5924 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5870 TTATTTATTA
5880 ATATTTATAATA-ATATAAAATT
1 ATATTTATAATATATATAAAATT
*
5902 ATATTTTTAATATTATATAAAAT
1 ATATTTATAATA-TATATAAAAT
5925 AATCAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTATAATATATATAAAATT
Found at i:6664 original size:787 final size:787
Alignment explanation
Indices: 5151--7655 Score: 4787
Period size: 787 Copynumber: 3.2 Consensus size: 787
5141 ATCCAATCCG
* *
5151 ATCAGATTAGGTCGAAATTCGTCGAGTTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
1 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
*
5216 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGAATTTTAATATCTAGAAA
66 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
* *
5281 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCCCTCTATGTCAGTCGCATCCCTTGT
131 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
5346 CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
196 CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
*
5411 AAATTATGAACCGGATACTGATCTGAAAATACAGGTATCTGACTTATGGGTAGCTAAATGTAATA
261 AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
* **
5476 AGCCGAGACACCGACCGGCATTTTGGTATTTGAAAATTTTTGGATACTCGATTTTGAACACCACT
326 AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAACACCACT
5541 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGAAATTGGTTTTCC
391 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGAAATTGGTTTTCC
5606 CTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCAC
456 CTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCAC
5671 GTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTAA
521 GTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTAA
5736 AATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATACT
586 AATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATACT
5801 TAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTAATATCATTTTCATCAAAATA
651 TAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTAATATCATTTTCATCAAAATA
*
5866 TTATTTATTTATTAATATTTATAATAATATAAAATTATATTTTTAATATTATATAAAATAATCAA
716 TTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAA
5931 TTATATT
781 TTATATT
5938 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
1 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
6003 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
66 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
6068 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
131 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
*
6133 CGGTCCCTTACATCGATGTTTAGCCGAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
196 CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
6198 AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
261 AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
6263 AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAACACCACT
326 AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAACACCACT
6328 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGAAATTGGTTTTCC
391 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGAAATTGGTTTTCC
6393 CTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCAC
456 CTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCAC
6458 GTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTAA
521 GTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTAA
6523 AATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATACT
586 AATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATACT
6588 TAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTAATATCATTTTCATCAAAATA
651 TAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTAATATCATTTTCATCAAAATA
6653 TTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAA
716 TTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAA
6718 TTATATT
781 TTATATT
6725 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
1 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
6790 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
66 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
6855 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
131 TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
6920 CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
196 CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
6985 AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
261 AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
*
7050 AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAGCACCACT
326 AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAACACCACT
*
7115 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGACGTATTTGGAATTAC-AGAATTGGTTTTC
391 ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGA-AATTGGTTTTC
* * * * * * *
7179 CCTAAATTCCCGTATTTGTTTCACATAATTCGTTTTCTGGAAAATGTTTTCCCGTGTTTGTTTTA
455 CCTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCA
*
7244 CGTAATTGGTTTTCCGGAATGTAATTCATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTA
520 CGTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTA
7309 AAATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATAC
585 AAATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATAC
7374 TTAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTTAATATCATTTTCATCAAAA
650 TTAAAATAATTTTATTTTATGAATTTAATATTAATAAAATA-TTTTAATATCATTTTCATCAAAA
7439 TATTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATC
714 TATTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATC
*
7504 AAATATATT
779 AATTATATT
7513 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
1 ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
7578 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
66 ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
7643 TTCTATTAATTTG
131 TTCTATTAATTTG
7656 ATAAGATTTT
Statistics
Matches: 1693, Mismatches: 23, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
786 1 0.00
787 1453 0.86
788 239 0.14
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (787 bp):
ATCAGATTAGGTCGAAACTCGTCGAATTCGGGTCTCATGCCCATCCTTAATGATTCTGGGTGTAC
ATTTATACATTCTATCAAATTTGTCGCAATTCAAAAATAATTCAATGATTTTTAATATCTAGAAA
TTCTATTAATTTGGTCGAACATAAAATCACCATCATCGCCTCTCTATGTCAGTCGCATCCCTTAT
CGGTCCCTTACATCGATGTTTAGCCAAATGTAATTTTAAATTTTTATATAATTTTTTAAATAAAA
AAATTATGAACCGGATACTGATCTGAAAATACATGTATCTGACTTATGGGTAGCTAAATGTAATA
AGCCGAGACACCGACCGACATTTTGGTACCTGAAAATTTTTGGATACTCGATTTTGAACACCACT
ACGTATAAACGCTAAATTTAGGGTGTGTTTGCTTGTCGTATTTGGAATTACGAAATTGGTTTTCC
CTAAATTTCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGTTTCAC
GTAATTGGTTTTCCGGAATGTAATTTATTTTTCTAGTAACAGAATTTCCTTTGTGTTTTCTGTAA
AATGACTTACAGATTCATTTTCCGTAAATCATTTTCCGAACTTTTCACTTCAAAGAATAAATACT
TAAAATAATTTTATTTTATGAATTTAATATTAATAAAATATTTTAATATCATTTTCATCAAAATA
TTATTTATTTATTAATATTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAA
TTATATT
Found at i:6693 original size:22 final size:23
Alignment explanation
Indices: 6662--6705 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6652 ATTATTTATT
6662 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
6685 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
6706 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:6702 original size:31 final size:31
Alignment explanation
Indices: 6647--6712 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
6637 CATTTTCATC
6647 AAAATAT--TATTTATTTATTAATATT-TAT
1 AAAATATAATATTTATTTATTAATATTATAT
6675 AATAATATAATATTATATTT-TTAATATTATAT
1 AA-AATATAATATT-TATTTATTAATATTATAT
6707 AAAATA
1 AAAATA
6713 ATCAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 2 0.06
29 5 0.15
31 16 0.48
32 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATATAATATTTATTTATTAATATTATAT
Found at i:6724 original size:31 final size:32
Alignment explanation
Indices: 6654--6712 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
6644 ATCAAAATAT
6654 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
6685 TATTATATTT-TTAATATTATATAA-AATA
1 TATTATATTTATTAATATT-TATAATAATA
6713 ATCAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:7481 original size:22 final size:23
Alignment explanation
Indices: 7450--7493 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
7440 ATTATTTATT
7450 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
7473 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
7494 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:7490 original size:31 final size:31
Alignment explanation
Indices: 7435--7500 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
7425 CATTTTCATC
7435 AAAATAT--TATTTATTTATTAATATT-TAT
1 AAAATATAATATTTATTTATTAATATTATAT
7463 AATAATATAATATTATATTT-TTAATATTATAT
1 AA-AATATAATATT-TATTTATTAATATTATAT
7495 AAAATA
1 AAAATA
7501 ATCAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 2 0.06
29 5 0.15
31 16 0.48
32 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATATAATATTTATTTATTAATATTATAT
Found at i:7512 original size:31 final size:32
Alignment explanation
Indices: 7442--7500 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
7432 ATCAAAATAT
7442 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
7473 TATTATATTT-TTAATATTATATAA-AATA
1 TATTATATTTATTAATATT-TATAATAATA
7501 ATCAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:8792 original size:37 final size:36
Alignment explanation
Indices: 8729--8848 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
8719 ATCCCATTAT
* * *
8729 CATTTTTC-AACAAGCATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
8765 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
8801 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
8836 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
8849 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:8804 original size:21 final size:21
Alignment explanation
Indices: 8780--8840 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
8770 TTCAAAGAAA
8780 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
8801 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
8815 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
8836 CATTT
1 CATTT
8841 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:8857 original size:35 final size:36
Alignment explanation
Indices: 8747--8875 Score: 142
Period size: 35 Copynumber: 3.6 Consensus size: 36
8737 AACAAGCATC
* *
8747 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAG-AACAGT
*
8784 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-AACAGT
***
8819 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
8854 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
8876 AATAATTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.17
35 44 0.52
37 26 0.31
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAACAGT
Found at i:12434 original size:17 final size:17
Alignment explanation
Indices: 12412--12448 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12402 CAATTTCCAC
12412 TGAACTCAACTAGGTTG
1 TGAACTCAACTAGGTTG
*
12429 TGAACTCAACTGGGTTG
1 TGAACTCAACTAGGTTG
12446 TGA
1 TGA
12449 TTGTGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (17 bp):
TGAACTCAACTAGGTTG
Found at i:13430 original size:37 final size:36
Alignment explanation
Indices: 13367--13485 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
13357 ATCCCATTAT
* * *
13367 CATTTTTC-AACAAGCATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
13403 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
13439 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
13474 CATTTTTTCAAA
1 CA-TTTTTCAAA
13486 ATTGGTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.47
36 13 0.17
37 27 0.36
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:13442 original size:21 final size:21
Alignment explanation
Indices: 13418--13478 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
13408 TTCAAAGAAA
13418 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
13439 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
13453 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
13474 CATTT
1 CATTT
13479 TTTCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:13495 original size:35 final size:37
Alignment explanation
Indices: 13385--13513 Score: 153
Period size: 35 Copynumber: 3.6 Consensus size: 37
13375 AACAAGCATC
* *
13385 TACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCAT-TTTTTCAAAGAAACAGT
*
13422 TACCAAACTTTGAAAACCA--TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAAACAGT
***
13457 TACCAAACTTTGAAAACCATTTTTTC-AA-AATTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGAAACAGT
13492 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACCATTTT
13514 AATAATTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
34 14 0.17
35 46 0.55
36 2 0.02
37 22 0.26
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (37 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGAAACAGT
Found at i:14629 original size:4 final size:4
Alignment explanation
Indices: 14616--14645 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
14606 CGGACCACAG
14616 TTTC -TTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
14646 TCCTATTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:15397 original size:17 final size:18
Alignment explanation
Indices: 15364--15399 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
15354 AATTCCAAGA
15364 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
15382 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
15399 A
1 A
15400 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:16959 original size:3 final size:3
Alignment explanation
Indices: 16951--17010 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
16941 TTTGGGCCTG
*
16951 TAA TAA TAA TAA TAAA TAA T-A TAA TAA TAA TAG TAA TAAA TAA -AA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
*
16996 TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA
17011 AAAACCCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:16977 original size:21 final size:21
Alignment explanation
Indices: 16951--17009 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
16941 TTTGGGCCTG
16951 TAATAATAATAATAAATAATA
1 TAATAATAATAATAAATAATA
*
16972 TAATAATAATAGT-AATAA-A
1 TAATAATAATAATAAATAATA
16991 TAA-AATAATAATAAA-AATA
1 TAATAATAATAATAAATAATA
17010 AAAAACCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 10 0.29
19 7 0.21
20 5 0.15
21 12 0.35
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
TAATAATAATAATAAATAATA
Found at i:16987 original size:24 final size:24
Alignment explanation
Indices: 16951--17010 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
16941 TTTGGGCCTG
*
16951 TAATAATAATAATAAATAATATAA
1 TAATAATAATAATAAATAAAATAA
*
16975 TAATAATAGTAATAAATAAAATAA
1 TAATAATAATAATAAATAAAATAA
*
16999 TAATAAAAATAA
1 TAATAATAATAA
17011 AAAACCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TAATAATAATAATAAATAAAATAA
Found at i:17632 original size:123 final size:125
Alignment explanation
Indices: 17360--17912 Score: 755
Period size: 123 Copynumber: 4.5 Consensus size: 125
17350 TAAGGCAATC
* *
17360 TTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGCTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * * *
17424 CTCTCTTTGGGAAATGAATGTTGATGCTGATCTATCTACTTCTGTGATAGAGTTACGCAAAAGG
65 CTTTCTCT-GGAAA--AGTGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* * * *
17488 TTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAATTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
17553 TTTCTCTGGAAAAGTG-T-ATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
66 TTTCTCTGGAAAAGTGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
*
17611 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGATTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * *
17676 ACTT-T-T-GAAAA-TGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAAG
66 -TTTCTCTGGAAAAGTGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* * * *
17733 TTGAACAAGTTGTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* * *
17798 TTTCTCTGGCAAAGTG-T-ATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
66 TTTCTCTGGAAAAGTGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* *
17856 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
17913 CTATTAAATC
Statistics
Matches: 384, Mismatches: 33, Indels: 21
0.88 0.08 0.05
Matches are distributed among these distances:
120 2 0.01
121 8 0.02
122 101 0.26
123 190 0.49
124 8 0.02
125 5 0.01
127 5 0.01
128 62 0.16
129 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (125 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
TTTCTCTGGAAAAGTGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
Found at i:17796 original size:245 final size:249
Alignment explanation
Indices: 17360--17912 Score: 864
Period size: 245 Copynumber: 2.2 Consensus size: 249
17350 TAAGGCAATC
* *
17360 TTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGCTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
17424 CTCTCTTTGGGAAATGAATGTTGATGCTGATCTATCTACTTCTGTGATAGAGTTACGCAAAAGGT
65 CACTCTTT-GGAAA-GAATGTTGATGCTGATCTATCTACTTCTGTGATAGAATCAAGCAAAAAGT
* *
17489 TGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAATTTCTTCTCATTATGAACT
128 TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTCATTATGAACT
17554 TTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
193 TTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
*
17611 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGATTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
17676 ACT-TTT-G-AA-AATGTTGATGTTGATCTATCTCCTTCTGTGATAGAATCAAGCAAAAAGTTGA
66 ACTCTTTGGAAAGAATGTTGATGCTGATCTATCTACTTCTGTGATAGAATCAAGCAAAAAGTTGA
* * *
17737 ACAAGTTGTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTTATTATGAACTTTC
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTCATTATGAACTTTC
* * *
17802 TCTGGCAAAGTGTATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
196 TCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* *
17856 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
17913 CTATTAAATC
Statistics
Matches: 280, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
245 211 0.75
247 2 0.01
248 1 0.00
250 3 0.01
251 60 0.21
252 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (249 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC
ACTCTTTGGAAAGAATGTTGATGCTGATCTATCTACTTCTGTGATAGAATCAAGCAAAAAGTTGA
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTCTCATTATGAACTTTC
TCTGGAAAAGTGTATGCTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
Found at i:18378 original size:22 final size:22
Alignment explanation
Indices: 18349--18408 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
18339 AAAAGAAAAC
18349 CTATCATCTTTGAAGAGAGAAT
1 CTATCATCTTTGAAGAGAGAAT
*
18371 TTATCATCTTTGAAGAGAGAAT
1 CTATCATCTTTGAAGAGAGAAT
*
18393 CTATCATATTTGAAGA
1 CTATCATCTTTGAAGA
18409 ATGTAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (22 bp):
CTATCATCTTTGAAGAGAGAAT
Found at i:19885 original size:75 final size:75
Alignment explanation
Indices: 19768--19999 Score: 340
Period size: 75 Copynumber: 3.1 Consensus size: 75
19758 CATGCCCTAA
* * * * * *
19768 CATTTGTTAATAC-AACGTTCAAAATGCGCCAACATTCTTCATTCTGATTGAAATGGGCTTTCAG
1 CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTCATTCTGATTGAAATGGGCTTTCAG
19832 CATACCCCAG
66 CATACCCCAG
*
19842 CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTCATTCTGATTGAATTGGGCTTTCAG
1 CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTCATTCTGATTGAAATGGGCTTTCAG
*
19907 CATGCCCCAG
66 CATACCCCAG
* * * *
19917 CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTGATTATGATTGAAATGGGTTTTCAA
1 CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTCATTCTGATTGAAATGGGCTTTCAG
*
19982 CATACCCCAA
66 CATACCCCAG
19992 CATTTGCT
1 CATTTGCT
20000 TTTTTGTTGA
Statistics
Matches: 142, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 11 0.08
75 131 0.92
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (75 bp):
CATTTGCTGATACAAACGTTCAAAATACGTCAATATTCCTCATTCTGATTGAAATGGGCTTTCAG
CATACCCCAG
Found at i:27214 original size:17 final size:18
Alignment explanation
Indices: 27181--27216 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
27171 AATTCCAAGA
27181 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
27199 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
27216 A
1 A
27217 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:28570 original size:3 final size:3
Alignment explanation
Indices: 28562--28625 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
28552 TTTGGGCCTG
28562 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
28609 -AA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
28626 AAAACCCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:33218 original size:422 final size:417
Alignment explanation
Indices: 32458--33225 Score: 1128
Period size: 422 Copynumber: 1.8 Consensus size: 417
32448 TGGTGACAAA
* *
32458 TTTTGTAACTATAAGTGTTAATAATTATTACAAAAATATTGTCACAAAAAATAATGATATTCACA
1 TTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGTCACAAAAAATAATGATATTCAAA
* *
32523 TTTTTTTGACAAATTAAATTTGTAGTTATAAATTTTAACTATAGTGATATCATATATTGTCATAA
66 TTTTTGTGACAAATTAAACTTGTAGTTATAAATTTTAACTATAGTGATATCATATATTGTCATAA
* * * *
32588 CTATTTTTCTCCACTTTTTTTGTTTCAAAATTTATATTAACAATTTTTATAATTATAATTTATAG
131 ATATTTTTCTCCACTTTTTTTGTTTCAAAAGTGATATTAACAAGTTTTATAATTATAATTTATAG
* * *
32653 TTATTTTTATAGAAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGTAATAAATTATT
196 TTACTGTTATAGAAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAATAAATTATT
* *
32718 TTTGTACTTATATATTTTAATCATTCTAAAAAATTATACTATCAGAAACATTTCACCATGTTATT
261 TTTGTACTTATATATTTTAATCATTATAAAAAATTATACTATCAGAAACATTTCACCATATTATT
*
32783 TAGTGTAAAAAATGTTATATAGTAACAAAATATATTGTCATAAAGATTTTTCTCCATATTGTTTT
326 TAGTGCAAAAAATGTTATATAGTAACAAAATATATTGTCATAAAGATTTTTCTCCATATTGTTTT
32848 ACGCCAAAAAATCCTATGGTAATACTT
391 ACGCCAAAAAATCCTATGGTAATACTT
* * *
32875 TTTTTTAACTATAAGTGTTTATAATTATTACAAAATACATTGTTACAAAAAATAATGATATTCAA
1 TTTTGTAACTATAAGTGTTAATAATTATTACAAAA-ACATTGTCACAAAAAATAATGATATTCAA
* * *
32940 ATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAATTATAGTGATGA-CATATATTGTGAT
65 ATTTTTGTGACAAATTAAACTTGTAGTTATAAATTTTAACTATAGTGAT-ATCATATATTGTCAT
* * * *
33004 AAATATTTTTTTCCACTTTTTTTTTTTGTTTCAAAAAGTGATATTGATAAGTTTTGTAATTATAA
129 AAATATTTTTCTCCAC----TTTTTTTGTTTC-AAAAGTGATATTAACAAGTTTTATAATTATAA
* * *
33069 TTTATAGTTACTGTTATAGAAAAAAA-TATCACATCATATAGTAAAATTAAAGTTTTTTGTAATC
189 TTTATAGTTACTGTTATAGAAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAATA
* * * *
33133 AATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTATTAG-AACAATTTCTCC
254 AATTATTTTTGTACTTATATATTTTAATCATTATAAAAAATTATACTATCAGAAAC-ATTTCACC
* * * *
33197 CTATTTTTTGGTGCCAAAAATGTTATATA
318 ATATTATTTAGTGCAAAAAATGTTATATA
33226 ATAAAAGTTT
Statistics
Matches: 308, Mismatches: 35, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
417 33 0.11
418 97 0.31
419 1 0.00
421 3 0.01
422 124 0.40
423 50 0.16
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (417 bp):
TTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGTCACAAAAAATAATGATATTCAAA
TTTTTGTGACAAATTAAACTTGTAGTTATAAATTTTAACTATAGTGATATCATATATTGTCATAA
ATATTTTTCTCCACTTTTTTTGTTTCAAAAGTGATATTAACAAGTTTTATAATTATAATTTATAG
TTACTGTTATAGAAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAATAAATTATT
TTTGTACTTATATATTTTAATCATTATAAAAAATTATACTATCAGAAACATTTCACCATATTATT
TAGTGCAAAAAATGTTATATAGTAACAAAATATATTGTCATAAAGATTTTTCTCCATATTGTTTT
ACGCCAAAAAATCCTATGGTAATACTT
Found at i:36657 original size:31 final size:31
Alignment explanation
Indices: 36622--36686 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
36612 GAAAGATAAT
* * *
36622 TTATGATAATTTATTTAGACAAAATAACAAA
1 TTATGATAATTTATATAAACAAAAGAACAAA
36653 TTATGATAATTTATATAAACAAAAGAACAAA
1 TTATGATAATTTATATAAACAAAAGAACAAA
36684 TTA
1 TTA
36687 AATTTAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (31 bp):
TTATGATAATTTATATAAACAAAAGAACAAA
Found at i:37026 original size:196 final size:196
Alignment explanation
Indices: 36684--37051 Score: 468
Period size: 196 Copynumber: 1.9 Consensus size: 196
36674 AAAGAACAAA
* * *
36684 TTAAATTTAGTTAAAATAAAAAATTATGACAAATGTGTTTAGTCAAAATATTTTTTCAAAATAAC
1 TTAAATTTAGTCAAAATAAAAAATTATGACAAATGTATTTAGTCAAAATATTTTCTCAAAATAAC
* * * * *
36749 AAATTATGACAATTTTAATTAGTTATAACAACAAATTATAATAAATATTAATTTCTTAATATAAA
66 AAATTATGACAAATTTAATTAATCAAAACAACAAATTATAACAAATATTAATTTCTTAATATAAA
* ** * *
36814 AAGTTATGGCAAATAATATTTTTTCACAATAATCATTTATAACAAATTTATTTAGTCACAATAAC
131 AAATTATGAAAAATAATATTTTTTCACAATAATAAATTATAACAAATTTATTTAGTCACAATAAC
36879 T
196 T
** * * *
36880 TTAAATTTAGTCAAAATAAAAAATTATGTTAAATTTATTTTGTCACAATATTTTCTCAAAA-AAC
1 TTAAATTTAGTCAAAATAAAAAATTATGACAAATGTATTTAGTCAAAATATTTTCTCAAAATAAC
** * * * * * * *
36944 ATCTTTTGATAAATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTTATTATAAA
66 AAATTATGACAAATTTAATTAATCAAAACAACAAATTATAACAAATATTAATTTCTTAATAT-AA
*
37009 AAAATTTTGAAAAATAATATTTTTTCACAATAATAAATTATAA
130 AAAATTATGAAAAATAATATTTTTTCACAATAATAAATTATAA
37052 AAAAAAATAT
Statistics
Matches: 143, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
195 51 0.36
196 92 0.64
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (196 bp):
TTAAATTTAGTCAAAATAAAAAATTATGACAAATGTATTTAGTCAAAATATTTTCTCAAAATAAC
AAATTATGACAAATTTAATTAATCAAAACAACAAATTATAACAAATATTAATTTCTTAATATAAA
AAATTATGAAAAATAATATTTTTTCACAATAATAAATTATAACAAATTTATTTAGTCACAATAAC
T
Found at i:55860 original size:23 final size:23
Alignment explanation
Indices: 55809--55861 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
55799 TGGATTATGC
*
55809 CACAAGATCAGAGAAAATGCGTG
1 CACAAGAGCAGAGAAAATGCGTG
* *
55832 CTCAAGAGCAGAGAAAAATGTGT-
1 CACAAGAGCAGAG-AAAATGCGTG
55855 CACAAGA
1 CACAAGA
55862 ATAGAGATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (23 bp):
CACAAGAGCAGAGAAAATGCGTG
Found at i:56902 original size:137 final size:140
Alignment explanation
Indices: 56730--57006 Score: 524
Period size: 137 Copynumber: 2.0 Consensus size: 140
56720 AAATTTAAAA
56730 GCTTTTAAAATTTATTTTTATTTTTTAATATTTTTGATGAATAATATTTAAAAAATATTTGTTAT
1 GCTTTTAAAATTTATTTTTATTTTTTAATATTTTTGATGAATAATATTTAAAAAATATTTGTTAT
*
56795 AATCAGCAGTAATTAATTTATTAATAGATTAACTCTTGAATCAAATATT-AAAAAAA-TTAATTC
66 AATCAGCAGTAATTAATTTATTAATAGATCAACTCTTGAATCAAATATTAAAAAAAATTTAATTC
56858 TAATTTATTT
131 TAATTTATTT
56868 GCTTTT-AAATTTATTTTTATTTTTTAATATTTTTGATGAATAATATTTAAAAAATATTTGTTAT
1 GCTTTTAAAATTTATTTTTATTTTTTAATATTTTTGATGAATAATATTTAAAAAATATTTGTTAT
56932 AATCAGCAGTAATTAATTTATTAATAGATCAACTCTTGAATCAAATATTAAAAAAAATTTAATTC
66 AATCAGCAGTAATTAATTTATTAATAGATCAACTCTTGAATCAAATATTAAAAAAAATTTAATTC
56997 TAATTTATTT
131 TAATTTATTT
57007 TTACTTTTAT
Statistics
Matches: 136, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
137 106 0.78
138 13 0.10
139 17 0.12
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.48
Consensus pattern (140 bp):
GCTTTTAAAATTTATTTTTATTTTTTAATATTTTTGATGAATAATATTTAAAAAATATTTGTTAT
AATCAGCAGTAATTAATTTATTAATAGATCAACTCTTGAATCAAATATTAAAAAAAATTTAATTC
TAATTTATTT
Found at i:58495 original size:59 final size:60
Alignment explanation
Indices: 58414--58529 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
58404 AAATAGCCCC
* * *
58414 TTGACTATAGGGTGTTATTTTGTTGAGTC-TTCAACCATTAAAAGTTATAAAATGGTTCA
1 TTGACTATAGAGTATTATTTTGTTGAGTCTTTCAACCATTAAAAGTTACAAAATGGTTCA
**
58473 TTGACTATAGAGTATTGA-TTTGTTGAGTCTTTCAACTGTTAAAAGTTACAAAATGGT
1 TTGACTATAGAGTATT-ATTTTGTTGAGTCTTTCAACCATTAAAAGTTACAAAATGGT
58530 CACATGACTA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 25 0.50
60 25 0.50
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (60 bp):
TTGACTATAGAGTATTATTTTGTTGAGTCTTTCAACCATTAAAAGTTACAAAATGGTTCA
Found at i:58538 original size:60 final size:59
Alignment explanation
Indices: 58415--58540 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 59
58405 AATAGCCCCT
* * * *
58415 TGACTATAGGGTGTTATTTTGTTGAGTCTTCAACCATTAAAAGTTATAAAATGGTTCAT
1 TGACTATAGAGTATTATTTTGTTGAGTCTTCAACCATTAAAAGTTACAAAATGGTTCAA
**
58474 TGACTATAGAGTATTGA-TTTGTTGAGTCTTTCAACTGTTAAAAGTTACAAAATGG-TCACA
1 TGACTATAGAGTATT-ATTTTGTTGAGTC-TTCAACCATTAAAAGTTACAAAATGGTTCA-A
58534 TGACTAT
1 TGACTAT
58541 TTATATGTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 27 0.47
60 31 0.53
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (59 bp):
TGACTATAGAGTATTATTTTGTTGAGTCTTCAACCATTAAAAGTTACAAAATGGTTCAA
Found at i:61554 original size:22 final size:22
Alignment explanation
Indices: 61528--61569 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
61518 TTTCAAAAGG
61528 TATTA-TTTTCCTATTCGAAAAC
1 TATTACTTTT-CTATTCGAAAAC
61550 TATTACTTTTCTATTCGAAA
1 TATTACTTTTCTATTCGAAA
61570 GCAGAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (22 bp):
TATTACTTTTCTATTCGAAAAC
Found at i:64703 original size:158 final size:156
Alignment explanation
Indices: 64482--64810 Score: 482
Period size: 158 Copynumber: 2.1 Consensus size: 156
64472 CGGTATAGAA
* * * *
64482 ATGATAAAACCGATAAAGCGCTACGGATACATTTAAAGTGTTGGTACTTAATATAAGGATCGACA
1 ATGATAAAACCGGTAAAGCGCTACGGATACATTGAAAGTGTCGATACTTAATATAAGGATCGACA
* *
64547 CTTCGTGAA-TTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTAAAAAAATGTA
66 CTT-GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTT--AAAAATATA
* *
64611 TCGATCCAAAATGATATACCAGGTAAAAAT
128 TCGATCC-AAACGATATAACAGGTAAAAAT
* * *
64641 ATGATAAAACCGGTAAA-CGTTACGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACA
1 ATGATAAAACCGGTAAAGCGCTACGGATACATTGAAAGTGTCGATACTTAATATAAGGATCGACA
** *
64705 CTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAATATATCG
66 CTTGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAATATATCG
64770 ATCCAAACGATATAACAGGTAAAAAT
131 ATCCAAACGATATAACAGGTAAAAAT
64796 ATGATAAAACCGGTA
1 ATGATAAAACCGGTA
64811 TCAAAATGAT
Statistics
Matches: 155, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
155 35 0.23
156 15 0.10
157 5 0.03
158 84 0.54
159 16 0.10
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (156 bp):
ATGATAAAACCGGTAAAGCGCTACGGATACATTGAAAGTGTCGATACTTAATATAAGGATCGACA
CTTGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAATATATCG
ATCCAAACGATATAACAGGTAAAAAT
Found at i:64810 original size:20 final size:19
Alignment explanation
Indices: 64787--64833 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
64777 CGATATAACA
64787 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
64807 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
64827 GGTAAAA
1 GGTAAAA
64834 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:64835 original size:17 final size:19
Alignment explanation
Indices: 64796--64838 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
64786 AGGTAAAAAT
64796 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
64816 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
64833 ATGATA
1 ATGATA
64839 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:67009 original size:21 final size:21
Alignment explanation
Indices: 66983--67047 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
66973 AATACAATCA
*
66983 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
67004 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
67025 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
67046 AG
1 AG
67048 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Done.