Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013823.1 Corchorus capsularis cultivar CVL-1 contig13844, 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: 142342
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2467 original size:24 final size:24
Alignment explanation
Indices: 2440--2486 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2430 GTTATTTAAA
2440 TTTATGCTT-TATCTTTAATTTTCC
1 TTTAT-CTTATATCTTTAATTTTCC
* *
2464 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTAATTTTC
2487 AAGTTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTATCTTATATCTTTAATTTTCC
Found at i:4042 original size:30 final size:30
Alignment explanation
Indices: 4006--4063 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3996 AGTTCGTGAT
*
4006 TTGAAGATTTCTTGAA-GATAATTTCAAGAC
1 TTGAAGA-TTATTGAAGGATAATTTCAAGAC
*
4036 TTGAAGATTATTGAAGGATTATTTCAAG
1 TTGAAGATTATTGAAGGATAATTTCAAG
4064 GAGCAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (30 bp):
TTGAAGATTATTGAAGGATAATTTCAAGAC
Found at i:5368 original size:22 final size:23
Alignment explanation
Indices: 5329--5371 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5319 ATTCACTGTT
*
5329 TTTTCTTTAATTGTTTTCTTAAA
1 TTTTCTTTAATTGCTTTCTTAAA
*
5352 TTTTC-TTGATTGCTTTCTTA
1 TTTTCTTTAATTGCTTTCTTA
5372 GTTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTCTTTAATTGCTTTCTTAAA
Found at i:8165 original size:48 final size:48
Alignment explanation
Indices: 8090--8627 Score: 666
Period size: 48 Copynumber: 11.2 Consensus size: 48
8080 TTGTCAGCCA
* *
8090 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * *
8138 GGAAGTGAGGAAAGACCAACTTAGGTCGAAAAGATTGCTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * * *
8186 GGAAGTGAAGAAAGACCAATTTGGGTCGGAAGGATTTTTGACTCAAAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * *
8234 GGAAGTGAGGAATGACCAACTTAGGTCGAAAAGATTTCTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * *
8282 GGAAGTGGGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * *
8330 GGAATTGAGGAAATACCAACTTAGGTCGAAAAGATTTCTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * *
8378 GGAAGTGAGGAAAGACTAACTTGGG-CTGAAAAGCTTGCTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTC-GGAAAGATTTCTGACTCACAT
* * *
8426 GGAAAGTGAGGAAAGACCAACTTGGGTCAGAAGGATTTTTGACTCACAT
1 GG-AAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * *
8475 GGAAGTGAGGAATGACCAACTTGGGTTGGAAGGATTTTTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * * * *
8523 GGAAGTGAGGAATGGCCAACTTGGCTCGAAAAGATTGCTGACTCACTT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
* * * * *
8571 GGAAGTAAGTAAAGACCAATTTAGGTC-GAAAGATTGCTGACTCACAT
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
8618 GGAAGTGAGG
1 GGAAGTGAGG
8628 TTGACTTTTG
Statistics
Matches: 418, Mismatches: 69, Indels: 7
0.85 0.14 0.01
Matches are distributed among these distances:
47 27 0.06
48 351 0.84
49 39 0.09
50 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.23
Consensus pattern (48 bp):
GGAAGTGAGGAAAGACCAACTTGGGTCGGAAAGATTTCTGACTCACAT
Found at i:8254 original size:96 final size:96
Alignment explanation
Indices: 8090--8627 Score: 735
Period size: 96 Copynumber: 5.6 Consensus size: 96
8080 TTGTCAGCCA
*
8090 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGGAAAGACC
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGGAATGACC
*
8155 AACTTAGGTCGAAAAGATTGCTGACTCACAT
66 AACTTAGGTCGAAAAGATTTCTGACTCACAT
* * *
8186 GGAAGTGAAGAAAGACCAATTTGGGTCGGAAGGATTTTTGACTCAAATGGAAGTGAGGAATGACC
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGGAATGACC
8251 AACTTAGGTCGAAAAGATTTCTGACTCACAT
66 AACTTAGGTCGAAAAGATTTCTGACTCACAT
* *
8282 GGAAGTGGGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAATTGAGGAAAT-AC
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGG-AATGAC
8346 CAACTTAGGTCGAAAAGATTTCTGACTCACAT
65 CAACTTAGGTCGAAAAGATTTCTGACTCACAT
* * * * ** *
8378 GGAAGTGAGGAAAGACTAACTTGGG-CTGAAAAGCTTGCTGACTCACATGGAAAGTGAGGAAAGA
1 GGAAGTGAGGAAAGACCAACTTGGGTC-GGAAGGATTTTTGACTCACATGG-AAGTGAGGAATGA
* * *
8442 CCAACTTGGGTC-AGAAGGATTTTTGACTCACAT
64 CCAACTTAGGTCGA-AAAGATTTCTGACTCACAT
* * *
8475 GGAAGTGAGGAATGACCAACTTGGGTTGGAAGGATTTTTGACTCACATGGAAGTGAGGAATGGCC
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGGAATGACC
* *
8540 AACTT-GGCTCGAAAAGATTGCTGACTCACTT
66 AACTTAGG-TCGAAAAGATTTCTGACTCACAT
* * * * * **
8571 GGAAGTAAGTAAAGACCAATTTAGGTC-GAAAGATTGCTGACTCACATGGAAGTGAGG
1 GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGG
8628 TTGACTTTTG
Statistics
Matches: 389, Mismatches: 45, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
95 30 0.08
96 278 0.71
97 81 0.21
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.23
Consensus pattern (96 bp):
GGAAGTGAGGAAAGACCAACTTGGGTCGGAAGGATTTTTGACTCACATGGAAGTGAGGAATGACC
AACTTAGGTCGAAAAGATTTCTGACTCACAT
Found at i:8764 original size:68 final size:67
Alignment explanation
Indices: 8677--8846 Score: 268
Period size: 68 Copynumber: 2.5 Consensus size: 67
8667 AGGCTTAAAT
*
8677 TGACTCGTATGTAAACGAGTTTGGCTTGTGGAAAAGCCCCTAATGCTTGGATGGAACCAAGGCTG
1 TGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCCCCTAATGCTTGGATGGAACCAAGGCT-
8742 AAC
65 AAC
* * *
8745 TGACTCGTATGGAAACGAGTTTGGCTAGTGGAAAAGCCCCTGATGCTTGGATGGAACCAAGGCTA
1 TGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCCCCTAATGCTTGGATGGAACCAAGGCTA
8810 AC
66 AC
* * *
8812 TGACTTGTATCAAAACGAGTTTGGGTTGTGGAAAA
1 TGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAA
8847 CTCAAAGCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 33 0.35
68 61 0.65
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (67 bp):
TGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCCCCTAATGCTTGGATGGAACCAAGGCTA
AC
Found at i:11161 original size:43 final size:42
Alignment explanation
Indices: 11107--11243 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
11097 TCTTTTAATG
* *
11107 GAAAAGCATTTTATCAAAACCTTTTGAAAATCATGACTCCTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAA-CATGACTCTTTT
* * *
11150 GAGAACCATTTTATCAAAACCTTTTG-AAACCT---TTTTTT
1 GAAAACCATTTTATCAAAACCTTTTGAAAACATGACTCTTTT
*
11188 GGAAAACCATTTTATCAAAACCTTTCGAAAACCATGACTCTTTT
1 -GAAAACCATTTTATCAAAACCTTTTGAAAA-CATGACTCTTTT
11232 GAAAACCATTTT
1 GAAAACCATTTT
11244 GTTGGACTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
38 4 0.05
39 24 0.30
40 3 0.04
41 4 0.05
42 3 0.04
43 36 0.46
44 5 0.06
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (42 bp):
GAAAACCATTTTATCAAAACCTTTTGAAAACATGACTCTTTT
Found at i:11877 original size:75 final size:74
Alignment explanation
Indices: 11731--11877 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 74
11721 GCTTTCACTA
* * * * **
11731 AAACTGATTTTGGAACATCTTTGATTAAAATTCATCATTCCTTTGCTCATACCTCGAAATCATTG
1 AAACTAATTTTGGAACATCTTTGATTAAAACTCATCATTCCTTTGCTCATACCTCCAAATAAAGG
11796 TTTTGACTT
66 TTTTGACTT
* *
11805 AAACTAATTTT-GAACCATCTTTTGATTAAAACTCATCATTCCTTTGCTCATA-GTCCAGATAAA
1 AAACTAATTTTGGAA-CATC-TTTGATTAAAACTCATCATTCCTTTGCTCATACCTCCAAATAAA
11868 GGTTATTGAC
64 GGTT-TTGAC
11878 CCTTCCACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
73 3 0.05
74 23 0.37
75 36 0.58
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (74 bp):
AAACTAATTTTGGAACATCTTTGATTAAAACTCATCATTCCTTTGCTCATACCTCCAAATAAAGG
TTTTGACTT
Found at i:13566 original size:16 final size:17
Alignment explanation
Indices: 13547--13579 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13537 AATGTCATGG
13547 TGAATGAATGAA-CAAA
1 TGAATGAATGAAGCAAA
*
13563 TGAATGCATGAAGCAAA
1 TGAATGAATGAAGCAAA
13580 AAATGGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
TGAATGAATGAAGCAAA
Found at i:16960 original size:21 final size:20
Alignment explanation
Indices: 16915--16962 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16905 GCGTTGGGGG
* *
16915 CCCATGTGGTATGCTTGGCA
1 CCCATGTGGTATGCCTCGCA
*
16935 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGC-A
16956 CCCATGT
1 CCCATGT
16963 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.12, C:0.31, G:0.27, T:0.29
Consensus pattern (20 bp):
CCCATGTGGTATGCCTCGCA
Found at i:29494 original size:15 final size:15
Alignment explanation
Indices: 29461--29528 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
29451 TGCTAGGGTG
* *
29461 AATGGCGCAAACAAC
1 AATGGTGCAAACCAC
* *
29476 AATGGTGCGAACCAT
1 AATGGTGCAAACCAC
*
29491 AATGGCGCAAACCAC
1 AATGGTGCAAACCAC
29506 AATGGTGCAAACCAC
1 AATGGTGCAAACCAC
29521 AATGGTGC
1 AATGGTGC
29529 GAACAATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.24, T:0.13
Consensus pattern (15 bp):
AATGGTGCAAACCAC
Found at i:29497 original size:30 final size:30
Alignment explanation
Indices: 29461--29534 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
29451 TGCTAGGGTG
* *
29461 AATGGCGCAAACAACAATGGTGCGAACCAT
1 AATGGCGCAAACAACAATGGTGCAAACCAC
*
29491 AATGGCGCAAACCACAATGGTGCAAACCAC
1 AATGGCGCAAACAACAATGGTGCAAACCAC
* *
29521 AATGGTGCGAACAA
1 AATGGCGCAAACAA
29535 TCATGTTGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (30 bp):
AATGGCGCAAACAACAATGGTGCAAACCAC
Found at i:42152 original size:9 final size:9
Alignment explanation
Indices: 42138--42176 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
42128 TTAATTTCTT
*
42138 TTAATTTAA
1 TTAATTAAA
42147 TTAATTAAA
1 TTAATTAAA
**
42156 TTAAAGAAA
1 TTAATTAAA
42165 TTAATTAAA
1 TTAATTAAA
42174 TTA
1 TTA
42177 TGTTGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:47744 original size:48 final size:48
Alignment explanation
Indices: 47692--47794 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 48
47682 GGAAAAAAAG
* *
47692 AAGAAAACTTGCACCTTTCGACCGGGAAAGGCGATTT-TGGAATAAATA
1 AAGAAAACTTGCACCTTCCGACCAGGAAAGGC-ATTTCTGGAATAAATA
* * * *
47740 AAGAAGACTTGCGCCTTCCGACCAGGAAGGGCATTTCTGGAATAAATG
1 AAGAAAACTTGCACCTTCCGACCAGGAAAGGCATTTCTGGAATAAATA
47788 AAGAAAA
1 AAGAAAA
47795 TTGGAAACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 4 0.09
48 43 0.91
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (48 bp):
AAGAAAACTTGCACCTTCCGACCAGGAAAGGCATTTCTGGAATAAATA
Found at i:51085 original size:23 final size:23
Alignment explanation
Indices: 51037--51085 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
51027 AAAGGGATGG
**
51037 ATTTACTTAAAAATGAACTATGA
1 ATTTACTTAAAAATGAACTACAA
*
51060 ATTTACTTTAAAATGAACTACAA
1 ATTTACTTAAAAATGAACTACAA
51083 ATT
1 ATT
51086 GACCAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (23 bp):
ATTTACTTAAAAATGAACTACAA
Found at i:52998 original size:26 final size:26
Alignment explanation
Indices: 52968--53020 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
52958 CCAAGTCATT
52968 ACAATAAACCGAGCTAATCCAAGCTC
1 ACAATAAACCGAGCTAATCCAAGCTC
* **
52994 ACAATCAACCGAGCTTCTCCAAGCTC
1 ACAATAAACCGAGCTAATCCAAGCTC
53020 A
1 A
53021 ACTCAAGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.17
Consensus pattern (26 bp):
ACAATAAACCGAGCTAATCCAAGCTC
Found at i:54621 original size:81 final size:82
Alignment explanation
Indices: 54528--54698 Score: 299
Period size: 82 Copynumber: 2.1 Consensus size: 82
54518 GTAGACCCGA
*
54528 GACCCGAATGACCCGAAAACCGTATGA-CCAAACCCAAATGACCTAAATCTGAATGACCCGAGAA
1 GACCCGAATGACCCGAAAACCGTATGACCCAAACCCAAATGACCTAAATCCGAATGACCCGAGAA
*
54592 AACTGCCTTACCTATTT
66 AACTGCCTGACCTATTT
*
54609 GACCCGAATGACCCGAAACCCGTATGACCCAAACCCAAATGACCTAAATCCGAATGACCCGAGAA
1 GACCCGAATGACCCGAAAACCGTATGACCCAAACCCAAATGACCTAAATCCGAATGACCCGAGAA
54674 AACTGCCTGACCTATTT
66 AACTGCCTGACCTATTT
*
54691 TACCCGAA
1 GACCCGAA
54699 CCCGAAACCC
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
81 26 0.31
82 59 0.69
ACGTcount: A:0.36, C:0.32, G:0.15, T:0.17
Consensus pattern (82 bp):
GACCCGAATGACCCGAAAACCGTATGACCCAAACCCAAATGACCTAAATCCGAATGACCCGAGAA
AACTGCCTGACCTATTT
Found at i:54644 original size:15 final size:15
Alignment explanation
Indices: 54610--54668 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
54600 TACCTATTTG
54610 ACCCGAATGACCCGAA
1 ACCCGAATGACCC-AA
*
54626 ACCCGTATGACCCAA
1 ACCCGAATGACCCAA
* *
54641 ACCCAAATGACCTAA
1 ACCCGAATGACCCAA
*
54656 ATCCGAATGACCC
1 ACCCGAATGACCC
54669 GAGAAAACTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 24 0.67
16 12 0.33
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.12
Consensus pattern (15 bp):
ACCCGAATGACCCAA
Found at i:60304 original size:8 final size:8
Alignment explanation
Indices: 60285--60315 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
60275 TTTCCCATAT
60285 AAAATATCC
1 AAAAT-TCC
60294 AAAATTCC
1 AAAATTCC
60302 AAAATTCC
1 AAAATTCC
60310 AAAATT
1 AAAATT
60316 TTCGGGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATTCC
Found at i:62941 original size:23 final size:23
Alignment explanation
Indices: 62895--62941 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
62885 TCACATCAAG
* * *
62895 GGGGTCCTCCCCGTTCTCGTCAA
1 GGGGACCTCCCCGTTCGCGGCAA
62918 GGGGACCTCCCCGTTCGCGGCAA
1 GGGGACCTCCCCGTTCGCGGCAA
62941 G
1 G
62942 CATCAGGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.38, G:0.32, T:0.19
Consensus pattern (23 bp):
GGGGACCTCCCCGTTCGCGGCAA
Found at i:64159 original size:32 final size:32
Alignment explanation
Indices: 64118--64186 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
64108 CATACTTAGA
64118 TAAGGAAGAATCAAGAAGAGGAGAAAGAAGGG
1 TAAGGAAGAATCAAGAAGAGGAGAAAGAAGGG
64150 TAAGGAAGAATCAAGAAGAGGAGAAAGAAGGG
1 TAAGGAAGAATCAAGAAGAGGAGAAAGAAGGG
*
64182 AAAGG
1 TAAGG
64187 TTTGTTCGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.54, C:0.03, G:0.38, T:0.06
Consensus pattern (32 bp):
TAAGGAAGAATCAAGAAGAGGAGAAAGAAGGG
Found at i:66135 original size:67 final size:67
Alignment explanation
Indices: 66027--66160 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
66017 GTGCAGGTGA
66027 GAATTCCATAAACATGATCTCTTGCTTTTGATGGGATTTGTTCTATGAAGGTTGAAAATGCTGAT
1 GAATTCCATAAACATGATCTCTTGCTTTTGATGGGATTTGTTCTATGAAGGTTGAAAATGCTGAT
66092 AT
66 AT
*
66094 GAATTCCATAAACATGATCTCTTGCTTTTGTTGGGATTTGTTCTATGAAGGTTGAAAATGCTGAT
1 GAATTCCATAAACATGATCTCTTGCTTTTGATGGGATTTGTTCTATGAAGGTTGAAAATGCTGAT
66159 AT
66 AT
66161 TATAACTTGG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (67 bp):
GAATTCCATAAACATGATCTCTTGCTTTTGATGGGATTTGTTCTATGAAGGTTGAAAATGCTGAT
AT
Found at i:71422 original size:4 final size:4
Alignment explanation
Indices: 71415--71445 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
71405 TTCGGCCCTT
*
71415 TTTA TTTA TTTA TTTA TTTA TTTA TATA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
71446 TTATATAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:77860 original size:859 final size:860
Alignment explanation
Indices: 76193--77902 Score: 3134
Period size: 859 Copynumber: 2.0 Consensus size: 860
76183 AAACTATCTA
* **
76193 ATGCACCCAAGGCTTATCATGGAGGGAATGAAGCGCCAAGGACTTATCATGGACTTGAAGATGGC
1 ATGCACCCAAGGCTTATCATGGAGGGAATGAAACGCCAAGGACTTATCATGGACTTGAAGAAAGC
*
76258 TATGGAGAGCAAGGAAAGGATGTGCAAGGGTTGCAAGGAAGCATGAAGATGCAAGAAGATCATGG
66 TATGGAGAGCAAGGAAAGGATGTGCAAAGGTTGCAAGGAAGCATGAAGATGCAAGAAGATCATGG
* *
76323 AGATATCGTTGAGCATGTTCCAAGCACCAAAAAGATGCTATTCGATCCATTGAAGAAGCCTAATG
131 AGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCATTGAAGAAGCCTAATG
*
76388 GTTCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCAAAGTCAT
196 GTTCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTCTTCAAAGTCAT
*
76453 CTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTCTGATGATCATTTGAGCGAGAAAAC
261 CTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTCTGATAATCATTTGAGCGAGAAAAC
76518 ACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATG
326 ACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATG
*
76583 GCATTAGCACATTAGTTTTAGTTTGTTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTATTTT
391 GCATTAGCACATTAGTTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTATTTT
*
76648 TATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACAAAGTCCAATCCTTAGTTATTTTTCTAT
456 TATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACAAAGTCCAATCCTTAGCTATTTTTCTAT
76713 TGGTTGTATTTTTGGATAGATTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACGAAAATT
521 TGGTTGTATTTTTGGATAGATTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACGAAAATT
* *
76778 AGGGTATTCGAGTAGATTATGCGTTGTTCTTGTGCCTATATAAGGCCACCAATATCTCTTGTAAA
586 AGGGTATTAGAGTAGATTATGCGTTGGTCTTGTGCCTATATAAGGCCACCAATATCTCTTGTAAA
76843 AGTGAAGTCAAGTTATCAATAAAATTGAGAGCTTTATTCACCCATATCGATTATTTGGCTTCATT
651 AGTGAAGTCAAGTTATCAATAAAATTGAGAGCTTTATTCACCCATATCGATTATTTGGCTTCATT
*
76908 GTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
716 GTTCTAGTTTGAGCAAACTTAGGATTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
*
76973 ATTGCTTAATTGTTTGTGAATATTGTGATCTTAAGAGTTCAATTGCATGTCTAATTGGATACTTG
781 ATTGCTTAATTGTTTGTGAATATTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTGGATACTTG
77038 GGGCGATCTCAAATG
846 GGGCGATCTCAAATG
*
77053 ATGCGCCCAAGGCTTATCATGGAGGGAATGAAACGCCAAGGACTTATCATGGACTTGAAGAAAGC
1 ATGCACCCAAGGCTTATCATGGAGGGAATGAAACGCCAAGGACTTATCATGGACTTGAAGAAAGC
*
77118 TATGGAGAGCAAGGAAAGGATGTGCAAAGGTTGCAAGGAAGCATGAAGATGCATGAAGATCATGG
66 TATGGAGAGCAAGGAAAGGATGTGCAAAGGTTGCAAGGAAGCATGAAGATGCAAGAAGATCATGG
* *
77183 AGATATCGTTGAGAATGTTCCATGCACCAAAAAGATGATATTCGATCCATTGAAGATGCCTAATG
131 AGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCATTGAAGAAGCCTAATG
*
77248 GTTCAATGACAAGATCGAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTCTTCAAAGTCAT
196 GTTCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTCTTCAAAGTCAT
* *
77313 CTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTTTGATAATGATTTGAGCGAG-AAAC
261 CTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTCTGATAATCATTTGAGCGAGAAAAC
*
77377 ACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTTATTCTAGATGGCCGGATTGACATCATG
326 ACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATG
*
77442 GCATTAGCCCATTAGTTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTATTTT
391 GCATTAGCACATTAGTTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTATTTT
*
77507 TATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCAATCCTTAGCTATTTTTCTAT
456 TATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACAAAGTCCAATCCTTAGCTATTTTTCTAT
* *
77572 TGGTTGTATTTTTGGATAGTTTCTAGAAGGTTCTTTTGTGTAGCCTTTATATTTGGACGAAAATT
521 TGGTTGTATTTTTGGATAGATTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACGAAAATT
* *
77637 AGGGTTTTAGAGTAGATTATGCGTTGGTCTTGTGTCTATATAAGGCCACCAATATCTCTTGTAAA
586 AGGGTATTAGAGTAGATTATGCGTTGGTCTTGTGCCTATATAAGGCCACCAATATCTCTTGTAAA
*
77702 AGTGAAGTCAAGTTATCAATAAAATTGAGAGGTTTATTCACCCATATCGATTATTTGGCTTCATT
651 AGTGAAGTCAAGTTATCAATAAAATTGAGAGCTTTATTCACCCATATCGATTATTTGGCTTCATT
77767 GTTCTAGTTTGAGCAAACTTAGGATTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
716 GTTCTAGTTTGAGCAAACTTAGGATTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
* *
77832 ATTGCTTAATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTTCAGGTCTAATTGGATACTTG
781 ATTGCTTAATTGTTTGTGAATATTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTGGATACTTG
77897 GGGCGA
846 GGGCGA
77903 CGAACGAAGG
Statistics
Matches: 819, Mismatches: 31, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
859 514 0.63
860 305 0.37
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (860 bp):
ATGCACCCAAGGCTTATCATGGAGGGAATGAAACGCCAAGGACTTATCATGGACTTGAAGAAAGC
TATGGAGAGCAAGGAAAGGATGTGCAAAGGTTGCAAGGAAGCATGAAGATGCAAGAAGATCATGG
AGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCATTGAAGAAGCCTAATG
GTTCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTCTTCAAAGTCAT
CTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTCTGATAATCATTTGAGCGAGAAAAC
ACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATG
GCATTAGCACATTAGTTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTATTTT
TATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACAAAGTCCAATCCTTAGCTATTTTTCTAT
TGGTTGTATTTTTGGATAGATTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACGAAAATT
AGGGTATTAGAGTAGATTATGCGTTGGTCTTGTGCCTATATAAGGCCACCAATATCTCTTGTAAA
AGTGAAGTCAAGTTATCAATAAAATTGAGAGCTTTATTCACCCATATCGATTATTTGGCTTCATT
GTTCTAGTTTGAGCAAACTTAGGATTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTGTG
ATTGCTTAATTGTTTGTGAATATTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTGGATACTTG
GGGCGATCTCAAATG
Found at i:78953 original size:30 final size:30
Alignment explanation
Indices: 78913--78975 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
78903 TCTTCAAGGG
* *
78913 GGAGGAAATGATGTGCCCAAGG-CTTATCAT
1 GGAGGAAATGAAGCG-CCAAGGACTTATCAT
* *
78943 GGAGGGAATGAAGCGTCAAGGACTTATCAT
1 GGAGGAAATGAAGCGCCAAGGACTTATCAT
78973 GGA
1 GGA
78976 CTTGAAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (30 bp):
GGAGGAAATGAAGCGCCAAGGACTTATCAT
Found at i:80576 original size:859 final size:859
Alignment explanation
Indices: 78918--80616 Score: 2983
Period size: 859 Copynumber: 2.0 Consensus size: 859
78908 AAGGGGGAGG
* **
78918 AAATGATGTGCCCAAGGCTTATCATGGAGGGAATGAAGCGTCAAGGACTTATCATGGACTTGAAG
1 AAATGATGCGCCCAAGGCTTATCATGGAGGGAATGAAGCACCAAGGACTTATCATGGACTTGAAG
*
78983 ATGGCTATGGAGAGCAAGGAAAGGATGAGCAAGGGTTGCAAGGAAGCATGAAGATTCATGAAGAT
66 ATGGCTATGGAGAGCAAGGAAAGGATGAGCAAGGGTTGCAAGGAAGCATGAAGATGCATGAAGAT
* *
79048 CATGGAGATATCGTTGAGCATGTTCCAAGCACCAAAAAGATGTTATTCGATCCACTGAAGATGCC
131 CATGGAGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCACTGAAGATGCC
*
79113 TAATGGTTCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCGAA
196 TAATGGTCCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCGAA
* * *
79178 GTCATCTTGATGGTATGAAGACCATTCAAGTTCAATTCAAGCGCTTTGATGATGATTTGAGCGAG
261 GTCATCTTGATGATATGAAGACCATTCAAGTTCAATTCAAGCGCTTTGATAATGATTTAAGCGAG
*
79243 AAAACACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTTATTCTAGATGGCCAGATTGACA
326 AAAACACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCAGATTGACA
*
79308 TCATGGCATTAGCCCATTAGTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAATTAGCTTA
391 TCATGGCATTAGCCCATTAGTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAACTAGCTTA
79373 TTTTTATGTTTAGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCAATCCTTAGCTATTTTT
456 TTTTTATGTTTAGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCAATCCTTAGCTATTTTT
*
79438 CTATTGGTTGTATTTTTGGTTAGTTTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACAAA
521 CTATTGGTTGTATTTTTGGATAGTTTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACAAA
* *
79503 AATTAGGGTTTTAGAGTAGATTATACGTTGTTCTTGTGCCTATATAAGGCCACCAATATCTCTTT
586 AATTAGGGTTTTAGAGTAGATTATACGTTGGTCCTGTGCCTATATAAGGCCACCAATATCTCTTT
* * *
79568 ATAAAGTGAAGTCAAGTTATAAATAAAATTGAGAGGTTTATTCACCCATATCGATTATTTGGCTT
651 ATAAAATCAAGTCAAGTTATAAATAAAATTGAGAGGTTTATTCACCCAAATCGATTATTTGGCTT
79633 CATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTAGAAAACAATTAGGT
716 CATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTAGAAAACAATTAGGT
*
79698 TGTGATTGCTTCATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTAGATA
781 TGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTAGATA
79763 CTTGGGGTGATCTC
846 CTTGGGGTGATCTC
* *
79777 AAATGATGCGCCCAGGGCTTATCATGGAGGGAATGAAGCACCAAGGACTTATTATGGACTTGAAG
1 AAATGATGCGCCCAAGGCTTATCATGGAGGGAATGAAGCACCAAGGACTTATCATGGACTTGAAG
*
79842 ATGGCTATGGAGAGCAAGGAAAGGATGTGCAAGGGTTGCAAGGAAGCATGAAGATGCATGAAGAT
66 ATGGCTATGGAGAGCAAGGAAAGGATGAGCAAGGGTTGCAAGGAAGCATGAAGATGCATGAAGAT
* *
79907 CATGGAGATATCGTTGAGAATGTTCCATGCACCAAAAAGATGATATTCGATCCATTGAAGATGCC
131 CATGGAGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCACTGAAGATGCC
79972 TAATGGTCCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCGAA
196 TAATGGTCCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCGAA
* *
80037 GTCATCTTGATGATATGAAGACCATTCAAGTTCAATTGAAGCGCTTTGATAATGATTTAAGTGAG
261 GTCATCTTGATGATATGAAGACCATTCAAGTTCAATTCAAGCGCTTTGATAATGATTTAAGCGAG
* *
80102 AAAACACCAATCAATTACAAGTTCATCATTTTGCTTGCTATTGATTCTAGATGGCCGGATTGACA
326 AAAACACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCAGATTGACA
80167 TCATGGCATTAGCCCATTAGTTTTAGTTTGCTTT-TTTGGGCTTAATTCTATCTTAAACTAGCTT
391 TCATGGCATTAGCCCATTAG-TTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAACTAGCTT
* *
80231 ATTTTTATGTTTGGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCGATCCTTAGCTATTTT
455 ATTTTTATGTTTAGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCAATCCTTAGCTATTTT
* *
80296 TCTATTGGTTGTATTTTT-GATAGTTTCTAGAAGGTTCTTTTGTGTAGCCTTTATATTTGGACGA
520 TCTATTGGTTGTATTTTTGGATAGTTTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACAA
* *
80360 AAATTAGGGTTTTCGAGTAGATTATTCGTTGGTCCTGTGCCTATATAAGGCCACCAATATCTCTT
585 AAATTAGGGTTTTAGAGTAGATTATACGTTGGTCCTGTGCCTATATAAGGCCACCAATATCTCTT
* * *
80425 GTA-AAAATCAAGTTAAGTGT-TCAATAAAGTTGAGAGGTTTATTCACCCCAAATCGATTATTTG
650 -TATAAAATCAAGTCAAGT-TATAAATAAAATTGAGAGGTTTATTCA-CCCAAATCGATTATTTG
* *
80488 GCTTCATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGTAAACAATT
712 GCTTCATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTAGAAAACAATT
80553 AGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATT
777 AGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATT
80617 GAGAGGCCGA
Statistics
Matches: 797, Mismatches: 39, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
858 139 0.17
859 645 0.81
860 13 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (859 bp):
AAATGATGCGCCCAAGGCTTATCATGGAGGGAATGAAGCACCAAGGACTTATCATGGACTTGAAG
ATGGCTATGGAGAGCAAGGAAAGGATGAGCAAGGGTTGCAAGGAAGCATGAAGATGCATGAAGAT
CATGGAGATATCGTTGAGAATGTTCCAAGCACCAAAAAGATGATATTCGATCCACTGAAGATGCC
TAATGGTCCAATGACAAGATCAAGAGCTAAGGAGTTCAAGGATGCACTATTGGGCCTTGTTCGAA
GTCATCTTGATGATATGAAGACCATTCAAGTTCAATTCAAGCGCTTTGATAATGATTTAAGCGAG
AAAACACCAATCAATTACAAGTTCATCACTTTGCTTGCTATTGATTCTAGATGGCCAGATTGACA
TCATGGCATTAGCCCATTAGTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAAACTAGCTTA
TTTTTATGTTTAGATGTTATTTGGGTTGGGCCTTGGTTGACTAAGTCCAATCCTTAGCTATTTTT
CTATTGGTTGTATTTTTGGATAGTTTCTAGAAGGTTCTTTTGTGTACCCTTTATATTTGGACAAA
AATTAGGGTTTTAGAGTAGATTATACGTTGGTCCTGTGCCTATATAAGGCCACCAATATCTCTTT
ATAAAATCAAGTCAAGTTATAAATAAAATTGAGAGGTTTATTCACCCAAATCGATTATTTGGCTT
CATTGTTCTAGTTTGAGCAAACATAGGGTTCTTCAATCTTGTAGAGTCCTAGAAAACAATTAGGT
TGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAAGAGTTCAATTGCAGGTCTAATTAGATA
CTTGGGGTGATCTC
Found at i:94500 original size:11 final size:10
Alignment explanation
Indices: 94484--94536 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
94474 TTGCTCTTGA
94484 AATAATTCTTC
1 AATAA-TCTTC
94495 AATAATCTTC
1 AATAATCTTC
94505 -A-AATCTTC
1 AATAATCTTC
*
94513 AAATTATCTTC
1 -AATAATCTTC
94524 AATAAATCTTC
1 AAT-AATCTTC
94535 AA
1 AA
94537 ACACGAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 9 0.25
11 19 0.53
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (10 bp):
AATAATCTTC
Found at i:94523 original size:19 final size:18
Alignment explanation
Indices: 94490--94525 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
94480 TTGAAATAAT
94490 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
94508 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
94526 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:98103 original size:23 final size:23
Alignment explanation
Indices: 98077--98123 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
98067 GTTTAAGGGC
*
98077 TAATTTGTTTCATTCTTACAAGT
1 TAATTTGTCTCATTCTTACAAGT
98100 TAATTTGTCTCATTCTTACAAGT
1 TAATTTGTCTCATTCTTACAAGT
98123 T
1 T
98124 CATAAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (23 bp):
TAATTTGTCTCATTCTTACAAGT
Found at i:99138 original size:24 final size:23
Alignment explanation
Indices: 99093--99139 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
99083 GATTTTGACA
*
99093 TTTTACCCTCTAAACTTTAATTT
1 TTTTACCCTCTAAACTTCAATTT
99116 TTTTACCC-CTTAAACTTGCAATTT
1 TTTTACCCTC-TAAACTT-CAATTT
99140 GAAATCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.71
24 5 0.24
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTACCCTCTAAACTTCAATTT
Found at i:99290 original size:18 final size:18
Alignment explanation
Indices: 99264--99304 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
99254 TGCCACATGC
*
99264 CATTTTGGTCCAACGTGG
1 CATTGTGGTCCAACGTGG
**
99282 CATTGTGGTCTGACGTGG
1 CATTGTGGTCCAACGTGG
99300 CATTG
1 CATTG
99305 CCACATTGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.34
Consensus pattern (18 bp):
CATTGTGGTCCAACGTGG
Found at i:99526 original size:20 final size:19
Alignment explanation
Indices: 99484--99522 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
99474 TTAAGAACAG
99484 ATTTTTCTCCTTACATTCC
1 ATTTTTCTCCTTACATTCC
99503 ATTTTTCTCCTTACATTCC
1 ATTTTTCTCCTTACATTCC
99522 A
1 A
99523 ATTTACCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTCTCCTTACATTCC
Found at i:100145 original size:153 final size:153
Alignment explanation
Indices: 99867--100174 Score: 607
Period size: 153 Copynumber: 2.0 Consensus size: 153
99857 CATCACTTAA
99867 ATGCAATCATTGTGAGATCGTCGTCAATATTGTACAAAAAGGATGAAAAACAAAAAGGCACAAAG
1 ATGCAATCATTGTGAGATCGTCGTCAATATTGTACAAAAAGGATGAAAAACAAAAAGGCACAAAG
99932 GATCTATATTCAACAAAATTGACAAGGAATACAAGACAATCGAACAGATTGAAACTTTAGAAAAA
66 GATCTATATTCAACAAAATTGACAAGGAATACAAGACAATCGAACAGATTGAAACTTTAGAAAAA
99997 TCAGACTAACTAAAAAATTGTAC
131 TCAGACTAACTAAAAAATTGTAC
100020 ATGCAATCATTGTGAGATCGTCGTCAATATTGTACAAAAAGGATGAAAAACAAAAAGGCACAAAG
1 ATGCAATCATTGTGAGATCGTCGTCAATATTGTACAAAAAGGATGAAAAACAAAAAGGCACAAAG
*
100085 GATCTATATTCAACAAAATTGACAAGGAATACAAGACAATCGAACTGATTGAAACTTTAGAAAAA
66 GATCTATATTCAACAAAATTGACAAGGAATACAAGACAATCGAACAGATTGAAACTTTAGAAAAA
100150 TCAGACTAACTAAAAAATTGTAC
131 TCAGACTAACTAAAAAATTGTAC
100173 AT
1 AT
100175 AGTTATGTTT
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (153 bp):
ATGCAATCATTGTGAGATCGTCGTCAATATTGTACAAAAAGGATGAAAAACAAAAAGGCACAAAG
GATCTATATTCAACAAAATTGACAAGGAATACAAGACAATCGAACAGATTGAAACTTTAGAAAAA
TCAGACTAACTAAAAAATTGTAC
Found at i:106608 original size:14 final size:14
Alignment explanation
Indices: 106589--106615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
106579 GAAAAAAGAC
106589 CAATATAATTTATT
1 CAATATAATTTATT
106603 CAATATAATTTAT
1 CAATATAATTTAT
106616 ATTATTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
CAATATAATTTATT
Found at i:107393 original size:16 final size:16
Alignment explanation
Indices: 107374--107472 Score: 96
Period size: 16 Copynumber: 6.2 Consensus size: 16
107364 CGCCCAACCT
107374 GAGACCCGGTA-GACCC
1 GAGACCC-GTATGACCC
*
107390 GAGACCCGAATGACCC
1 GAGACCCGTATGACCC
*
107406 GAAACCCGTATGACCC
1 GAGACCCGTATGACCC
* *
107422 GAGACCTGAATGACCC
1 GAGACCCGTATGACCC
* * *
107438 GAAACCCGAATAACCC
1 GAGACCCGTATGACCC
107454 GA-ACCCAG-ATGACCC
1 GAGACCC-GTATGACCC
107469 GAGA
1 GAGA
107473 AAACTGTCTG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
15 14 0.20
16 56 0.80
ACGTcount: A:0.33, C:0.35, G:0.23, T:0.08
Consensus pattern (16 bp):
GAGACCCGTATGACCC
Found at i:107404 original size:9 final size:9
Alignment explanation
Indices: 107392--107456 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 9
107382 GTAGACCCGA
107392 GACCCGAAT
1 GACCCGAAT
107401 GACCCGAA-
1 GACCCGAAT
*
107409 -ACCCGTAT
1 GACCCGAAT
107417 GACCCG-A-
1 GACCCGAAT
*
107424 GACCTGAAT
1 GACCCGAAT
107433 GACCCGAA-
1 GACCCGAAT
107441 -ACCCGAAT
1 GACCCGAAT
*
107449 AACCCGAA
1 GACCCGAA
107457 CCCAGATGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 18 0.38
8 2 0.04
9 27 0.57
ACGTcount: A:0.35, C:0.35, G:0.20, T:0.09
Consensus pattern (9 bp):
GACCCGAAT
Found at i:107413 original size:32 final size:32
Alignment explanation
Indices: 107377--107470 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
107367 CCAACCTGAG
107377 ACCCGGTAGACCCGAGACCCGAATGACCCGAA
1 ACCCGGTAGACCCGAGACCCGAATGACCCGAA
*
107409 ACCC-GTATGACCCGAGACCTGAATGACCCGAA
1 ACCCGGTA-GACCCGAGACCCGAATGACCCGAA
*
107441 ACCCGAATA-ACCCGA-ACCC-AGATGACCCGA
1 ACCCG-GTAGACCCGAGACCCGA-ATGACCCGA
107471 GAAAACTGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
30 1 0.02
31 15 0.27
32 37 0.67
34 2 0.04
ACGTcount: A:0.33, C:0.37, G:0.21, T:0.09
Consensus pattern (32 bp):
ACCCGGTAGACCCGAGACCCGAATGACCCGAA
Found at i:108900 original size:2 final size:2
Alignment explanation
Indices: 108895--108961 Score: 68
Period size: 2 Copynumber: 34.5 Consensus size: 2
108885 ACGTTTCTGT
* *
108895 TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
108936 TA -A TA TA TGA TA TG TA T- TA TA CA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA T
108962 TACTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
1 3 0.06
2 48 0.91
3 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123009 original size:2 final size:2
Alignment explanation
Indices: 123002--123031 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
122992 GAAACCACAT
123002 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
123032 GGCAGATGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:124849 original size:16 final size:16
Alignment explanation
Indices: 124789--124916 Score: 73
Period size: 16 Copynumber: 7.9 Consensus size: 16
124779 TCAGGTTGTT
124789 TTTGAGGTTCGGGTTTAA
1 TTTG-GGTTCGGG-TTAA
* *
124807 GTTGGGTTCGGATTAAA
1 TTTGGGTTCGGGTT-AA
* *
124824 TTT-GGATCGGGTTGA
1 TTTGGGTTCGGGTTAA
124839 TTTGGGTTCGGGTTAAA
1 TTTGGGTTCGGGTT-AA
* * *
124856 TTTGAGTT-AGGTTGA
1 TTTGGGTTCGGGTTAA
* *
124871 TTCGGGTTCGGGTCAA
1 TTTGGGTTCGGGTTAA
* *
124887 TTT-TGTGTCAGGTTAA
1 TTTGGGT-TCGGGTTAA
* *
124903 TTCGAGTTCGGGTT
1 TTTGGGTTCGGGTT
124917 CGGATTGGGT
Statistics
Matches: 81, Mismatches: 23, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
15 13 0.16
16 44 0.54
17 21 0.26
18 3 0.04
ACGTcount: A:0.16, C:0.08, G:0.34, T:0.41
Consensus pattern (16 bp):
TTTGGGTTCGGGTTAA
Found at i:124906 original size:32 final size:32
Alignment explanation
Indices: 124810--124915 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 32
124800 GGTTTAAGTT
* * * *
124810 GGGTTCGGATTAAATTTG-GATCGGGTTGATTT
1 GGGTTCGGGTCAAATTTGAG-TCAGGTTGATTC
* *
124842 GGGTTCGGGTTAAATTTGAGTTAGGTTGATTC
1 GGGTTCGGGTCAAATTTGAGTCAGGTTGATTC
* * *
124874 GGGTTCGGGTCAATTTTGTGTCAGGTTAATTC
1 GGGTTCGGGTCAAATTTGAGTCAGGTTGATTC
*
124906 GAGTTCGGGT
1 GGGTTCGGGT
124916 TCGGATTGGG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 62 0.98
33 1 0.02
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (32 bp):
GGGTTCGGGTCAAATTTGAGTCAGGTTGATTC
Found at i:125090 original size:20 final size:20
Alignment explanation
Indices: 125057--125095 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
125047 CATAGATAAA
*
125057 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
125077 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
125096 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:125147 original size:16 final size:16
Alignment explanation
Indices: 125128--125185 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
125118 GAGTTCAGGT
125128 TTTTTCGGGTTTCAGA
1 TTTTTCGGGTTTCAGA
* *
125144 TTTTTTGGG-TTCTGA
1 TTTTTCGGGTTTCAGA
* * *
125159 TTTTTCGGATTTGAGC
1 TTTTTCGGGTTTCAGA
125175 TTTTTCGGGTT
1 TTTTTCGGGTT
125186 CGGGTTTTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.09, C:0.10, G:0.26, T:0.55
Consensus pattern (16 bp):
TTTTTCGGGTTTCAGA
Found at i:125166 original size:31 final size:31
Alignment explanation
Indices: 125128--125186 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
125118 GAGTTCAGGT
* *
125128 TTTTTCGGGTTTCAGATTTTTTGGGTTCTGA
1 TTTTTCGGATTTCAGATTTTTCGGGTTCTGA
* *
125159 TTTTTCGGATTTGAGCTTTTTCGGGTTC
1 TTTTTCGGATTTCAGATTTTTCGGGTTC
125187 GGGTTTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.54
Consensus pattern (31 bp):
TTTTTCGGATTTCAGATTTTTCGGGTTCTGA
Found at i:125193 original size:15 final size:15
Alignment explanation
Indices: 125128--125194 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
125118 GAGTTCAGGT
*
125128 TTTTTCGGGTTTCAGA
1 TTTTTCGGG-TTCGGA
* *
125144 TTTTTTGGGTTCTGA
1 TTTTTCGGGTTCGGA
* * *
125159 TTTTTCGGATTTGAGC
1 TTTTTCGGGTTCG-GA
*
125175 TTTTTCGGGTTCGGG
1 TTTTTCGGGTTCGGA
125190 TTTTT
1 TTTTT
125195 GTGGGTTCAG
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
15 20 0.50
16 20 0.50
ACGTcount: A:0.07, C:0.10, G:0.27, T:0.55
Consensus pattern (15 bp):
TTTTTCGGGTTCGGA
Found at i:125194 original size:16 final size:16
Alignment explanation
Indices: 125115--125207 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
125105 TTTTTTCAGG
*
125115 TTCGAGTTCAGGTTTT
1 TTCGGGTTCAGGTTTT
*
125131 TTCGGGTTTCAGATTTT
1 TTCGGG-TTCAGGTTTT
* *
125148 TT-GGGTTC-TGATTT
1 TTCGGGTTCAGGTTTT
* * *
125162 TTCGGATT-TGAGCTTT
1 TTCGGGTTCAG-GTTTT
*
125178 TTCGGGTTCGGGTTTT
1 TTCGGGTTCAGGTTTT
125194 TGT-GGGTTCAGGTT
1 T-TCGGGTTCAGGTT
125208 CGGGCGGGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 5 0.08
15 7 0.12
16 34 0.58
17 13 0.22
ACGTcount: A:0.09, C:0.11, G:0.30, T:0.51
Consensus pattern (16 bp):
TTCGGGTTCAGGTTTT
Found at i:125194 original size:31 final size:31
Alignment explanation
Indices: 125128--125194 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
125118 GAGTTCAGGT
* * *
125128 TTTTTCGGGTTTCAGATTTTTTGGGTTCTGA
1 TTTTTCGGATTTCAGATTTTTCGGGTTCGGA
* * *
125159 TTTTTCGGATTTGAGCTTTTTCGGGTTCGGG
1 TTTTTCGGATTTCAGATTTTTCGGGTTCGGA
125190 TTTTT
1 TTTTT
125195 GTGGGTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.07, C:0.10, G:0.27, T:0.55
Consensus pattern (31 bp):
TTTTTCGGATTTCAGATTTTTCGGGTTCGGA
Found at i:126439 original size:21 final size:22
Alignment explanation
Indices: 126414--126461 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
126404 GAATTTCGAG
* * *
126414 AACCTTTTTAT-AATTTTTTTT
1 AACCTTCTTATGAAATTTTGTT
126435 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
126457 AACCT
1 AACCT
126462 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:126691 original size:23 final size:22
Alignment explanation
Indices: 126661--126745 Score: 107
Period size: 23 Copynumber: 3.8 Consensus size: 22
126651 GATAAGCTCG
126661 CTATAAAATTTTGATAAATTTTC
1 CTATAAAATTTTGATAAA-TTTC
*
126684 CTATAAAATTTTGATAAATCTC
1 CTATAAAATTTTGATAAATTTC
*
126706 CGTATAAAATTTTGATAACTTTC
1 C-TATAAAATTTTGATAAATTTC
* * *
126729 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
126746 CTACAAACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
22 18 0.33
23 37 0.67
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (22 bp):
CTATAAAATTTTGATAAATTTC
Found at i:126699 original size:45 final size:44
Alignment explanation
Indices: 126642--126745 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
126632 ATAATCACAC
* *
126642 TAAAATTGTGATAAGCT-CGCTATAAAATTTTGATAAATTTTCCTA
1 TAAAATTTTGATAAGCTCCG-TATAAAATTTTGAT-AACTTTCCTA
* *
126687 TAAAATTTTGATAAATCTCCGTATAAAATTTTGATAACTTTCTTA
1 TAAAATTTTGAT-AAGCTCCGTATAAAATTTTGATAACTTTCCTA
* *
126732 TGAAATCTTGATAA
1 TAAAATTTTGATAA
126746 CTACAAACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.04
45 29 0.57
46 18 0.35
47 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (44 bp):
TAAAATTTTGATAAGCTCCGTATAAAATTTTGATAACTTTCCTA
Found at i:126793 original size:22 final size:22
Alignment explanation
Indices: 126434--126869 Score: 153
Period size: 22 Copynumber: 20.0 Consensus size: 22
126424 TAATTTTTTT
* * *
126434 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCCTATGAAATTTTGA
* *
126456 TAACCTCCCTAAGGAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* **
126478 -AGAACTCAATATGAAATTTTGA
1 TA-ACCTCCCTATGAAATTTTGA
* *
126500 TAACTTCCCAATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
** * * *
126522 TAACGAACACTATGAGATGTTGA
1 TAAC-CTCCCTATGAAATTTTGA
* * * *
126545 TAATCTCCATATGATATATTGA
1 TAACCTCCCTATGAAATTTTGA
* ** * *
126567 TAACCACGTTATGAAAATTTAA
1 TAACCTCCCTATGAAATTTTGA
* *
126589 AAACCTCCATATG-AATTGTT-A
1 TAACCTCCCTATGAAATT-TTGA
* * * *
126610 GTAATCACACTTTGAAATTTTGA
1 -TAACCTCCCTATGAAATTTTGA
* * * *
126633 TAATCACACTA--AAATTGTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
126653 TAAGCTCGCTATAAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
** * *
126675 TAAATTTTCCTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* * *
126698 TAAATCTCCGTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* * * *
126721 TAACTTTCTTATGAAATCTTGA
1 TAACCTCCCTATGAAATTTTGA
* *
126743 TAA-----CTA-CAAACTTTGA
1 TAACCTCCCTATGAAATTTTGA
**
126759 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCCTATGAAATTTTGA
*
126781 TAACC-CCATTATGAAATTTTGA
1 TAACCTCC-CTATGAAATTTTGA
* * *
126803 TCTACAT-ACTATGAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
*
126825 TAACC-CTCTTATGAAATTTTGA
1 TAACCTC-CCTATGAAATTTTGA
* * *
126847 AAACCTTCATATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
126869 T
1 T
126870 TACTCCATAA
Statistics
Matches: 303, Mismatches: 89, Indels: 44
0.69 0.20 0.10
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
20 16 0.05
21 12 0.04
22 202 0.67
23 61 0.20
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCCTATGAAATTTTGA
Found at i:127027 original size:22 final size:22
Alignment explanation
Indices: 126977--127028 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
126967 TCACATTTTG
126977 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
126998 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
127020 AAAATTTTG
1 AAAATTTTG
127029 TTGACCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:127046 original size:22 final size:22
Alignment explanation
Indices: 126975--127047 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
126965 AATCACATTT
* * *
126975 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
126997 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
127019 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
127041 TGAAATT
1 TGAAATT
127048 CTAATAATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:127102 original size:14 final size:14
Alignment explanation
Indices: 127085--127111 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
127075 AATCTTGTTT
127085 TGAAATTTTGATAC
1 TGAAATTTTGATAC
127099 TGAAATTTTGATA
1 TGAAATTTTGATA
127112 ATCTTCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TGAAATTTTGATAC
Found at i:127150 original size:25 final size:22
Alignment explanation
Indices: 127099--127159 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
127089 ATTTTGATAC
*
127099 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAATATTCCTA
127121 T-AAATTTTGATAATATGATCTCTA
1 TGAAATTTTGATAATAT--TC-CTA
*
127145 TGAAATTTCGATAAT
1 TGAAATTTTGATAAT
127160 CACTCTGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 14 0.42
22 1 0.03
23 2 0.06
24 4 0.12
25 12 0.36
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAATATTCCTA
Found at i:127246 original size:22 final size:22
Alignment explanation
Indices: 127217--127272 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
127207 AAATTGAGAC
*
127217 TTTT-ATAAGCTTCA-TATGAAA
1 TTTTGATAA-CTTCACTATAAAA
**
127238 TTTTGATAACCACACTATAAAA
1 TTTTGATAACTTCACTATAAAA
127260 TTTTGATAACTTC
1 TTTTGATAACTTC
127273 CCAATAGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTTGATAACTTCACTATAAAA
Found at i:127315 original size:22 final size:23
Alignment explanation
Indices: 127290--127344 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
127280 AAACCTTCTA
*
127290 ATGAAATTTTGT-TAACCACATT
1 ATGAAATTTTGTATAACCACACT
* * *
127312 ATGAAA-ATCGTATAACCTCACT
1 ATGAAATTTTGTATAACCACACT
127334 ATGAAATTTTG
1 ATGAAATTTTG
127345 AAATCTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 3 0.12
22 20 0.80
23 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (23 bp):
ATGAAATTTTGTATAACCACACT
Found at i:127444 original size:24 final size:22
Alignment explanation
Indices: 127383--127544 Score: 123
Period size: 22 Copynumber: 7.3 Consensus size: 22
127373 TTGTGATAAT
* *
127383 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
127405 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
127427 TAACCTAATCCTATGAAATTTTGG
1 TAACC-AA-CCTATGAAATTTTAA
**
127451 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
127473 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
127495 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
127517 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
127539 TAACCA
1 TAACCA
127545 CATAGAGACA
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.03
22 95 0.79
23 5 0.04
24 17 0.14
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:127875 original size:31 final size:29
Alignment explanation
Indices: 127816--127875 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
127806 AATTTAGAAT
* * *
127816 TATGTTTTAAAAAAGGGTATAATTGGAAA
1 TATGTTTTAAAAAAGGGCACAATCGGAAA
127845 TATGTTTTAAAAATAAGGGCACAATCGGAAA
1 TATGTTTT-AAAA-AAGGGCACAATCGGAAA
127876 ATATAAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 14 0.54
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (29 bp):
TATGTTTTAAAAAAGGGCACAATCGGAAA
Found at i:128753 original size:70 final size:70
Alignment explanation
Indices: 128677--128901 Score: 315
Period size: 70 Copynumber: 3.1 Consensus size: 70
128667 TAACTAAAAT
*
128677 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGAGTTTTT
128742 AGTTG
66 AGTTG
*
128747 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATA
128812 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * *
128825 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGAGTTTTT
128890 AGTTG
66 AGTTG
128895 AGTAAAA
1 AGTAAAA
128902 CTATAAAAAC
Statistics
Matches: 139, Mismatches: 8, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
70 66 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 62 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:128753 original size:78 final size:77
Alignment explanation
Indices: 128671--128909 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
128661 TTTTTTTAAC
*
128671 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
128736 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
128749 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
128814 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* *
128827 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGAG
128885 TTTTTAGTTGAG
66 TTTTTAGTTGAG
128897 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
128910 ACCTAAACAA
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 87 0.56
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Done.