Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004994.1 Hibiscus syriacus cultivar Beakdansim tig00011207_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: 73889
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6010 original size:16 final size:16
Alignment explanation
Indices: 5975--6022 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5965 TAAGAGAATT
* *
5975 TAATTATTGATTATAC
1 TAATTATTTATTAAAC
*
5991 TAATTATTTATTAAAG
1 TAATTATTTATTAAAC
*
6007 TAATAATATTATTAAA
1 TAATTAT-TTATTAAA
6023 ATATTAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (16 bp):
TAATTATTTATTAAAC
Found at i:6540 original size:35 final size:35
Alignment explanation
Indices: 6494--6563 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
6484 GCTACGTGAG
6494 GTGGAGTGATTACTAATTACTGATACTAAGACTAT
1 GTGGAGTGATTACTAATTACTGATACTAAGACTAT
6529 GTGGAGTGATTACTAATTACTGATACTAAGACTAT
1 GTGGAGTGATTACTAATTACTGATACTAAGACTAT
6564 ATGTGCATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (35 bp):
GTGGAGTGATTACTAATTACTGATACTAAGACTAT
Found at i:6865 original size:16 final size:17
Alignment explanation
Indices: 6834--6889 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
6824 ATAAAATGTA
*
6834 AATAAAAGAAATACTAC
1 AATAAAAGATATACTAC
6851 AATAAAA-ATATACTAC
1 AATAAAAGATATACTAC
* *
6867 AATAAAAGATACAATAC
1 AATAAAAGATATACTAC
6884 AATAAA
1 AATAAA
6890 TGAAAGAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 15 0.43
17 20 0.57
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.20
Consensus pattern (17 bp):
AATAAAAGATATACTAC
Found at i:9097 original size:13 final size:13
Alignment explanation
Indices: 9081--9123 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
9071 GTCATAAATC
9081 TATGTCGCGCATT
1 TATGTCGCGCATT
* * *
9094 TATGACACTCATT
1 TATGTCGCGCATT
9107 TATGTCGCGCATT
1 TATGTCGCGCATT
9120 TATG
1 TATG
9124 ACGTTCATTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (13 bp):
TATGTCGCGCATT
Found at i:9132 original size:13 final size:13
Alignment explanation
Indices: 9090--9132 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9080 CTATGTCGCG
*
9090 CATTTATGACACT
1 CATTTATGACGCT
* *
9103 CATTTATGTCGCG
1 CATTTATGACGCT
*
9116 CATTTATGACGTT
1 CATTTATGACGCT
9129 CATT
1 CATT
9133 GAGCGTCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (13 bp):
CATTTATGACGCT
Found at i:9208 original size:83 final size:85
Alignment explanation
Indices: 9104--9352 Score: 285
Period size: 85 Copynumber: 3.0 Consensus size: 85
9094 TATGACACTC
* * *
9104 ATTTATGTCGCGCATTTATGACGTT-CATTGAGCGTCATTGAAGCCCCCGTCATAAAT-TAAG-A
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCCCCCGTCATAAATCT--GCA
*
9166 TGACATACA-TT-TGTGTCATAA
63 TGACACACATTTGTGTGTCATAA
* * *
9187 ATTTATGACTCGCATGTATGACTTACATTGAGCTTCATTGAAGCCCCCGTCATAAATCTGCTTGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTCATAAATCTGCATGA
9252 CACACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* * * * ** *
9272 ATTTATGACACGCATGTATGACTTACATTGTGTGTCATTGAAGCACACGTCATTAAAAATG-ACG
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTCA-TAAATCTGCATG
*
9336 ACACACATTCGTGTGTC
65 ACACACATTTGTGTGTC
9353 GTGATTGTAT
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
82 3 0.02
83 58 0.41
84 3 0.02
85 73 0.51
86 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTCATAAATCTGCATGA
CACACATTTGTGTGTCATAA
Found at i:9310 original size:85 final size:82
Alignment explanation
Indices: 9104--9324 Score: 268
Period size: 83 Copynumber: 2.6 Consensus size: 82
9094 TATGACACTC
* * * *
9104 ATTTATGTCGCGCATTTATGACGTT-CATTGAGCGTCATTGAAGCCCCCGTCATAAATTAAGATG
1 ATTTATGACACGCATGTATGAC-TTACATTGAGTGTCATTGAAGCCCCCGTCATAAATT-AGATG
*
9168 ACATACATTTGTGTCATAA
64 ACACACATTTGTGTCATAA
* *
9187 ATTTATGACTCGCATGTATGACTTACATTGAGCT-TCATTGAAGCCCCCGTCATAAATCT-GCTT
1 ATTTATGACACGCATGTATGACTTACATTGAG-TGTCATTGAAGCCCCCGTCATAAAT-TAG-AT
9250 GACACACATTTGTGTGTCATAA
63 GACACACA-TT-TGTGTCATAA
* * *
9272 ATTTATGACACGCATGTATGACTTACATTGTGTGTCATTGAAGCACACGTCAT
1 ATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCAT
9325 TAAAAATGAC
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
82 3 0.02
83 57 0.47
84 4 0.03
85 57 0.47
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (82 bp):
ATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCGTCATAAATTAGATGAC
ACACATTTGTGTCATAA
Found at i:9379 original size:2 final size:2
Alignment explanation
Indices: 9372--9432 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
9362 TTTCGTAAAT
9372 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
9414 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
9433 GTAGATTGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14214 original size:15 final size:15
Alignment explanation
Indices: 14189--14244 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
14179 GATGCTTTCT
14189 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTTGACG
14205 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
* *
14220 TTTTCTTCCTAGACG
1 TTTTCTTCTTTGACG
14235 TTTTCTTCTT
1 TTTTCTTCTT
14245 ACCCCATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.07, C:0.23, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:17122 original size:20 final size:20
Alignment explanation
Indices: 17097--17136 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17087 ATAAAATTCC
17097 CTTAACTTATTATTATATTT
1 CTTAACTTATTATTATATTT
*
17117 CTTAACTTATTATTTTATTT
1 CTTAACTTATTATTATATTT
17137 TTATCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTAACTTATTATTATATTT
Found at i:18749 original size:50 final size:51
Alignment explanation
Indices: 18685--18798 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 51
18675 GTATGTACTA
* * * * *
18685 AATAAAATAATAATAAACTAAAGA-TATTGTTTTGATTCTATC-TAATTCTT
1 AATAAAATAATAATAAACTAAAAATTA-TATTTTAACTCTATCTTAATTCCT
18735 AATAAAATAATAATAAACTAAAAATTATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAAATTATATTTTAACTCTATCTTAATTCCT
*
18786 AATAGAATAATAA
1 AATAAAATAATAA
18799 ATTTAATCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 35 0.62
51 21 0.38
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATTATATTTTAACTCTATCTTAATTCCT
Found at i:20388 original size:31 final size:31
Alignment explanation
Indices: 20344--20416 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
20334 TTCAATATCC
*
20344 AAGTGTCCAAAACTTAATAAAACT-ATAACGT
1 AAGTGACCAAAACTTAATAAAA-TGATAACGT
*
20375 AAGTTACCAAAACTTAATAAAATGATAACGT
1 AAGTGACCAAAACTTAATAAAATGATAACGT
20406 AAGTGACCAAA
1 AAGTGACCAAA
20417 TTTTAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 37 0.97
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAATGATAACGT
Found at i:23240 original size:12 final size:12
Alignment explanation
Indices: 23223--23247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23213 AGGCAACATA
23223 TTTTTTCTTTCT
1 TTTTTTCTTTCT
23235 TTTTTTCTTTCT
1 TTTTTTCTTTCT
23247 T
1 T
23248 GTCTTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:25594 original size:12 final size:12
Alignment explanation
Indices: 25577--25613 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
25567 TACAAAAATA
25577 AAAAATAATAAT
1 AAAAATAATAAT
25589 AAAAATAATAAT
1 AAAAATAATAAT
25601 AAATAAT-ATAAT
1 AAA-AATAATAAT
25613 A
1 A
25614 TAATAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:25600 original size:15 final size:15
Alignment explanation
Indices: 25576--25621 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
25566 CTACAAAAAT
25576 AAAA-AATAATAATA
1 AAAATAATAATAATA
25590 AAAATAATAATAA-A
1 AAAATAATAATAATA
*
25604 TAATATAAT-ATAATA
1 -AAAATAATAATAATA
25619 AAA
1 AAA
25622 TGTTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:25604 original size:10 final size:10
Alignment explanation
Indices: 25573--25619 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
25563 GACCTACAAA
*
25573 AATAAAAAAT
1 AATAATAAAT
25583 AATAATAAAAAT
1 AATAAT--AAAT
25595 AATAATAAAT
1 AATAATAAAT
25605 AAT-ATAATAT
1 AATAATAA-AT
25615 AATAA
1 AATAA
25620 AATGTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 4 0.12
10 17 0.53
11 1 0.03
12 10 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAATAAAT
Found at i:26626 original size:31 final size:31
Alignment explanation
Indices: 26588--26743 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
26578 CCCGAAGGAC
*
26588 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
*
26619 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
26650 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
26681 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
26712 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
26743 C
1 C
26744 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:26947 original size:23 final size:24
Alignment explanation
Indices: 26921--26967 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
26911 ATATACTTGT
*
26921 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
26944 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
26968 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:27599 original size:21 final size:21
Alignment explanation
Indices: 27569--27613 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27559 ATTCTGTCGT
* *
27569 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
27590 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
27611 TTG
1 TTG
27614 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:29153 original size:15 final size:16
Alignment explanation
Indices: 29123--29159 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29113 GTTAATTAAC
29123 TTAAAT-TATTAAATA
1 TTAAATATATTAAATA
*
29138 -TAAATATATTATATA
1 TTAAATATATTAAATA
29153 TTAAATA
1 TTAAATA
29160 AATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 8 0.42
16 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATATATTAAATA
Found at i:29995 original size:26 final size:26
Alignment explanation
Indices: 29966--30015 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
29956 TATTTTTAAC
29966 ACCTTTAATATATGTGTAAAAAAATT
1 ACCTTTAATATATGTGTAAAAAAATT
29992 ACCTTTAATATATGTGTAAAAAAA
1 ACCTTTAATATATGTGTAAAAAAA
30016 ATTAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
ACCTTTAATATATGTGTAAAAAAATT
Found at i:31426 original size:2 final size:2
Alignment explanation
Indices: 31419--31482 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
31409 ATACCCAAAT
31419 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
31461 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
31483 CAATAAAGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31588 original size:95 final size:98
Alignment explanation
Indices: 31473--31733 Score: 343
Period size: 95 Copynumber: 2.7 Consensus size: 98
31463 TATATATATA
* * *
31473 TATATATATACAATAAAGCTTGAGTTGTCCTTATAAAGCAATTGGTTAAACGCCCTGGCTTTATG
1 TATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCTGGCTTTATG
* * *
31538 GATAAGATTCAGCTAACTTGATAAAGTTGA-T-
66 GATAAGATTCAGCTAACATAATAAAGGTGATTG
* *
31569 TATA-ATATACAATAAAGCTTGAGTTGTCCCTCTATAGTAATTGGTTAAATGCCCTGGCTTTATG
1 TATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCTGGCTTTATG
* *
31633 GATAATATTCAGCTAGCATAATAAAGGTGATTG
66 GATAAGATTCAGCTAACATAATAAAGGTGATTG
* * * *
31666 TAATATATATACAATGATA--TTGAGTTGTCCCTCTAGAGTAATTGGTTAAACGCCCCGTCTTTA
1 T-ATATATATACAAT-AAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCTGGCTTTA
31729 TGGAT
64 TGGAT
31734 TCAGCTAGTC
Statistics
Matches: 145, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 80 0.55
96 5 0.03
97 1 0.01
98 48 0.33
99 9 0.06
100 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (98 bp):
TATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGCCCTGGCTTTATG
GATAAGATTCAGCTAACATAATAAAGGTGATTG
Found at i:32511 original size:3 final size:3
Alignment explanation
Indices: 32503--32542 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
32493 TTGTCTGGGA
32503 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
32543 ATAATAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:35621 original size:84 final size:84
Alignment explanation
Indices: 35466--36909 Score: 1592
Period size: 84 Copynumber: 17.3 Consensus size: 84
35456 CTATTGGCAG
* **
35466 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATACCTTCGAGTTCGA-TGATACTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT-ACGCTCAGCT
* *
35530 CAAAGGCAGATCATTTGCAA
65 CCAAGGCACATCATTTGCAA
* * * * *
35550 CATAGCTTAAGTCGAGAAGGG-TATCTGCCAACCAAAACACCTTCGAGTTCGACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
35614 CCAAGGCACATTATTTGCAA
65 CCAAGGCACATCATTTGCAA
* * * * * * *
35634 CATAGCTCAAGGCAAGAAGGGCTATTTACCAACAAAAGACCTTTGAATTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
35699 CAAGGCATATCATTTGTAA
66 CAAGGCACATCATTTGCAA
* * * * **
35718 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATATCTTAGAGTTCGATTACATTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
35783 AAAGGCACACCATTTGCAG
66 CAAGGCACATCATTTGCAA
* * * *
35802 CATATCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
35867 CAAGGCACATCATTTACAA
66 CAAGGCACATCATTTGCAA
* * * *
35886 CATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
35951 CAAGGCACATAATTTGCAG
66 CAAGGCACATCATTTGCAA
* *
35970 TATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
36035 CAAGGCACATCATTTACAA
66 CAAGGCACATCATTTGCAA
* **
36054 CATAACTCAAGGATAGAAGGGTTATCTATCAA-AAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
36118 CAAGGCACATCATTTGCAG
66 CAAGGCACATCATTTGCAA
* * * *
36137 CATAACTCAAGGCTAGAAGGGTTATCTGCTAACAAAAGACCTTCGAGTTTGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
36202 AAAGGCACAACGTTTGCAG
66 CAAGGCACATCATTTGCAA
* * * * *
36221 CATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGATCTTCGAGTTCGACTATGCTTAACTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
36286 CAAGGCACATCAATTACAA
66 CAAGGCACATCATTTGCAA
* * * * * * *
36305 CATAACGCAAGGCAAGAAGGGATATTTTCCAACAAAA-ACCTTCAAGTTCGACTATGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
36369 TAATGCACATCATTTGCTA
66 CAAGGCACATCATTTGCAA
* *
36388 CATAACTCAAGGATAGAAGGGTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
36453 CAAGGCACATCATTTACAA
66 CAAGGCACATCATTTGCAA
* * * * * *
36472 CATAACTCAAGGCTAGAAGGGTTATATGTCAAC-AAAGACCTTCGATTTCGATTACACTCACCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
36536 AAAGGCACATCATTTACAA
66 CAAGGCACATCATTTGCAA
* * * * * * *
36555 TATAACTCAATGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTTAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
36619 AAAGGCATCATCATTTGCAG
66 CAAGGCA-CATCATTTGCAA
* * * * * * * *
36639 CATAGCTCAAGGCAAGAAGGGTTATTTG-C--C-AAAGACCTTCAAGTTCAATTCCACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
36700 AAAGGCACCGTCATTTGCAG
66 CAAGGCA-CATCATTTGCAA
* * * * ** * * *
36720 CACAGCTCAAGGCAAGAAGGGCTAT-TTTC--C-AAAGACCTTTGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
36781 AAAGGCACTATCATTTGCAG
66 CAAGGCAC-ATCATTTGCAA
* * *** * * *
36801 CATAGCTCAAGGCAAGAAGAACTATCT-TC--C-AAAGACCTTAGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
36862 GAAGGCACATCATTTGCAG
66 CAAGGCACATCATTTGCAA
*
36881 CATAACTCAAGGCCAGAAGGGTTATCTGC
1 CATAACTCAAGGCTAGAAGGGTTATCTGC
36910 TAAAGATCTT
Statistics
Matches: 1174, Mismatches: 176, Indels: 23
0.86 0.13 0.02
Matches are distributed among these distances:
80 35 0.03
81 173 0.15
82 1 0.00
83 263 0.22
84 693 0.59
85 9 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCACATCATTTGCAA
Found at i:36209 original size:251 final size:251
Alignment explanation
Indices: 35462--36909 Score: 1624
Period size: 251 Copynumber: 5.8 Consensus size: 251
35452 GAAACTATTG
* * *
35462 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATACCTTCGAGTTCGATGATACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
35527 GCTCAAAGGCAGATCATTTGCAACATAGCTTAAGTCG-AGAAGGG-TATCTGCCAACCAAAACAC
66 GCTCAAAGGCACATCATTTACAACATAACTCAAG--GAAGAAGGGCTATCTGTCAA-CAAAAGAC
* * *
35590 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAACATAGCTCAAGGCAAGAAGGG
128 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGG
* * * * * * * *
35655 CTATTTACCAACAAAAGACCTTTGAATTCGACTACGCTCAGCTCCAAGGCATATCATTT
193 TTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
* * * * * *
35714 GTAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATATCTTAGAGTTCGATTACATTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
35779 GCTCAAAGGCACACCATTTGCAGCATATCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCT
66 GCTCAAAGGCACATCATTTACAACATAACTCAAGG-AAGAAGGGCTATCTGTCAACAAAAGACCT
* * * *
35844 TCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGCT
130 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTT
* * * * *
35909 ATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATAATTT
195 ATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
* * * *
35966 GCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * *
36031 GCTCCAAGGCACATCATTTACAACATAACTCAAGGATAGAAGGGTTATCTATCAA-AAAAGACCT
66 GCTCAAAGGCACATCATTTACAACATAACTCAAGGA-AGAAGGGCTATCTGTCAACAAAAGACCT
*
36095 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTT
130 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTT
* * * * *
36160 ATCTGCTAACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAACGTTT
195 ATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
* * * ** *
36217 GCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGATCTTCGAGTTCGACTATGCTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
36282 ACTCCAAGGCACATCAATTACAACATAACGCAAGGCAAGAAGGGATAT-TTTCCAACAAAA-ACC
66 GCTCAAAGGCACATCATTTACAACATAACTCAAGG-AAGAAGGGCTATCTGT-CAACAAAAGACC
* * * *
36345 TTCAAGTTCGACTATGCTCAGCTCTAATGCACATCATTTGCTA-CATAACTCAAGG-ATAGAAGG
129 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC-AGCATAACTCAAGGCA-AGAAGG
* * *
36408 GTTATCTGCCAACAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
192 GTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
* * * * *
36468 ACAACATAACTCAAGGCTAGAAGGGTTATATGTCAAC-AAAGACCTTCGATTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * ** *
36532 CCTCAAAGGCACATCATTTACAATATAACTCAATGCTAGAAGGGTTATCTGTCAAC-AAAGACCT
66 GCTCAAAGGCACATCATTTACAACATAACTCAA-GGAAGAAGGGCTATCTGTCAACAAAAGACCT
* * * ** *
36596 TCGAGTTCGATTACACTTAGCTTAAAGGCATCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGT
130 TCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTCAAGGCAAGAAGGGT
* * * * * *
36661 TATTTG-C--C-AAAGACCTTCAAGTTCAATTCCACTCAGCTCAAAGGCACCGTCATTT
194 TATCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTT
* * * * ** *
36716 GCAGCACAGCTCAAGGCAAGAAGGGCTAT-TTTC--C-AAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * **
36777 GCTCAAAGGCACTATCATTTGCAGCATAGCTCAAGGCAAGAAGAACTATCT-TC--C-AAAGACC
66 GCTCAAAGGCAC-ATCATTTACAACATAACTCAAGG-AAGAAGGGCTATCTGTCAACAAAAGACC
* * * *
36838 TTAGAGTTTGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTCAAGGCCAGAAGGGT
129 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGT
36903 TATCTGC
194 TATCTGC
36910 TAAAGATCTT
Statistics
Matches: 1031, Mismatches: 146, Indels: 47
0.84 0.12 0.04
Matches are distributed among these distances:
242 37 0.04
243 32 0.03
245 40 0.04
246 27 0.03
247 36 0.03
248 31 0.03
249 3 0.00
250 94 0.09
251 399 0.39
252 322 0.31
253 10 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (251 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTTACAACATAACTCAAGGAAGAAGGGCTATCTGTCAACAAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTA
TCTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
Found at i:37562 original size:35 final size:35
Alignment explanation
Indices: 37523--37643 Score: 106
Period size: 37 Copynumber: 3.3 Consensus size: 35
37513 TTATATATAT
37523 ATATATATATATTATAGTTTGCAAATGA-TTTGGAA
1 ATATATATATATTATAGTTTG-AAATGATTTTGGAA
*
37558 ATATATA-ATA-TATAGTTTTGAAAAATGATTTTTTGAA
1 ATATATATATATTATAG-TTTG--AAATGA-TTTTGGAA
* * *
37595 A-ATGTATATATTATATAGTTTGAAATCATTTTGAAA
1 ATATATATATA-T-TATAGTTTGAAATGATTTTGGAA
37631 ATATATAATATAT
1 ATATAT-ATATAT
37644 GGTTTTTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
33 5 0.07
34 7 0.10
35 13 0.19
36 11 0.16
37 19 0.28
38 5 0.07
39 4 0.06
40 5 0.07
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (35 bp):
ATATATATATATTATAGTTTGAAATGATTTTGGAA
Found at i:37674 original size:2 final size:2
Alignment explanation
Indices: 37667--37705 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37657 TGTTGAAAAC
37667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37706 GTTTTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37676 original size:73 final size:73
Alignment explanation
Indices: 37519--37685 Score: 180
Period size: 73 Copynumber: 2.3 Consensus size: 73
37509 GTATTTATAT
* *
37519 ATATATATATATATATTATAGTTTGCAAATGATTTGGAAATATATAATATATAGTTTTGAAAAAT
1 ATATATATATATATA-TATAGTTTGCAAATCATTTGAAAATATATAATATATAGTTTTGAAAAAT
***
37584 GATTTTTTGAA
65 G--TTTGAAAA
* * *
37595 A-ATGTATATAT-TATATAGTTTG-AAATCATTTTGAAAATATATAATATATGGTTTTTAAAACA
1 ATATATATATATATATATAGTTTGCAAATCA-TTTGAAAATATATAATATATAGTTTTGAAAA-A
37657 TG-TTGAAAA
64 TGTTTGAAAA
37666 CATATATATATATATATATA
1 -ATATATATATATATATATA
37686 TATATATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
71 4 0.05
72 6 0.08
73 46 0.60
74 11 0.14
75 9 0.12
76 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (73 bp):
ATATATATATATATATATAGTTTGCAAATCATTTGAAAATATATAATATATAGTTTTGAAAAATG
TTTGAAAA
Found at i:37729 original size:96 final size:93
Alignment explanation
Indices: 37599--37775 Score: 282
Period size: 96 Copynumber: 1.9 Consensus size: 93
37589 TTTGAAAATG
* *
37599 TATATATTATATAGTTTGAAATCATTTTGAAAATATATAATATATGGTTTTTAAAACATGTTGAA
1 TATATATTATATAGTTTGAAAACATTTTGAAAATATATAATATATGGGTTTTAAAACATGTTGAA
37664 AACATATATATATATATATATATATATA
66 AACATATATATATATATATATATATATA
* * *
37692 TATATATATATATAGTTTTTTAAAACATTTTGAAAATATATAGTATATGGGTTTTAAAACATTTT
1 TATATAT-TATATAG--TTTGAAAACATTTTGAAAATATATAATATATGGGTTTTAAAACATGTT
37757 GAAAACATATATATATATA
63 GAAAACATATATATATATA
37776 GTTTTTTTAA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
93 7 0.09
94 7 0.09
96 62 0.82
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (93 bp):
TATATATTATATAGTTTGAAAACATTTTGAAAATATATAATATATGGGTTTTAAAACATGTTGAA
AACATATATATATATATATATATATATA
Found at i:37746 original size:36 final size:33
Alignment explanation
Indices: 37588--37903 Score: 187
Period size: 34 Copynumber: 9.1 Consensus size: 33
37578 AAAAATGATT
* * *
37588 TTTTGAAAATGTATATATTATATAG-TTTGAAATCA
1 TTTTGAAAA--TATATA-TATATGGTTTTTAAAACA
37623 TTTTGAAAATATATAATATATGGTTTTTAAAACA
1 TTTTGAAAATATAT-ATATATGGTTTTTAAAACA
* * * * * * *
37657 TGTTGAAAACATATATATAT-ATATAT-ATATA
1 TTTTGAAAATATATATATATGGTTTTTAAAACA
* * *
37688 -TAT--ATATATATATATATAGTTTTTTAAAACA
1 TTTTGAAAATATATATATAT-GGTTTTTAAAACA
*
37719 TTTTGAAAATATATAGTATATGGGTTTTAAAACA
1 TTTTGAAAATATATA-TATATGGTTTTTAAAACA
*
37753 TTTTGAAAACATATATATATATAGTTTTTTTAAAAACA
1 TTTTG-AAA-ATATATATATAT-G-GTTTTT-AAAACA
*
37791 TTTTAAAATAAATATATAATATATGGTTTTTAAAACA
1 TTTT--GA-AAATATAT-ATATATGGTTTTTAAAACA
* * * *
37828 TTTTAAAAACATATATGTTATATAG-TTTTAAAATA
1 TTTT-GAAA-ATATAT-ATATATGGTTTTTAAAACA
* *
37863 TTTTTGAAAATATTACATTATATGGTTTTGAAAAACA
1 -TTTTGAAAATA-TATA-TATATGGTTTT-TAAAACA
37900 TTTT
1 TTTT
37904 TTAAAAATCA
Statistics
Matches: 220, Mismatches: 37, Indels: 47
0.72 0.12 0.15
Matches are distributed among these distances:
28 12 0.05
30 4 0.02
31 6 0.03
32 5 0.02
33 17 0.08
34 48 0.22
35 44 0.20
36 34 0.15
37 19 0.09
38 15 0.07
39 8 0.04
40 8 0.04
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (33 bp):
TTTTGAAAATATATATATATGGTTTTTAAAACA
Found at i:37769 original size:38 final size:37
Alignment explanation
Indices: 37691--37903 Score: 192
Period size: 36 Copynumber: 5.8 Consensus size: 37
37681 ATATATATAT
*
37691 ATATATATATATATAGTTTTTTAAAACATTTTG-AAA-
1 ATATATATATATAT-GGTTTTTAAAACATTTTGAAAAC
* *
37727 ATATATA-GTATATGGGTTTTAAAACATTTTGAAAAC
1 ATATATATATATATGGTTTTTAAAACATTTTGAAAAC
* *
37763 ATATATATATATA-GTTTTTTTAAAAACATTTT-AAAAT
1 ATATATATATATATG-GTTTTT-AAAACATTTTGAAAAC
* *
37800 AAATATATAATATATGGTTTTTAAAACATTTTAAAAAC
1 ATATATAT-ATATATGGTTTTTAAAACATTTTGAAAAC
* * * *
37838 ATATATGT-TATATAG-TTTTAAAATATTTTTGAAAAT
1 ATATATATATATATGGTTTTTAAAACA-TTTTGAAAAC
* *
37874 AT-TACAT-TATATGGTTTTGAAAAACATTTT
1 ATATATATATATATGGTTTT-TAAAACATTTT
37904 TTAAAAATCA
Statistics
Matches: 145, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
34 16 0.11
35 26 0.18
36 38 0.26
37 34 0.23
38 30 0.21
39 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATATATATATATGGTTTTTAAAACATTTTGAAAAC
Found at i:37806 original size:37 final size:35
Alignment explanation
Indices: 37695--37903 Score: 169
Period size: 38 Copynumber: 5.8 Consensus size: 35
37685 ATATATATAT
*
37695 ATATATATATAGTTTTTTAAAACATTTTGAAAAT-
1 ATATATATATAGGTTTTTAAAACATTTTGAAAATA
* *
37729 ATATAGTATAT-GGGTTTTAAAACATTTTGAAAACA
1 ATATA-TATATAGGTTTTTAAAACATTTTGAAAATA
*
37764 TATATATATATAGTTTTTTTAAAAACATTTT-AAAATAA
1 -ATATATATATAG-GTTTTT-AAAACATTTTGAAAAT-A
* *
37802 ATATATAATATATGGTTTTTAAAACATTTTAAAAACA
1 ATATAT-ATATA-GGTTTTTAAAACATTTTGAAAATA
* *
37839 TATATGTTATATA-G-TTTTAAAATATTTTTGAAAATA
1 -ATAT-ATATATAGGTTTTTAAAACA-TTTTGAAAATA
* * *
37875 TTACAT-TATATGGTTTTGAAAAACATTTT
1 ATATATATATA-GGTTTT-TAAAACATTTT
37904 TTAAAAATCA
Statistics
Matches: 141, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
33 4 0.03
34 26 0.18
35 22 0.16
36 23 0.16
37 30 0.21
38 34 0.24
39 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (35 bp):
ATATATATATAGGTTTTTAAAACATTTTGAAAATA
Found at i:37902 original size:109 final size:111
Alignment explanation
Indices: 37691--37903 Score: 267
Period size: 109 Copynumber: 1.9 Consensus size: 111
37681 ATATATATAT
* * * *
37691 ATATATATATATATAGTTTTTTAAAACATTTTGAAAATATATAGTATATGGGTTTTAAAACATTT
1 ATATATATATATATAGGTTTTTAAAACATTTTAAAAACATATAGTATATGAGTTTTAAAACATTT
* * *
37756 TGAAAACATATATATATATAGTTTTTTTAAAAACATTTTAAAATAA
66 TGAAAACATACATATATATAGTGTTTTGAAAAACATTTTAAAATAA
*
37802 ATATATA-ATATAT-GGTTTTTAAAACATTTTAAAAACATATATGTTATAT-AGTTTTAAAATAT
1 ATATATATATATATAGGTTTTTAAAACATTTTAAAAACATATA-G-TATATGAGTTTTAAAACA-
*
37864 TTTTGAAAATATTACAT-TATAT-G-GTTTTGAAAAACATTTT
63 TTTTGAAAACA-TACATATATATAGTGTTTTGAAAAACATTTT
37904 TTAAAAATCA
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
109 40 0.45
110 18 0.20
111 27 0.30
112 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (111 bp):
ATATATATATATATAGGTTTTTAAAACATTTTAAAAACATATAGTATATGAGTTTTAAAACATTT
TGAAAACATACATATATATAGTGTTTTGAAAAACATTTTAAAATAA
Found at i:37951 original size:75 final size:70
Alignment explanation
Indices: 37691--37944 Score: 183
Period size: 75 Copynumber: 3.4 Consensus size: 70
37681 ATATATATAT
* * * * *
37691 ATATATATATATATAGTTTTTTAAAACATTTTGAAAATA-TATAGTATATGGGTTTT-AAAACAT
1 ATATATA-AAATATAG--TTTTAAAATATTTTTAAAATATTACATTATAT-GGTTTTAAAAACAT
*
37754 TTTGAAAAC
62 TTTAAAAAC
* * * * *
37763 ATATAT-ATATATAGTTTTTTTAAAA-ACATTTTAAAATAAATATATAATATATGGTTTTTAAAA
1 ATATATAAAATATAG---TTTTAAAATA-TTTTTAAAAT--AT-TACATTATATGGTTTTAAAAA
37826 CATTTTAAAAAC
59 CATTTTAAAAAC
***
37838 ATATATGTTATATAGTTTTAAAATATTTTTGAAAATATTACATTATATGGTTTTGAAAAACATTT
1 ATATATAAAATATAGTTTTAAAATATTTTT-AAAATATTACATTATATGGTTTT-AAAAACA--T
37903 TTTAAAAATC
62 TTTAAAAA-C
*
37913 ATATATAAAATGTAGTTTTAAAAAATATTTTT
1 ATATATAAAATATAGTTTT--AAAATATTTTT
37945 TTATATTTTA
Statistics
Matches: 153, Mismatches: 13, Indels: 27
0.79 0.07 0.14
Matches are distributed among these distances:
70 9 0.06
71 32 0.21
72 14 0.09
73 13 0.08
74 21 0.14
75 46 0.30
76 7 0.05
77 11 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (70 bp):
ATATATAAAATATAGTTTTAAAATATTTTTAAAATATTACATTATATGGTTTTAAAAACATTTTA
AAAAC
Found at i:37952 original size:10 final size:11
Alignment explanation
Indices: 37937--38006 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 11
37927 GTTTTAAAAA
37937 ATATTTT-TTT
1 ATATTTTATTT
37947 ATATTTTATTT
1 ATATTTTATTT
37958 -TATTTTATTT
1 ATATTTTATTT
37968 -TAATTATTATTT
1 AT-ATT-TTATTT
37980 ATTATTTATTATTT
1 A-TA-TT-TTATTT
37994 AT-TTGTTATTT
1 ATATT-TTATTT
38005 AT
1 AT
38007 TACTTATTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
10 18 0.34
11 16 0.30
12 6 0.11
13 2 0.04
14 11 0.21
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (11 bp):
ATATTTTATTT
Found at i:37958 original size:5 final size:5
Alignment explanation
Indices: 37938--37979 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
37928 TTTTAAAAAA
37938 TATTT T-TTT ATATTT TATTT TATTT TATTT TAATTAT TATTT
1 TATTT TATTT -TATTT TATTT TATTT TATTT T-ATT-T TATTT
37980 ATTATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 3 0.09
5 19 0.58
6 9 0.27
7 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:37965 original size:17 final size:17
Alignment explanation
Indices: 37938--37997 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
37928 TTTTAAAAAA
* *
37938 TATTTTTTTATATTTTAT
1 TATTATTTTAT-TTTAAT
37956 T-TTATTTTATTTTAAT
1 TATTATTTTATTTTAAT
*
37972 TATTA-TTTATTATTTAT
1 TATTATTTTATT-TTAAT
37989 TATTTATTT
1 TA-TTATTT
37998 GTTATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 12 0.34
17 17 0.49
18 4 0.11
19 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTATTTTATTTTAAT
Found at i:37983 original size:7 final size:7
Alignment explanation
Indices: 37971--38018 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
37961 TTTATTTTAA
37971 TTATTAT
1 TTATTAT
37978 TTATTAT
1 TTATTAT
37985 TTATTA-
1 TTATTAT
37991 -T-TTAT
1 TTATTAT
*
37996 TTGTTAT
1 TTATTAT
*
38003 TTATTAC
1 TTATTAT
38010 TTATTAT
1 TTATTAT
38017 TT
1 TT
38019 TTGTTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
4 3 0.09
5 1 0.03
6 1 0.03
7 30 0.86
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:39413 original size:14 final size:13
Alignment explanation
Indices: 39390--39418 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39380 TATTTAATTT
39390 TTTATTTTTTTCC
1 TTTATTTTTTTCC
39403 TTTATTTTTTTCC
1 TTTATTTTTTTCC
39416 TTT
1 TTT
39419 TGATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTTCC
Found at i:42411 original size:31 final size:29
Alignment explanation
Indices: 42376--42466 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 29
42366 AATTATTTGA
*
42376 AATATTTGTTATTATGGTTTTAATTTTTTCT
1 AATATTTATTATTATGGTTTT-ATTTTTT-T
* ** *
42407 AATATTTATTATTTTGGGCTTATTTCTTT
1 AATATTTATTATTATGGTTTTATTTTTTT
* *
42436 AATATTTATTATTA-GGTTCTATTTTTAT
1 AATATTTATTATTATGGTTTTATTTTTTT
42464 AAT
1 AAT
42467 TTATTTTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 12 0.24
29 14 0.29
30 6 0.12
31 17 0.35
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62
Consensus pattern (29 bp):
AATATTTATTATTATGGTTTTATTTTTTT
Found at i:42599 original size:30 final size:31
Alignment explanation
Indices: 42512--42600 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 31
42502 TTGTCAATAT
* *
42512 TTTTTTTCTAACATTTGTTATTA-AATGCCCAA
1 TTTTTTT-TAATATTTGTTATTAGGA-GCCCAA
* * * * * *
42544 TTATTTTCAATATTTATCATCAGGAGTCC-A
1 TTTTTTTTAATATTTGTTATTAGGAGCCCAA
42574 TTTTTTTTAATATTTGTTATTAGGAGC
1 TTTTTTTTAATATTTGTTATTAGGAGC
42601 ACTTTTAAAA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
30 22 0.52
31 13 0.31
32 7 0.17
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
TTTTTTTTAATATTTGTTATTAGGAGCCCAA
Found at i:43229 original size:21 final size:20
Alignment explanation
Indices: 43143--43300 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
43133 AAATGACCAA
**
43143 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
43162 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
43182 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
43202 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
43223 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
43244 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
43264 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
43285 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
43301 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:43329 original size:20 final size:20
Alignment explanation
Indices: 43267--43460 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
43257 CGATTTTCCA
* ** *
43267 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
43287 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
43307 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43327 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
43347 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
43367 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
43387 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
43407 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
43427 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
43448 AAATCGCAACGCG
1 AAATCGCAACGCG
43461 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:43351 original size:60 final size:60
Alignment explanation
Indices: 43267--43460 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
43257 CGATTTTCCA
* ** * * *
43267 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * *** *
43327 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* **
43387 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
43448 AAATCGCAACGCG
1 AAATCGCAACGCG
43461 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:43882 original size:33 final size:33
Alignment explanation
Indices: 43843--43913 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43833 TTCACTTAGA
*
43843 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
43876 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
43909 TTTCA
1 TTTCA
43914 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:44053 original size:14 final size:14
Alignment explanation
Indices: 44034--44088 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
44024 AGAATGACTG
44034 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
44048 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
44067 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
44081 TCGCAACG
1 TCGCAACG
44089 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:44063 original size:33 final size:33
Alignment explanation
Indices: 44034--44104 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
44024 AGAATGACTG
44034 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
**
44067 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
44100 TCGCA
1 TCGCA
44105 TTGCGATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
Found at i:45977 original size:93 final size:93
Alignment explanation
Indices: 45818--46100 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
45808 TAGATTGCTT
*
45818 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45883 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
45911 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
45976 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46004 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46069 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46096 AGTAA
1 AGTAA
46101 TGCAATCCAT
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 183 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:46208 original size:19 final size:19
Alignment explanation
Indices: 46148--46277 Score: 100
Period size: 20 Copynumber: 7.3 Consensus size: 19
46138 TAGTTTACTT
* *
46148 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-GAAAA
*
46168 TCGCAACGCGAAACCAAAAA
1 TCGCAACGCGAAA-CGAAAA
*
46188 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
46207 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACGAAAA
*
46221 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
46240 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACGAAAA
*
46254 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
46273 TCGCA
1 TCGCA
46278 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 4 0.04
17 4 0.04
18 4 0.04
19 27 0.30
20 29 0.32
21 1 0.01
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACGAAAA
Found at i:46228 original size:33 final size:32
Alignment explanation
Indices: 46185--46277 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
46175 GCGAAACCAA
**
46185 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
46217 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
46250 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
46278 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:46295 original size:19 final size:19
Alignment explanation
Indices: 46273--46406 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
46263 GAAACCAAAA
*
46273 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
46292 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
46308 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
46324 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
46340 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
46357 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
46376 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
46396 TCGTGTTGCGA
1 TCGCGTTGCGA
46407 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 11 0.12
17 8 0.08
18 7 0.07
19 39 0.41
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:46314 original size:14 final size:14
Alignment explanation
Indices: 46295--46350 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
46285 TTTCATTTCG
46295 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
46309 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
46325 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
46341 CGTTGCGATT
1 CGTTGCGATT
46351 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:46359 original size:33 final size:33
Alignment explanation
Indices: 46278--46369 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
46268 CAAAATCGCA
*
46278 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
46311 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
46343 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
46370 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:48333 original size:13 final size:14
Alignment explanation
Indices: 48317--48351 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
48307 ATTGTTTAAT
48317 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
48330 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
48344 TGATTTGT
1 TGATTTGT
48352 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48474 original size:19 final size:19
Alignment explanation
Indices: 48458--48555 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
48448 AAAAATGACT
48458 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48477 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48496 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
48510 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48529 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
48549 ATCGCAA
1 ATCGCAA
48556 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48587 original size:53 final size:53
Alignment explanation
Indices: 48458--48573 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
48448 AAAAATGACT
48458 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
48510 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
48563 ATCGCAATGCG
1 ATCGCAATGCG
48574 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:48616 original size:32 final size:32
Alignment explanation
Indices: 48580--48810 Score: 254
Period size: 32 Copynumber: 6.9 Consensus size: 32
48570 TGCGTTTATA
48580 ATTTCGCATTGCGATTCTCTCGTTGCGATTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTC
* * *
48612 ATTTCGCATTGCGATT-T-TCATTTCGCATTGC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTC
* * *
48643 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGA-TTTC
48683 ATTTCGCATTGCGATTCTCTCGTTGCGATTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTC
48715 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
*
48748 ATTTCCGCATTGCGATT-TCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGA-TTTC
48781 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
48811 GTAATTTCCG
Statistics
Matches: 170, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
30 6 0.04
31 5 0.03
32 66 0.39
33 48 0.28
34 13 0.08
35 6 0.04
36 3 0.02
37 1 0.01
38 11 0.06
39 4 0.02
40 7 0.04
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (32 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTC
Found at i:48632 original size:19 final size:18
Alignment explanation
Indices: 48580--48796 Score: 188
Period size: 19 Copynumber: 12.9 Consensus size: 18
48570 TGCGTTTATA
48580 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
48597 -TCTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
48612 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
48631 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
48648 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
48664 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
48683 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
48700 -TCTCG--TTGCGATTTC
1 ATTTCGCATTGCGATTTC
48715 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
48732 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
48748 ATTTCCGCATTGCGATTTC
1 ATTT-CGCATTGCGATTTC
*
48767 A--T-G--TTGGGATTTTC
1 ATTTCGCATTGCGA-TTTC
48781 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
48797 CTCTCGTTGC
Statistics
Matches: 164, Mismatches: 10, Indels: 51
0.73 0.04 0.23
Matches are distributed among these distances:
13 5 0.03
14 29 0.18
15 7 0.04
16 31 0.19
17 17 0.10
18 16 0.10
19 53 0.32
20 6 0.04
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:48793 original size:84 final size:82
Alignment explanation
Indices: 48580--48796 Score: 294
Period size: 84 Copynumber: 2.6 Consensus size: 82
48570 TGCGTTTATA
*
48580 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATT-TCAT-GTTGGGATTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCG
48644 ATTCTCTCGTTGCGATTTTC
63 ATTCTCTCGTTGCGATTTTC
* * * * *
48664 ATTTCGCATTGCGATTTTCAT-TTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCG
1 ATTTCGCATTGCGA-TTTCATGTTGGGATTTC-ATT-TCGCATTGCGATTTCATTTCGCATTGCG
48728 ATTCTCTCGTTGCGATTTTC
63 ATTCTCTCGTTGCGATTTTC
48748 ATTTCCGCATTGCGATTTCATGTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTTCATGTTGGGA-TTTCATTTCGCATTGCGATT
48797 CTCTCGTTGC
Statistics
Matches: 115, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
83 6 0.05
84 77 0.67
85 29 0.25
86 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (82 bp):
ATTTCGCATTGCGATTTCATGTTGGGATTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATT
CTCTCGTTGCGATTTTC
Found at i:48818 original size:52 final size:51
Alignment explanation
Indices: 48580--48810 Score: 309
Period size: 52 Copynumber: 4.6 Consensus size: 51
48570 TGCGTTTATA
48580 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
48631 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
48683 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATT-T-TC
* * * *
48736 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTCA--T-G--TTGGGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
48781 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
48811 GTAATTTCCG
Statistics
Matches: 163, Mismatches: 7, Indels: 25
0.84 0.04 0.13
Matches are distributed among these distances:
45 9 0.06
46 13 0.08
47 9 0.06
48 2 0.01
49 1 0.01
50 3 0.02
51 50 0.31
52 67 0.41
53 9 0.06
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (51 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTCATTTCGCATTGCGATTTTC
Found at i:51311 original size:24 final size:24
Alignment explanation
Indices: 51277--51323 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51267 CTGAAACATC
51277 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
51301 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
51324 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:52032 original size:20 final size:20
Alignment explanation
Indices: 52004--52233 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
51994 AAATTTCAGT
* * *
52004 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
52024 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
52044 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
52064 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
52084 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
52104 GTTGCGATATACGGATAT-GC
1 GTTGCGATTTACGGAT-TCGC
* **
52124 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
* *
52144 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
52164 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
52184 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
52204 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
52224 GTTGCGATTT
1 GTTGCGATTT
52234 TGGAAAATCG
Statistics
Matches: 178, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
20 177 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:52250 original size:21 final size:21
Alignment explanation
Indices: 52220--52302 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
52210 ATTTTCATAT
*
52220 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
52241 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
52262 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
52283 TCGCGTTGCGATTTTAGAAA
1 TCGCATTGCGATTTTGGAAA
52303 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:52293 original size:42 final size:42
Alignment explanation
Indices: 52200--52297 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 42
52190 ATTTATGTGT
* *
52200 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
**
52241 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTTTGCAA-AA
52283 TCGCGTTGCG-ATTTT
1 TCGCGTTGCGAATTTT
52298 AGAAACTGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
40 1 0.02
41 14 0.30
42 29 0.62
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
Found at i:58005 original size:19 final size:19
Alignment explanation
Indices: 57981--58026 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
57971 TGCTATTTAA
57981 GCTCATTACTCGCCTCATT
1 GCTCATTACTCGCCTCATT
58000 GCTCATTACTCGCCTCATT
1 GCTCATTACTCGCCTCATT
58019 GCTCATTA
1 GCTCATTA
58027 AGCTCACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.35, G:0.11, T:0.37
Consensus pattern (19 bp):
GCTCATTACTCGCCTCATT
Found at i:62367 original size:43 final size:42
Alignment explanation
Indices: 62319--62623 Score: 353
Period size: 43 Copynumber: 7.1 Consensus size: 42
62309 GAACCAAAAT
* * *
62319 GCCGCAATAGGTTAAGATCTATAGCGGCATTTTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
*
62362 GCCGCAAAAGGTCGAGATCTATAGTGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
* * * *
62405 GCCGTAAAAGGTTGATATCTATAGCGGCGTTTTTGAAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
62448 GCCGCAATAGGTCAGATATATAGTGGCGTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAAC
** **
62491 ATCGCAAAAGGTCAGATCTATAGCGGTATTTTT-GATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
* *
62533 GCTGCAAAAGGTCAGATATATAGCGGCGTTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG--TTTTTGGAACAAAC
**
62577 GCCGCAAAA-GTCAGATCTATAGCGGCGTTTTTTTATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
62619 GCCGC
1 GCCGC
62624 TAATTTCCTT
Statistics
Matches: 221, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
41 8 0.04
42 58 0.26
43 133 0.60
44 20 0.09
45 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:62524 original size:85 final size:85
Alignment explanation
Indices: 62319--62623 Score: 389
Period size: 86 Copynumber: 3.6 Consensus size: 85
62309 GAACCAAAAT
* * * *
62319 GCCGCAATAGGTTAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTAT
1 GCCGCAAAAGG-TCAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAAAAGGTC-AGATATAT
62384 AGTGGCG-TTTTTGGAACAAAC
64 AGTGGCGTTTTTTGGAACAAAC
* * * * *
62405 GCCGTAAAAGGTTGATATCTATAGCGGCGTTTTTGAAACAAACGCCGCAATAGGTCAGATATATA
1 GCCGCAAAAGG-TCAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAAAAGGTCAGATATATA
62470 GTGGCGTTTTTTGGAACAAAC
65 GTGGCGTTTTTTGGAACAAAC
** * * *
62491 ATCGCAAAAGGTCAGATCTATAGCGGTATTTTTGATACAAACGCTGCAAAAGGTCAGATATATAG
1 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAAAAGGTCAGATATATAG
*
62556 CGGCGTTTTTTTGGAACAAAC
66 TGGCG-TTTTTTGGAACAAAC
* * *
62577 GCCGCAAAA-GTCAGATCTATAGCGGCGTTTTTTTATACAAACGCCGC
1 GCCGCAAAAGGTCAGATCTATAGCGGC-ATTTTTGAAACAAACGCCGC
62624 TAATTTCCTT
Statistics
Matches: 191, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
85 81 0.42
86 110 0.58
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (85 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAAAAGGTCAGATATATAG
TGGCGTTTTTTGGAACAAAC
Found at i:72118 original size:31 final size:31
Alignment explanation
Indices: 72049--72132 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
72039 CAAACATGAA
72049 AATAAGTTGGCCACCT-ACCAAG-AATTTTCC
1 AATAAGTTGGCCA-CTAACCAAGAAATTTTCC
* *
72079 AATGAGTTGGCCACTAACCAAGAAATTTTTC
1 AATAAGTTGGCCACTAACCAAGAAATTTTCC
*
72110 AATAAGTTGGCCACCAACCAAGA
1 AATAAGTTGGCCACTAACCAAGA
72133 TTAAATTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
29 2 0.04
30 18 0.38
31 28 0.58
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
AATAAGTTGGCCACTAACCAAGAAATTTTCC
Done.