Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 24 of 24
Found at i:3889514 original size:17 final size:18
Alignment explanation
Indices: 3889491--3889539 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3889481 AATTACTATT
*
3889491 TATTATATTTTTAAAATA
1 TATTATATTTTTAAAAAA
*
3889509 -ATTATATACTTTAAAAAA
1 TATTATAT-TTTTAAAAAA
*
3889527 TATTATTTTTTTA
1 TATTATATTTTTA
3889540 CCTACATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 7 0.28
18 12 0.48
19 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATATTTTTAAAAAA
Found at i:3889875 original size:11 final size:11
Alignment explanation
Indices: 3889859--3889892 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3889849 AAATCGATTT
3889859 AATTAATTAAA
1 AATTAATTAAA
*
3889870 AATTAATAAAA
1 AATTAATTAAA
3889881 AATTAAATTAAA
1 AATT-AATTAAA
3889893 TCAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:3892103 original size:29 final size:30
Alignment explanation
Indices: 3892071--3892134 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
3892061 AGTACCTATG
* *
3892071 CCAAAAGCACTTGTGTC-AAAGTATTTCTA
1 CCAAAAGCACTTGTGCCAAAAGTATCTCTA
*
3892100 CCAAAAGTACTTGTGCCAAAAGTATCTCTA
1 CCAAAAGCACTTGTGCCAAAAGTATCTCTA
3892130 CCAAA
1 CCAAA
3892135 GTACCTCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (30 bp):
CCAAAAGCACTTGTGCCAAAAGTATCTCTA
Found at i:3892106 original size:15 final size:15
Alignment explanation
Indices: 3892096--3892215 Score: 70
Period size: 14 Copynumber: 8.1 Consensus size: 15
3892086 TCAAAGTATT
*
3892096 TCTACCAAAAGTACT
1 TCTACCAAAAGTACC
* * *
3892111 TGTGCCAAAAGTATC
1 TCTACCAAAAGTACC
3892126 TCTACC-AAAGTACC
1 TCTACCAAAAGTACC
*
3892140 TCTACC-AATGTACC
1 TCTACCAAAAGTACC
* * * *
3892154 TATGCTATAAA-TACT
1 TCTACCA-AAAGTACC
*
3892169 TCTACCAAAA-TATC
1 TCTACCAAAAGTACC
*
3892183 TTTACC-AAAGTACTATC
1 TCTACCAAAAGTAC---C
3892200 TCTACCAAAAGTACC
1 TCTACCAAAAGTACC
3892215 T
1 T
3892216 TGCTAAAGTA
Statistics
Matches: 77, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
13 3 0.04
14 35 0.45
15 24 0.31
16 2 0.03
17 6 0.08
18 7 0.09
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (15 bp):
TCTACCAAAAGTACC
Found at i:3892135 original size:29 final size:29
Alignment explanation
Indices: 3891967--3892138 Score: 96
Period size: 29 Copynumber: 5.9 Consensus size: 29
3891957 CTGCCAAAGA
* * * *
3891967 GTGCTAAAGTATCTGTGCCAAAATTACTT
1 GTGCCAAAGTATCTCTACCAAAAGTACTT
* * * * * * *
3891996 ATGCTAAAGTATTTCTGCCCAACGTAGTT
1 GTGCCAAAGTATCTCTACCAAAAGTACTT
* * * * *
3892025 GTGCGAAAGT-TCTTTTGCCAAAATTACCT
1 GTGCCAAAGTATC-TCTACCAAAAGTACTT
* * * * * *
3892054 CTACCAAAGTACCTATGCCAAAAGCACTT
1 GTGCCAAAGTATCTCTACCAAAAGTACTT
* *
3892083 GTGTCAAAGTATTTCTACCAAAAGTACTT
1 GTGCCAAAGTATCTCTACCAAAAGTACTT
3892112 GTGCCAAAAGTATCTCTACC-AAAGTAC
1 GTGCC-AAAGTATCTCTACCAAAAGTAC
3892139 CTCTACCAAT
Statistics
Matches: 106, Mismatches: 34, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
28 1 0.01
29 91 0.86
30 14 0.13
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (29 bp):
GTGCCAAAGTATCTCTACCAAAAGTACTT
Found at i:3892147 original size:29 final size:29
Alignment explanation
Indices: 3892088--3892212 Score: 83
Period size: 29 Copynumber: 4.2 Consensus size: 29
3892078 CACTTGTGTC
* * * *
3892088 AAAGTATTTCTACCAAAAGTACTTGTGCCA
1 AAAGTATCTCTACC-AAAGTACCTCTACCA
3892118 AAAGTATCTCTACCAAAGTACCTCTACC-
1 AAAGTATCTCTACCAAAGTACCTCTACCA
* * * * * * *
3892146 AATGTACCTATGCTATAAATACTTCTACCA
1 AAAGTATCTCTACCA-AAGTACCTCTACCA
*
3892176 AAA-TATCTTTACCAAAGTACTATCTCTACCA
1 AAAGTATCTCTACCAAAGTAC---CTCTACCA
3892207 AAAGTA
1 AAAGTA
3892213 CCTTGCTAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
28 15 0.21
29 29 0.41
30 15 0.21
31 10 0.14
32 2 0.03
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAGTATCTCTACCAAAGTACCTCTACCA
Found at i:3892205 original size:17 final size:18
Alignment explanation
Indices: 3892179--3892213 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3892169 TCTACCAAAA
*
3892179 TATCTTTACC-AAAGTAC
1 TATCTCTACCAAAAGTAC
3892196 TATCTCTACCAAAAGTAC
1 TATCTCTACCAAAAGTAC
3892214 CTTGCTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (18 bp):
TATCTCTACCAAAAGTAC
Found at i:3893511 original size:133 final size:133
Alignment explanation
Indices: 3893207--3893512 Score: 321
Period size: 133 Copynumber: 2.3 Consensus size: 133
3893197 GGCACATAAA
* * * *
3893207 ACCATAACTAGTTGACTTCTCCATTAAGAGTATTTGCATTAAGGAAAGTGATGGAAGTTGCACAC
1 ACCATAAC-AGTTGGCTTCTCCATTAAGAGTATTTGTA-TAAGGAAAATGATGGAAGTGGCACAC
* * * ** * *
3893272 ATGACCCTAACGATCGACTTTTTAATTAGAAAAACTTGTGTACGGAGAGTGACAAAAGTGGTACT
64 AAGACCCTAACGATCAACTTTTTAATTAGAAAAACTTGTATAAAGAGAGTGACAAAAGTAGTACA
3893337 ATGGG
129 ATGGG
** * * **
3893342 ACCATAACAGTCAAG-TTTTCCATTAAGAGAATTTGTATAAGGAAAATGATGGAAGTGGCACGTA
1 ACCATAACAGT-TGGCTTCTCCATTAAGAGTATTTGTATAAGGAAAATGATGGAAGTGGCACACA
* * *
3893406 AGACCTTAAC-AGTCAACTTTTTCATTAGAAAAACTTGTATATAAGATAGTGACAAAAGTAGTA-
65 AGACCCTAACGA-TCAACTTTTTAATTAGAAAAACTTGTATA-AAGAGAGTGACAAAAGTAGTAC
3893469 AATGGG
128 AATGGG
* * * * *
3893475 ACTATGACAGTTGGCTTCTCTATTAAAAGTACTTGTAT
1 ACCATAACAGTTGGCTTCTCCATTAAGAGTATTTGTAT
3893513 TAGGGAGAAT
Statistics
Matches: 138, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
132 2 0.01
133 89 0.64
134 39 0.28
135 8 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (133 bp):
ACCATAACAGTTGGCTTCTCCATTAAGAGTATTTGTATAAGGAAAATGATGGAAGTGGCACACAA
GACCCTAACGATCAACTTTTTAATTAGAAAAACTTGTATAAAGAGAGTGACAAAAGTAGTACAAT
GGG
Found at i:3893575 original size:66 final size:67
Alignment explanation
Indices: 3893490--3893615 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 67
3893480 GACAGTTGGC
* *
3893490 TTCTCTATTAAAAGTACTTGTATTA-GGGAGAATGACGAAAA-TGACATAAGAGA-CACAATAAT
1 TTCTCTATTAAAAGAACTTGTA-TACGAGAGAATGAC-AAAAGTGACATAAGAGATCACAATAAT
3893552 CGAT
64 CGAT
* *
3893556 TTCTCTATTAGAAA-AACTTGTATACGAGAGAATGACAAAAGTGGCATATGAGATCACAAT
1 TTCTCTATTA-AAAGAACTTGTATACGAGAGAATGACAAAAGTGACATAAGAGATCACAAT
3893616 GGTTGACTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
65 6 0.12
66 37 0.71
67 9 0.17
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (67 bp):
TTCTCTATTAAAAGAACTTGTATACGAGAGAATGACAAAAGTGACATAAGAGATCACAATAATCG
AT
Found at i:3896352 original size:2 final size:2
Alignment explanation
Indices: 3896345--3896399 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
3896335 AAGCAACGCA
3896345 AT AT AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3896385 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3896400 AACAATGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3898690 original size:12 final size:12
Alignment explanation
Indices: 3898659--3898691 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3898649 AACTCGGCAA
*
3898659 AAAAGAACAAAT
1 AAAAGAATAAAT
3898671 AAAA-AATAAAT
1 AAAAGAATAAAT
3898682 AAAAGAATAA
1 AAAAGAATAA
3898692 CCAACTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAGAATAAAT
Found at i:3899823 original size:22 final size:23
Alignment explanation
Indices: 3899762--3899823 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
3899752 TTAAAAAATT
*
3899762 AAATTTAAATATTATTAATCTTAAA
1 AAATTTAAA-A-TATTACTCTTAAA
*
3899787 AAATTTATAAT-TTACTCTTAAA
1 AAATTTAAAATATTACTCTTAAA
3899809 AAA-TTAAAATATTAC
1 AAATTTAAAATATTAC
3899824 GTACTAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 6 0.18
22 17 0.52
23 1 0.03
24 1 0.03
25 8 0.24
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTTAAAATATTACTCTTAAA
Found at i:3900328 original size:18 final size:17
Alignment explanation
Indices: 3900301--3900334 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3900291 TTAAAAAAAT
*
3900301 AATATGATATGTAAATAA
1 AATATCATATG-AAATAA
3900319 AATATCATATGAAATA
1 AATATCATATGAAATA
3900335 TTGATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (17 bp):
AATATCATATGAAATAA
Found at i:3900376 original size:20 final size:20
Alignment explanation
Indices: 3900340--3900378 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3900330 AAATATTGAT
*
3900340 TTATTATATTTAAAATTTTG
1 TTATTATATATAAAATTTTG
3900360 TTATTATA-ATAATAATTTT
1 TTATTATATATAA-AATTTT
3900379 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTATTATATATAAAATTTTG
Found at i:3900559 original size:14 final size:15
Alignment explanation
Indices: 3900535--3900565 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3900525 AATTATATAT
3900535 TTTTATTAATTTTTA
1 TTTTATTAATTTTTA
3900550 TTTT-TTAATTTTTA
1 TTTTATTAATTTTTA
3900564 TT
1 TT
3900566 AAATAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTAATTTTTA
Found at i:3905334 original size:16 final size:17
Alignment explanation
Indices: 3905302--3905357 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
3905292 TTCGAATTCA
* *
3905302 AAATGAT-TCGAACTTG
1 AAATGATCTTGAATTTG
3905318 AAATGATCTT-AATTTG
1 AAATGATCTTGAATTTG
* *
3905334 AAATTAT-TTGAATTTA
1 AAATGATCTTGAATTTG
3905350 AAATGATC
1 AAATGATC
3905358 CGAACAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (17 bp):
AAATGATCTTGAATTTG
Found at i:3914131 original size:2 final size:2
Alignment explanation
Indices: 3914124--3914153 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3914114 ATTCAACCTA
3914124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3914154 TTAGAGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3917825 original size:72 final size:72
Alignment explanation
Indices: 3917708--3917852 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
3917698 ATTCATGGAA
* * * *
3917708 ATGAAACAGGCTTGGTTTCCATTGATCCTCAGGGAACAGCCGATCCCCACAGCGACACTCCTAAA
1 ATGAAACAGGCTTGATTTCCATTGATCCTCAGGGAACAGCCGATCCCCACAGCCACAATCCCAAA
3917773 GATCATG
66 GATCATG
* ** *
3917780 ATGAAACGGGCTTGATTTCCATTGATCCTGTGGGAACAGCCGATCCTCACAGCCACAATCCCAAA
1 ATGAAACAGGCTTGATTTCCATTGATCCTCAGGGAACAGCCGATCCCCACAGCCACAATCCCAAA
3917845 GATCATG
66 GATCATG
3917852 A
1 A
3917853 AAGAGGTTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (72 bp):
ATGAAACAGGCTTGATTTCCATTGATCCTCAGGGAACAGCCGATCCCCACAGCCACAATCCCAAA
GATCATG
Found at i:3922331 original size:23 final size:24
Alignment explanation
Indices: 3922299--3922344 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3922289 AACAACCACC
* *
3922299 AAAAATGAAAAGAGAGAAGAGAAT
1 AAAAATGAAAAGAAAAAAGAGAAT
3922323 AAAAA-GAAAAGAAAAAAGAGAA
1 AAAAATGAAAAGAAAAAAGAGAA
3922345 GAGAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (24 bp):
AAAAATGAAAAGAAAAAAGAGAAT
Found at i:3922335 original size:14 final size:15
Alignment explanation
Indices: 3922311--3922350 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3922301 AAATGAAAAG
3922311 AGAGAAGAGAATAAA
1 AGAGAAGAGAATAAA
*
3922326 A-AGAAAAGAA-AAA
1 AGAGAAGAGAATAAA
3922339 AGAGAAGAGAAT
1 AGAGAAGAGAAT
3922351 TATTCGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.19
14 16 0.76
15 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (15 bp):
AGAGAAGAGAATAAA
Found at i:3924841 original size:3 final size:3
Alignment explanation
Indices: 3924833--3924876 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3924823 GGCTCTCATA
3924833 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3924877 CCCATCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3927806 original size:2 final size:2
Alignment explanation
Indices: 3927799--3927837 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3927789 TATCGGTGTC
3927799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3927838 TAAAACTTGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3929471 original size:3 final size:3
Alignment explanation
Indices: 3929463--3929517 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
3929453 TTTAAAGCAT
3929463 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3929511 ATA ATA A
1 ATA ATA A
3929518 AATTTAAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3929877 original size:20 final size:20
Alignment explanation
Indices: 3929840--3929877 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3929830 ATATCATATT
*
3929840 TATATTATATTATATTTAAA
1 TATATTATATCATATTTAAA
*
3929860 TATATTATATCATGTTTA
1 TATATTATATCATATTTA
3929878 TTATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
TATATTATATCATATTTAAA
Found at i:3931628 original size:2 final size:2
Alignment explanation
Indices: 3931615--3931666 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3931605 GAAAGTTTAG
*
3931615 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3931657 GA GA GA -A GA G
1 GA GA GA GA GA G
3931667 TATGTGTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3931987 original size:19 final size:20
Alignment explanation
Indices: 3931944--3931979 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3931934 AAATTTAAAT
3931944 TATAA-ATTAATAATTATAA
1 TATAATATTAATAATTATAA
3931963 TATAATATTAA-AATTAT
1 TATAATATTAATAATTAT
3931980 TATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATATTAATAATTATAA
Found at i:3931987 original size:33 final size:29
Alignment explanation
Indices: 3931916--3931987 Score: 72
Period size: 33 Copynumber: 2.3 Consensus size: 29
3931906 TTATCATGAT
*
3931916 TTATATTAATAATATAAAAAATTTAAATTA
1 TTAT-TTAATAATATAAAAAATTAAAATTA
* *
3931946 TAAATTAATAATTATAATATAATATTAAAATTA
1 TTATTTAATAA-TATAA-A-AA-ATTAAAATTA
3931979 TTATTTAAT
1 TTATTTAAT
3931988 TTTTTATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 1 0.03
32 2 0.06
33 16 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATTTAATAATATAAAAAATTAAAATTA
Found at i:3932590 original size:35 final size:34
Alignment explanation
Indices: 3932497--3932605 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 34
3932487 TGTCAAATGA
* *
3932497 ATTATAATAAAAAATAT-TATTAAAAT-TATTGA-
1 ATTA-AATAATAAATATATATTAAAATATATTTAT
3932529 ATTAAAATATATATAAGTA-AT-TTAAAATGATATTTAT
1 ATT-AAATA-ATA-AA-TATATATTAAAAT-ATATTTAT
3932566 ATTAAATAATAAATATATATTAAAATTATATTTAT
1 ATTAAATAATAAATATATATTAAAA-TATATTTAT
3932601 ATTAA
1 ATTAA
3932606 GAATGAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 19
0.75 0.02 0.22
Matches are distributed among these distances:
32 7 0.11
33 5 0.08
34 13 0.20
35 25 0.39
36 11 0.17
37 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
ATTAAATAATAAATATATATTAAAATATATTTAT
Found at i:3932763 original size:23 final size:22
Alignment explanation
Indices: 3932726--3932780 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
3932716 ATGAGATAAA
3932726 AAAATTTTAAATATTAAA-ATT
1 AAAATTTTAAATATTAAATATT
3932747 AAAATTTTAAATTTATTAAATATT
1 AAAATTTTAAA--TATTAAATATT
*
3932771 -ATATTTTAAA
1 AAAATTTTAAA
3932781 AATAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 11 0.37
23 16 0.53
24 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATTTTAAATATTAAATATT
Found at i:3933703 original size:16 final size:16
Alignment explanation
Indices: 3933682--3933733 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3933672 ATCTTGTATT
*
3933682 AAATAATTTAAATTTA
1 AAATAATTTAATTTTA
3933698 AAATAATTTAATTTTA
1 AAATAATTTAATTTTA
* *
3933714 AATTAATTTTATTTTA
1 AAATAATTTAATTTTA
3933730 AAAT
1 AAAT
3933734 TAATAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAATTTAATTTTA
Found at i:3933808 original size:2 final size:2
Alignment explanation
Indices: 3933801--3933830 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3933791 CAAATAATTC
3933801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3933831 GAGATAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3935680 original size:21 final size:21
Alignment explanation
Indices: 3935647--3935686 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3935637 ATTATCCTTC
3935647 TTTCTTAAAAAAACTTCCCACT
1 TTTCTTAAAAAAAC-TCCCACT
*
3935669 TTTCTT-ATAAAACTCCCA
1 TTTCTTAAAAAAACTCCCA
3935687 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTCTTAAAAAAACTCCCACT
Found at i:3935693 original size:2 final size:2
Alignment explanation
Indices: 3935686--3935710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3935676 TAAAACTCCC
3935686 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 A
3935711 AATTTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3935914 original size:30 final size:30
Alignment explanation
Indices: 3935880--3935956 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
3935870 GTTTAGGTAC
*
3935880 AAATTAAAGATT-AAGAACTTACCTGAGTAA
1 AAATTAAAGATTAAAG-ACTTACCTGAATAA
**
3935910 AAATTAAA-ATTTAAAGACTTATTTGAATAA
1 AAATTAAAGA-TTAAAGACTTACCTGAATAA
*
3935940 AAATTAAAGTTTAAAGA
1 AAATTAAAGATTAAAGA
3935957 TTTATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.03
30 36 0.90
31 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATTAAAGATTAAAGACTTACCTGAATAA
Found at i:3936953 original size:2 final size:2
Alignment explanation
Indices: 3936948--3936993 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
3936938 AAAAAATGAC
*
3936948 TA TA TA TA TA TA TA TA TG TA TA TCA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
3936991 TA T
1 TA T
3936994 TGTTAGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3940577 original size:17 final size:17
Alignment explanation
Indices: 3940519--3940577 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
3940509 TATAATATTT
3940519 TTATAAATTTTAATATA
1 TTATAAATTTTAATATA
*
3940536 TTA-ATATTTT-ATATA
1 TTATAAATTTTAATATA
* *
3940551 ATATAAATTTTAAAATA
1 TTATAAATTTTAATATA
*
3940568 TTATATATTT
1 TTATAAATTT
3940578 ATTTTATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 7 0.21
16 12 0.35
17 15 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAAATTTTAATATA
Found at i:3940591 original size:17 final size:16
Alignment explanation
Indices: 3940565--3940632 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 16
3940555 AAATTTTAAA
3940565 ATATTATATATTTATTTT
1 ATATT-TATATTT-TTTT
3940583 ATATTTATATTATTTTT
1 ATATTTATATT-TTTTT
*
3940600 -TATATTATATTTTAATT
1 ATAT-TTATATTTT-TTT
*
3940617 ATTTTTATATTTTTTT
1 ATATTTATATTTTTTT
3940633 CGTATCATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 7 0.16
17 28 0.65
18 8 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATATTTATATTTTTTT
Found at i:3940603 original size:12 final size:12
Alignment explanation
Indices: 3940586--3940632 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
3940576 TTATTTTATA
3940586 TTTATATTATTT
1 TTTATATTATTT
*
3940598 TTTATATTATAT
1 TTTATATTATTT
3940610 TTTA-ATTA-TT
1 TTTATATTATTT
3940620 TTTATATT-TTT
1 TTTATATTATTT
3940631 TT
1 TT
3940633 CGTATCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 5 0.16
11 11 0.35
12 15 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:3940624 original size:34 final size:35
Alignment explanation
Indices: 3940565--3940632 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
3940555 AAATTTTAAA
*
3940565 ATATTATATATTTATTTTATATTTATATTATTTTTT
1 ATATTATATATTTATATTATATTTATATT-TTTTTT
*
3940601 ATATTATAT-TTTA-ATTATTTTTATATTTTTTT
1 ATATTATATATTTATATTATATTTATATTTTTTT
3940633 CGTATCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 4 0.13
36 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (35 bp):
ATATTATATATTTATATTATATTTATATTTTTTTT
Found at i:3942889 original size:50 final size:50
Alignment explanation
Indices: 3942809--3942908 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 50
3942799 ATTAGGTTAG
3942809 GCTTAACTAATGGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
1 GCTTAACTAATGGGGTCAATCAATCCATTC-TACCAAACCTAATAGGTGAT
*
3942860 GCTTAACTAAT-GGGTCAATCAATCCATTCTACCTAACCTAATAGGTGAT
1 GCTTAACTAATGGGGTCAATCAATCCATTCTACCAAACCTAATAGGTGAT
3942909 ATCAGTTTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 19 0.40
50 18 0.38
51 11 0.23
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (50 bp):
GCTTAACTAATGGGGTCAATCAATCCATTCTACCAAACCTAATAGGTGAT
Done.