Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold884
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: 70550
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:1477 original size:21 final size:21
Alignment explanation
Indices: 1448--1492 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1438 AAGTTTTCAT
*
1448 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1468 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1490 TTT
1 TTT
1493 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3727 original size:13 final size:13
Alignment explanation
Indices: 3709--3734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3699 CAATTTTTTG
3709 TGTATCGATACAT
1 TGTATCGATACAT
3722 TGTATCGATACAT
1 TGTATCGATACAT
3735 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5077 original size:15 final size:15
Alignment explanation
Indices: 5057--5091 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5047 AACCATCAAA
5057 GATGATAAAGATAAT
1 GATGATAAAGATAAT
* *
5072 GATGATGATGATAAT
1 GATGATAAAGATAAT
5087 GATGA
1 GATGA
5092 AGTTGACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
GATGATAAAGATAAT
Found at i:7596 original size:20 final size:20
Alignment explanation
Indices: 7545--7637 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
7535 ACCCTTAAAA
* *
7545 GTATCGATACACAATT-CAAA
1 GTATCGATACA-TATTGCAAT
7565 GTATCGATACATATTGCAAT
1 GTATCGATACATATTGCAAT
***
7585 GTATCGATACATGA-AAAAGAT
1 GTATCGATACAT-ATTGCA-AT
*
7606 GTATCGATACATGTTGCAAT
1 GTATCGATACATATTGCAAT
7626 GTATCGATACAT
1 GTATCGATACAT
7638 GAAAAAGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 41 0.68
21 16 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACATATTGCAAT
Found at i:7609 original size:21 final size:21
Alignment explanation
Indices: 7583--7658 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
7573 ACATATTGCA
7583 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
7604 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
7624 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
7645 ATGTATCGATACAT
1 ATGTATCGATACAT
7659 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:7616 original size:41 final size:41
Alignment explanation
Indices: 7565--7658 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
7555 ACAATTCAAA
7565 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
*
7606 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
7647 GTATCGATACAT
1 GTATCGATACAT
7659 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
Found at i:7638 original size:20 final size:20
Alignment explanation
Indices: 7565--7638 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
7555 ACAATTCAAA
*
7565 GTATCGATACATATTGCAAT
1 GTATCGATACATGTTGCAAT
****
7585 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
7606 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
7626 GTATCGATACATG
1 GTATCGATACATG
7639 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:7715 original size:13 final size:13
Alignment explanation
Indices: 7697--7722 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7687 TACAGCAAGT
7697 ATGTATCGATACA
1 ATGTATCGATACA
7710 ATGTATCGATACA
1 ATGTATCGATACA
7723 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9969 original size:21 final size:21
Alignment explanation
Indices: 9936--9980 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9926 TTGCAAGTTG
*
9936 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
9958 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
9978 AAA
1 AAA
9981 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:11811 original size:15 final size:15
Alignment explanation
Indices: 11793--11822 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11783 CCAAATTGAG
11793 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
11808 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
11823 ATCAATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:11818 original size:16 final size:16
Alignment explanation
Indices: 11782--11822 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
11772 GATAAAAATG
* *
11782 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
11798 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
11813 TCC-AAATGAA
1 TCCAAAATGAA
11823 ATCAATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:13898 original size:20 final size:21
Alignment explanation
Indices: 13829--13906 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
13819 AATGTCCAAA
*
13829 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
13849 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
13874 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
13894 TTGTATCGATACA
1 ATGTATCGATACA
13907 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:13913 original size:13 final size:13
Alignment explanation
Indices: 13895--13932 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
13885 CATTTTTCTT
13895 TGTATCGATACAA
1 TGTATCGATACAA
*
13908 TGTATCGATACAC
1 TGTATCGATACAA
13921 TGTATCGATACA
1 TGTATCGATACA
13933 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:15014 original size:32 final size:33
Alignment explanation
Indices: 14968--15031 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
14958 AGCCAAACTA
14968 GTATCGATACAC-AAAATATGTATCGATACAAT
1 GTATCGATACACAAAAATATGTATCGATACAAT
*
15000 GTATTGATACACAAAAAATATGTATCGATACA
1 GTATCGATACAC-AAAAATATGTATCGATACA
15032 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 11 0.38
34 18 0.62
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (33 bp):
GTATCGATACACAAAAATATGTATCGATACAAT
Found at i:17261 original size:21 final size:21
Alignment explanation
Indices: 17228--17277 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
17218 TTGCAAGTTG
*
17228 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
17250 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
17271 AAATAAA
1 AAATAAA
17278 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:19094 original size:15 final size:15
Alignment explanation
Indices: 19074--19104 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19064 TAAAAATGTC
*
19074 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
19089 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
19104 C
1 C
19105 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:21224 original size:13 final size:13
Alignment explanation
Indices: 21186--21224 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
21176 CATTTTTCTT
*
21186 TGTATCGATACAA
1 TGTATCGATACAG
*
21199 TGTATCGACACAG
1 TGTATCGATACAG
21212 TGTATCGATACAG
1 TGTATCGATACAG
21225 GGGGATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:23701 original size:20 final size:19
Alignment explanation
Indices: 23646--23701 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
23636 AAAACCCTTA
*
23646 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
23666 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
23686 AATGTATCGATACATG
1 AAAGTATCGATACATG
23702 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:23778 original size:19 final size:19
Alignment explanation
Indices: 23754--23817 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 19
23744 AGCCAAACTA
23754 GTATCGATACACAAAATAT
1 GTATCGATACACAAAATAT
23773 GTATCGAT--AC---A-AT
1 GTATCGATACACAAAATAT
23786 GTATCGATACACAAAAAATAT
1 GTATCGATACAC--AAAATAT
23807 GTATCGATACA
1 GTATCGATACA
23818 TTGGCTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 2 0.05
17 2 0.05
19 8 0.22
20 1 0.03
21 13 0.35
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (19 bp):
GTATCGATACACAAAATAT
Found at i:23789 original size:13 final size:13
Alignment explanation
Indices: 23771--23796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23761 TACACAAAAT
23771 ATGTATCGATACA
1 ATGTATCGATACA
23784 ATGTATCGATACA
1 ATGTATCGATACA
23797 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23795 original size:32 final size:33
Alignment explanation
Indices: 23754--23817 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 33
23744 AGCCAAACTA
23754 GTATCGATACAC-AAAATATGTATCGATACAAT
1 GTATCGATACACAAAAATATGTATCGATACAAT
23786 GTATCGATACACAAAAAATATGTATCGATACA
1 GTATCGATACAC-AAAAATATGTATCGATACA
23818 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 12 0.40
34 18 0.60
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (33 bp):
GTATCGATACACAAAAATATGTATCGATACAAT
Found at i:29235 original size:79 final size:79
Alignment explanation
Indices: 29142--29475 Score: 402
Period size: 79 Copynumber: 4.2 Consensus size: 79
29132 GAGATAAAGA
** * * *
29142 CGGGGTTGGAGTATCCTTTCAAAAATAATAGGGTTGGAGTATCCCTGATTGTGAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
* *
29207 TCTAAAAATAAAAT
66 TTTAGAAATAAAAT
* * * * * *
29221 TGGGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGAAGTATCTCCGATTACGAAAAATAGATAT
1 CGGGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
29286 TTTAGAAATAAAAT
66 TTTAGAAATAAAAT
* ** *
29300 CGGGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
*
29365 TTTGGAAATAAAAT
66 TTTAGAAATAAAAT
* * * *
29379 CGGGGTTGGAGTATCCCCTCAGAAATAA-CGAGGTTAGAGTATCCCCGATTATG-AAAATTTAGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAATAG-GGTTGGAGTATCCCCGATTATGAAAAATTGA-T
* *
29442 GTTTTGGAAATAAAAC
64 GTTTTAGAAATAAAAT
* *
29458 CAGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
29476 GATTGTGAAA
Statistics
Matches: 220, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
78 8 0.04
79 212 0.96
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAATAGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
TTTAGAAATAAAAT
Found at i:29473 original size:51 final size:51
Alignment explanation
Indices: 29415--29526 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 51
29405 AACGAGGTTA
*
29415 GAGTATCCCCGATTATG-AAAATTTAGTGTTTTGGAAATAAAACCAGAGTTG
1 GAGTATCCCCGATTATGAAAAATTGA-TGTTTTGGAAATAAAACCAGAGTTG
* * * *
29466 GAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTG
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCAGAGTTG
29517 GAGTATCCCC
1 GAGTATCCCC
29527 TCAGAAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 48 0.87
52 7 0.13
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAACCAGAGTTG
Found at i:29476 original size:130 final size:130
Alignment explanation
Indices: 29332--29605 Score: 512
Period size: 130 Copynumber: 2.1 Consensus size: 130
29322 AAATAACGGG
29332 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
*
29397 TCAGAAATAACGAGGTTAGAGTATCCCCGATTATGAAAATTTAGTGTTTTGGAAATAAAACCAGA
66 TCAGAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCAGA
29462 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
* * *
29527 TCAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGG
66 TCAGAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCAGA
29592 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
29606 TCGGAAATAA
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 140 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (130 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
TCAGAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCAGA
Found at i:29546 original size:209 final size:208
Alignment explanation
Indices: 29253--29683 Score: 605
Period size: 209 Copynumber: 2.1 Consensus size: 208
29243 AAATAATAGG
* *
29253 GTTGAAGTATCTCCGATTACGAAAAATAGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTACGAAAAATAGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
* * *
29318 TCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATT-GATGTTTTGGAAATAAAATCGG
66 TCAAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAG-TGTTTTGGAAATAAAACCGG
* * *
29382 GGTTGGAGTATCCCCTCAGAAATAACGAGG-TTAGAGTATCCCCGATTATGAAAATTTAGTGTTT
130 GGTTGGAGTATCCCCTCAGAAATAACG-GGATTAGAATATCCCCGATTATGAAAAATTAGT-ATT
29446 TGGAAATAAAACCAGA
193 TGGAAATAAAACCAGA
** * * * *
29462 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTACGAAAAATAGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
*
29527 TCAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGG
66 TCAAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGG
* * * * *
29592 GTTGGAGTATCCCCTCGGAAATAATGGGATTGGAATATCCCTGATTGTGAAAAATTAGTATTTGG
131 GTTGGAGTATCCCCTCAGAAATAACGGGATTAGAATATCCCCGATTATGAAAAATTAGTATTTGG
** *
29657 AAATAAAACTGGG
196 AAATAAAACCAGA
*
29670 GTTGGAGCATCCCC
1 GTTGGAGTATCCCC
29684 TCGGAAATAA
Statistics
Matches: 196, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
208 30 0.15
209 165 0.84
210 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (208 bp):
GTTGGAGTATCCCCGATTACGAAAAATAGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
TCAAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGG
GTTGGAGTATCCCCTCAGAAATAACGGGATTAGAATATCCCCGATTATGAAAAATTAGTATTTGG
AAATAAAACCAGA
Found at i:29686 original size:78 final size:79
Alignment explanation
Indices: 29462--29772 Score: 423
Period size: 79 Copynumber: 3.9 Consensus size: 79
29452 TAAAACCAGA
*
29462 GTTGGAGTATCCCCGATTGTGAAAAATT-GATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTAG-TGTTTTGGAAATAAAATCGGGGTTGGAGTATCCC
*
29526 CTCAGAAATAACGAG
65 CTCGGAAATAACGAG
*
29541 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
*
29606 TCGGAAATAATG-G
66 TCGGAAATAACGAG
* * * * *
29619 GATTGGAATATCCCTGATTGTGAAAAATTAGT-ATTTGGAAATAAAA-CTGGGGTTGGAGCATCC
1 G-TTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATC-GGGGTTGGAGTATCC
29682 CCTCGGAAATAACGAG
64 CCTCGGAAATAACGAG
* * * * * * *
29698 GTTAGTGTATCCTCAATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGGGTTAGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
29763 TCGGAAATAA
66 TCGGAAATAA
29773 AAACATGAAT
Statistics
Matches: 204, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.00
78 64 0.31
79 137 0.67
80 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
TCGGAAATAACGAG
Found at i:29695 original size:157 final size:158
Alignment explanation
Indices: 29463--29772 Score: 473
Period size: 157 Copynumber: 2.0 Consensus size: 158
29453 AAAACCAGAG
* *
29463 TTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCT
1 TTGGAATATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGCATCCCCT
* * *
29528 CAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGGG
66 CAGAAATAACGAGGTTAGAGTATCCCCAATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGGG
*
29593 TTGGAGTATCCCCTCGGAAATAATGGGA
131 TTAGAGTATCCCCTCGGAAATAATGGGA
*
29621 TTGGAATATCCCTGATTGTGAAAAATT-A-GTATTTGGAAATAAAA-CTGGGGTTGGAGCATCCC
1 TTGGAATATCCCCGATTGTGAAAAATTGATGT-TTTGGAAATAAAATC-GGGGTTGGAGCATCCC
* * * * *
29683 CTCGGAAATAACGAGGTTAGTGTATCCTCAATTATGAAAAATTGGTGTTTTGAAAATAAAATCGG
64 CTCAGAAATAACGAGGTTAGAGTATCCCCAATTATGAAAAATTAGTGTTTTGAAAATAAAACCGG
29748 GGTTAGAGTATCCCCTCGGAAATAA
129 GGTTAGAGTATCCCCTCGGAAATAA
29773 AAACATGAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
156 3 0.02
157 110 0.80
158 25 0.18
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (158 bp):
TTGGAATATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAGCATCCCCT
CAGAAATAACGAGGTTAGAGTATCCCCAATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGGG
TTAGAGTATCCCCTCGGAAATAATGGGA
Found at i:34437 original size:21 final size:21
Alignment explanation
Indices: 34411--34486 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
34401 CTGCCAAGAA
*
34411 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
34432 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
34452 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
34473 ATGTATCGATACAT
1 ATGTATCGATACAT
34487 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:34457 original size:20 final size:20
Alignment explanation
Indices: 34432--34504 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
34422 CATCTTTTTT
34432 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
34452 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
34473 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
34493 ATGTATCGATAC
1 ATGTATCGATAC
34505 TTTGAATTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:34468 original size:41 final size:41
Alignment explanation
Indices: 34411--34504 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
34401 CTGCCAAGAA
*
34411 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
34452 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
34493 ATGTATCGATAC
1 ATGTATCGATAC
34505 TTTGAATTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:37839 original size:31 final size:31
Alignment explanation
Indices: 37801--37964 Score: 157
Period size: 31 Copynumber: 5.9 Consensus size: 31
37791 AAAATAAATT
37801 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
1 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
37832 TTTATCAAGGGGGAG-AAA---TTTT-----
1 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
*
37854 TTTATTAAGGGGGAGAAAATCTTTTTAACCG
1 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
37885 TTTATCAAGGGGGAG-AAA---TTTT-----
1 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
*
37907 TTTATTAAGGGGGAGAAAATCTTTTTAACCG
1 TTTATCAAGGGGGAGAAAATCTTTTTAACCG
* * *
37938 TTTATCAAGGGGAAGAAATTTTTTTTA
1 TTTATCAAGGGGGAGAAAATCTTTTTA
37965 TCAAAGGGAA
Statistics
Matches: 108, Mismatches: 7, Indels: 36
0.72 0.05 0.24
Matches are distributed among these distances:
22 28 0.26
23 6 0.06
26 8 0.07
27 8 0.07
30 6 0.06
31 52 0.48
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (31 bp):
TTTATCAAGGGGGAGAAAATCTTTTTAACCG
Found at i:37863 original size:22 final size:23
Alignment explanation
Indices: 37832--37933 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 23
37822 TTTTTAACCG
37832 TTTATCAAGGGGGAG-AAATTTT
1 TTTATCAAGGGGGAGAAAATTTT
*
37854 TTTATTAAGGGGGAGAAAATCTTTTT
1 TTTATCAAGGGGGAGAAAA---TTTT
37880 AACCGTTTATCAAGGGGGAG-AAATTTT
1 -----TTTATCAAGGGGGAGAAAATTTT
* *
37907 TTTATTAAGGGGGAGAAAATCTT
1 TTTATCAAGGGGGAGAAAATTTT
37930 TTTA
1 TTTA
37934 ACCGTTTATC
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
22 28 0.42
23 13 0.20
26 4 0.06
27 4 0.06
30 3 0.05
31 14 0.21
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (23 bp):
TTTATCAAGGGGGAGAAAATTTT
Found at i:37874 original size:53 final size:53
Alignment explanation
Indices: 37799--37962 Score: 310
Period size: 53 Copynumber: 3.1 Consensus size: 53
37789 TGAAAATAAA
*
37799 TTTTTATCAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
1 TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
37852 TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
1 TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
*
37905 TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGAAGAAATT
1 TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
37958 TTTTT
1 TTTTT
37963 TATCAAAGGG
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 109 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (53 bp):
TTTTTATTAAGGGGGAGAAAATCTTTTTAACCGTTTATCAAGGGGGAGAAATT
Found at i:37979 original size:21 final size:23
Alignment explanation
Indices: 37938--37982 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
37928 TTTTTAACCG
*
37938 TTTATCAAGGGGAAGAAATTTTT
1 TTTATCAAAGGGAAGAAATTTTT
37961 TTTATCAAAGGG-A-AAATTTTT
1 TTTATCAAAGGGAAGAAATTTTT
37982 T
1 T
37983 AACGAAAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 11 0.52
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (23 bp):
TTTATCAAAGGGAAGAAATTTTT
Found at i:38539 original size:20 final size:20
Alignment explanation
Indices: 38516--38580 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
38506 CACACCCAGA
38516 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
38536 TGTATCGATACA--A-----
1 TGTATCGATACATTATGCTT
38549 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
38569 TGTATCGATACA
1 TGTATCGATACA
38581 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
15 1 0.03
18 1 0.03
20 24 0.63
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:38554 original size:13 final size:13
Alignment explanation
Indices: 38536--38593 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
38526 CATTATGCTT
38536 TGTATCGATACAA
1 TGTATCGATACAA
38549 TGTATCGATAC-A
1 TGTATCGATACAA
**
38561 T-TAT-G---CTT
1 TGTATCGATACAA
38569 TGTATCGATACAA
1 TGTATCGATACAA
38582 TGTATCGATACA
1 TGTATCGATACA
38594 TGTTCATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.08
10 2 0.06
11 3 0.08
12 2 0.06
13 24 0.67
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:38557 original size:33 final size:33
Alignment explanation
Indices: 38515--38594 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
38505 ACACACCCAG
38515 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATTATGCTTTGTATCGATACA
38548 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATTATGCTTTGTATCGATACA
38581 ATGTATCGATACAT
1 ATGTATCGATACAT
38595 GTTCATTGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTATGCTTTGTATCGATACA
Found at i:38624 original size:20 final size:20
Alignment explanation
Indices: 38578--38633 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
38568 TTGTATCGAT
*
38578 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
38597 TC-ATTGTATCGATTCATGG
1 ACAATTGTATCGATACATGG
38616 ACAATTGTATCGATACAT
1 ACAATTGTATCGATACAT
38634 AAAACTGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 14 0.47
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:38688 original size:20 final size:20
Alignment explanation
Indices: 38663--38729 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
38653 CTACCACTGT
38663 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
38683 TTGTATCG----AT---ACA
1 TTGTATCGATACATGGCACA
*
38696 TTATATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
38716 TTGTATCGATACAT
1 TTGTATCGATACAT
38730 TGCTTCAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.26
16 2 0.05
17 2 0.05
20 24 0.63
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:38702 original size:13 final size:13
Alignment explanation
Indices: 38680--38709 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38670 GATACATGGC
*
38680 ACATTGTATCGAT
1 ACATTATATCGAT
38693 ACATTATATCGAT
1 ACATTATATCGAT
38706 ACAT
1 ACAT
38710 GGCACATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:38708 original size:33 final size:33
Alignment explanation
Indices: 38666--38730 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
38656 CCACTGTTTG
38666 TATCGATACATGGCACATTGTATCGATACATTA
1 TATCGATACATGGCACATTGTATCGATACATTA
38699 TATCGATACATGGCACATTGTATCGATACATT
1 TATCGATACATGGCACATTGTATCGATACATT
38731 GCTTCAAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TATCGATACATGGCACATTGTATCGATACATTA
Found at i:41573 original size:12 final size:12
Alignment explanation
Indices: 41556--41583 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41546 TATCAAAAAG
41556 AGGGAGATTGAT
1 AGGGAGATTGAT
41568 AGGGAGATTGAT
1 AGGGAGATTGAT
41580 AGGG
1 AGGG
41584 TTTTGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.21
Consensus pattern (12 bp):
AGGGAGATTGAT
Found at i:41978 original size:33 final size:33
Alignment explanation
Indices: 41941--42005 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
41931 TACTACTGTT
** *
41941 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATAACAAATTGTATCGATACAA
41974 TGTATCGATACATAACAAATTGTATCGATACA
1 TGTATCGATACATAACAAATTGTATCGATACA
42006 TTGTCCTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATAACAAATTGTATCGATACAA
Found at i:41979 original size:13 final size:13
Alignment explanation
Indices: 41961--41985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41951 CATGGCACAT
41961 TGTATCGATACAA
1 TGTATCGATACAA
41974 TGTATCGATACA
1 TGTATCGATACA
41986 TAACAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:46110 original size:15 final size:15
Alignment explanation
Indices: 46087--46117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46077 GGTTATTATG
46087 AAATCAAATTTAAAT
1 AAATCAAATTTAAAT
*
46102 AAATTAAATTTAAAT
1 AAATCAAATTTAAAT
46117 A
1 A
46118 TTTTTATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATCAAATTTAAAT
Found at i:46224 original size:26 final size:26
Alignment explanation
Indices: 46195--46249 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
46185 ATTAGTATTA
* * * *
46195 AAATATTTAAATTTTAATTTAAATAT
1 AAATAATTAAATTTAAAATAAAATAT
46221 AAATAATTAAATTTAAAATAAAATAT
1 AAATAATTAAATTTAAAATAAAATAT
46247 AAA
1 AAA
46250 ATCAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATAATTAAATTTAAAATAAAATAT
Found at i:50381 original size:3 final size:3
Alignment explanation
Indices: 50373--50399 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
50363 TCATTATGAG
50373 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
50400 TAAAATAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52709 original size:26 final size:26
Alignment explanation
Indices: 52679--52733 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
52669 ACTTATCTAG
*
52679 AATCCCAAATAGAGTTAAACTTTATC
1 AATCCCAAATAAAGTTAAACTTTATC
* * *
52705 AATCCTAGATAAAGTTGAACTTTATC
1 AATCCCAAATAAAGTTAAACTTTATC
52731 AAT
1 AAT
52734 ACTATCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (26 bp):
AATCCCAAATAAAGTTAAACTTTATC
Found at i:55290 original size:152 final size:149
Alignment explanation
Indices: 55082--55369 Score: 418
Period size: 152 Copynumber: 1.9 Consensus size: 149
55072 TTCTTGAAAC
* * *
55082 TCCCATGTTTCTAAAACACAGAGTTTTCTACTACGTAAATATTTTTGAGTGAATTTTTCTTGGTT
1 TCCCATGTTTCTAAAACACAAAATTTTCTACTACGTAAATATTTTTGAGTGAATTTTT-TTCGTT
* ** *
55147 TTTAGTTTTTAAAATTTATCAAATATTATTAATTTAATTTGTATTAAATCACTTTTCAAAAATTC
65 TTTAATTTTTAAAATTTATCAAATATTATT-ATTTAATTCATATTAAATCA-GTTTCAAAAATTC
55212 ATTCATTTTTTATTTTTTTCCT
128 ATTCATTTTTTATTTTTTTCCT
* *
55234 TCCCATGTTTCTAAAATACAAAATTTTCTACTCCGTAAATATTTTTGGAAG-G-ATTTTTTTCGT
1 TCCCATGTTTCTAAAACACAAAATTTTCTACTACGTAAATATTTTT-G-AGTGAATTTTTTTCGT
*
55297 TTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTAAATTAGTTTCAAAAATTCA
64 TTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTAAATCAGTTTCAAAAATTCA
*
55362 TTTATTTT
129 TTCATTTT
55370 CATGAGTTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
149 20 0.16
150 17 0.14
151 34 0.28
152 48 0.39
153 2 0.02
154 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (149 bp):
TCCCATGTTTCTAAAACACAAAATTTTCTACTACGTAAATATTTTTGAGTGAATTTTTTTCGTTT
TTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTAAATCAGTTTCAAAAATTCATT
CATTTTTTATTTTTTTCCT
Found at i:58590 original size:9 final size:8
Alignment explanation
Indices: 58569--58608 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
58559 AAGGGTTTGG
58569 CTTTTTTT
1 CTTTTTTT
58577 -TTTTTTT
1 CTTTTTTT
*
58584 CTATTTTCT
1 CT-TTTTTT
58593 CTTTTTTT
1 CTTTTTTT
58601 CTTTTTTT
1 CTTTTTTT
58609 TTCTCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
CTTTTTTT
Found at i:58590 original size:10 final size:10
Alignment explanation
Indices: 58587--58623 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
58577 TTTTTTTCTA
58587 TTTTCTCTTT
1 TTTTCTCTTT
*
58597 TTTTCTTTTT
1 TTTTCTCTTT
*
58607 TTTTCTCTCT
1 TTTTCTCTTT
58617 TTTTCTC
1 TTTTCTC
58624 ACTACTTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:58599 original size:22 final size:20
Alignment explanation
Indices: 58572--58622 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
58562 GGTTTGGCTT
*
58572 TTTTTTTTTTTTCTATTTTCTC
1 TTTTTTTCTTTT-T-TTTTCTC
58594 TTTTTTTCTTTTTTTTTCTC
1 TTTTTTTCTTTTTTTTTCTC
*
58614 TCTTTTTCT
1 TTTTTTTCT
58623 CACTACTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 15 0.56
21 1 0.04
22 11 0.41
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTTCTC
Found at i:65391 original size:27 final size:27
Alignment explanation
Indices: 65357--65411 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
65347 ATAGTTTTAG
65357 ATTGAGTTTATAAATAAAGGAATAGAA
1 ATTGAGTTTATAAATAAAGGAATAGAA
* *
65384 ATTGAGTTTATAAATGAAGGATTAGAA
1 ATTGAGTTTATAAATAAAGGAATAGAA
65411 A
1 A
65412 GAGAATAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (27 bp):
ATTGAGTTTATAAATAAAGGAATAGAA
Found at i:65721 original size:15 final size:15
Alignment explanation
Indices: 65701--65746 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
65691 TCCGTTTTTA
65701 CGGATTCAGATATTG
1 CGGATTCAGATATTG
*
65716 CGGATTCAGATAATATT
1 CGGATTCAGAT-AT-TG
*
65733 CGGATTTAGATATT
1 CGGATTCAGATATT
65747 ATAATTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (15 bp):
CGGATTCAGATATTG
Found at i:65738 original size:17 final size:16
Alignment explanation
Indices: 65701--65744 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
65691 TCCGTTTTTA
65701 CGGATTCAGAT-ATTG
1 CGGATTCAGATAATTG
*
65716 CGGATTCAGATAATATT
1 CGGATTCAGATAAT-TG
*
65733 CGGATTTAGATA
1 CGGATTCAGATA
65745 TTATAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 12 0.48
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (16 bp):
CGGATTCAGATAATTG
Done.