Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold448
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: 1056520
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:989712 original size:20 final size:20
Alignment explanation
Indices: 989670--989708 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
989660 CGTGTAAATG
* *
989670 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
989690 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
989709 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:989777 original size:13 final size:13
Alignment explanation
Indices: 989759--989783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
989749 CAATTTTTTA
989759 TGTATCGATACAT
1 TGTATCGATACAT
989772 TGTATCGATACA
1 TGTATCGATACA
989784 AGTTTGGCTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:990500 original size:13 final size:12
Alignment explanation
Indices: 990482--990519 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
990472 CCTTTGCACC
990482 TTTTTTTTGTGT
1 TTTTTTTTGTGT
990494 TTGTTTTTTGT-T
1 TT-TTTTTTGTGT
990506 TTTTTTTTGTGT
1 TTTTTTTTGTGT
990518 TT
1 TT
990520 ACTTTTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 8 0.33
13 8 0.33
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:990532 original size:24 final size:24
Alignment explanation
Indices: 990482--990533 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
990472 CCTTTGCACC
** *
990482 TTTTTTTTGTGTTTGTTTTTTGTT
1 TTTTTTTTGTGTTTGACTTTTGCT
990506 TTTTTTTTGTGTTT-ACTTTTGACT
1 TTTTTTTTGTGTTTGACTTTTG-CT
990530 TTTT
1 TTTT
990534 AATCATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.04, C:0.04, G:0.13, T:0.79
Consensus pattern (24 bp):
TTTTTTTTGTGTTTGACTTTTGCT
Found at i:997592 original size:52 final size:52
Alignment explanation
Indices: 997392--997572 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
997382 TGAAATATGA
* *
997392 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
997444 AAATTTGCCTACATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
997496 AAATTTGCCTACATATATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
997548 AAATTTGCCTGCATGTATCAATACA
1 AAATTTGCCTACATATATCGATACA
997573 AAGATCAGTG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTACATATATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:997599 original size:13 final size:13
Alignment explanation
Indices: 997581--997605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
997571 CAAAGATCAG
997581 TGTATCGATACAA
1 TGTATCGATACAA
997594 TGTATCGATACA
1 TGTATCGATACA
997606 TTTGAATAAT
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:997685 original size:13 final size:13
Alignment explanation
Indices: 997667--997724 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
997657 ACAAAACTTA
997667 TGTATCGATACAT
1 TGTATCGATACAT
997680 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
997699 ATGTATCGATACAT
1 -TGTATCGATACAT
997713 TGTATCGATACA
1 TGTATCGATACA
997725 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:997705 original size:20 final size:20
Alignment explanation
Indices: 997680--997778 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 20
997670 ATCGATACAT
997680 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
997700 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
997713 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
997733 TGTATCGAT---ACA--TT-
1 TGTATCGATACAACACTTTA
*
997747 T-TATTGATACAACACTTTA
1 TGTATCGATACAACACTTTA
997766 TGTATCGATACAA
1 TGTATCGATACAA
997779 ATCGTTGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 28
0.68 0.02 0.30
Matches are distributed among these distances:
13 15 0.24
14 2 0.03
15 2 0.03
16 6 0.10
17 6 0.10
18 2 0.03
19 2 0.03
20 28 0.44
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:997706 original size:33 final size:33
Alignment explanation
Indices: 997643--997777 Score: 236
Period size: 33 Copynumber: 4.1 Consensus size: 33
997633 GGTAGTAGCT
*
997643 TACATTGTATCGATACAAAAC-TTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
997675 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
997708 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
* *
997741 TACATTTTATTGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
997774 TACA
1 TACA
997778 AATCGTTGAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 20 0.20
33 79 0.80
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (33 bp):
TACATTGTATCGATACAACACTTTATGTATCGA
Found at i:1004367 original size:9 final size:9
Alignment explanation
Indices: 1004353--1004381 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1004343 CGAGTCAATT
1004353 TCTTCATCA
1 TCTTCATCA
1004362 TCTTCATCA
1 TCTTCATCA
1004371 TCTTCATCA
1 TCTTCATCA
1004380 TC
1 TC
1004382 ATTAATGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (9 bp):
TCTTCATCA
Found at i:1006067 original size:32 final size:33
Alignment explanation
Indices: 1006026--1006088 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1006016 ATTTCATGGT
*
1006026 ATATCGATACAAAG-AACATTTATCGATACAAA
1 ATATCGATACAAAGCAACATTTATCAATACAAA
*
1006058 ATATCGATACTAAGCAACATTTATCAATACA
1 ATATCGATACAAAGCAACATTTATCAATACA
1006089 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (33 bp):
ATATCGATACAAAGCAACATTTATCAATACAAA
Found at i:1006605 original size:19 final size:19
Alignment explanation
Indices: 1006581--1006618 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1006571 GAAGTATTTG
*
1006581 CAATAAATTTGTTTTAGAA
1 CAATAAATTCGTTTTAGAA
1006600 CAATAAATTCGTTTTAGAA
1 CAATAAATTCGTTTTAGAA
1006619 ATAAGGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (19 bp):
CAATAAATTCGTTTTAGAA
Found at i:1007397 original size:13 final size:13
Alignment explanation
Indices: 1007379--1007403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1007369 ATATTGCTTA
1007379 GTATCAATACATT
1 GTATCAATACATT
1007392 GTATCAATACAT
1 GTATCAATACAT
1007404 GTTCATTGTA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
GTATCAATACATT
Found at i:1007555 original size:19 final size:20
Alignment explanation
Indices: 1007531--1007568 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1007521 TAAATTTCAA
1007531 ATGAA-TGCATCGATACATT
1 ATGAATTGCATCGATACATT
*
1007550 ATGAATTGTATCGATACAT
1 ATGAATTGCATCGATACAT
1007569 AGAAGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGAATTGCATCGATACATT
Found at i:1016057 original size:20 final size:19
Alignment explanation
Indices: 1016032--1016077 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
1016022 AATTACAGAC
1016032 ATTTTTTACCAACCAAATT
1 ATTTTTTACCAACCAAATT
*
1016051 AATTTTTTTCCAACCAAATT
1 -ATTTTTTACCAACCAAATT
1016071 ATTTTTT
1 ATTTTTT
1016078 GGATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTTACCAACCAAATT
Found at i:1021975 original size:32 final size:32
Alignment explanation
Indices: 1021934--1021997 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1021924 TATTTTTTTC
1021934 TTCAAATCGAATCTCTCCAAACGCCAATGGAA
1 TTCAAATCGAATCTCTCCAAACGCCAATGGAA
* *
1021966 TTCAAATCGAATCTTTCCAAACGTCAATGGAA
1 TTCAAATCGAATCTCTCCAAACGCCAATGGAA
1021998 AATATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (32 bp):
TTCAAATCGAATCTCTCCAAACGCCAATGGAA
Found at i:1022071 original size:24 final size:24
Alignment explanation
Indices: 1022046--1022105 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
1022036 TAATTAAATA
*
1022046 ATATTATTTATTATT-AAAGCATT
1 ATATTATTTAATATTCAAAGCATT
1022069 A-ATTATATTAATATTCAAAGCATT
1 ATATTAT-TTAATATTCAAAGCATT
1022093 ATAATTA-TTAATA
1 AT-ATTATTTAATA
1022106 AATTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.16
23 8 0.25
24 15 0.47
26 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (24 bp):
ATATTATTTAATATTCAAAGCATT
Found at i:1022206 original size:17 final size:19
Alignment explanation
Indices: 1022141--1022203 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1022131 AGTATAAATA
* * *
1022141 ATAATATAAATAAAATTCTA
1 ATAATATTAATAATATT-TT
*
1022161 ATAATTTTAATAATATTTT
1 ATAATATTAATAATATTTT
1022180 ATAATATTAA-AATATTTAT
1 ATAATATTAATAATATTT-T
1022199 ATAAT
1 ATAAT
1022204 TAATGTTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.19
19 16 0.43
20 14 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATATTAATAATATTTT
Found at i:1023840 original size:17 final size:17
Alignment explanation
Indices: 1023818--1023860 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1023808 TAAATTTAGT
1023818 TTTATTTATTAAAAATA
1 TTTATTTATTAAAAATA
*
1023835 TTTATTCT-TTAAAATTA
1 TTTATT-TATTAAAAATA
1023852 TTTGATTTA
1 TTT-ATTTA
1023861 AAAGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTATTTATTAAAAATA
Found at i:1024664 original size:22 final size:22
Alignment explanation
Indices: 1024611--1024667 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1024601 AAATTATAAT
* *
1024611 AAATTATTCAAATATTATTTTA
1 AAATTATTTAATTATTATTTTA
1024633 AAATTATTTAATTATTATTTTA
1 AAATTATTTAATTATTATTTTA
*
1024655 AAATTTTTTAATT
1 AAATTATTTAATT
1024668 TAATATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTATTTAATTATTATTTTA
Found at i:1030306 original size:2 final size:2
Alignment explanation
Indices: 1030299--1030330 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1030289 GCATGCGTGC
*
1030299 GT GT GT GT GT GT GT GT GT GT GT TT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1030331 TTTACATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
GT
Found at i:1037953 original size:44 final size:44
Alignment explanation
Indices: 1037905--1037988 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
1037895 AGCAACTCGA
*
1037905 ACATATTCAAACT-AAATAAAAATTAATTTAAATTCAAAATAAAT
1 ACATATTC-AACTCAAATAAAAATTAACTTAAATTCAAAATAAAT
*
1037949 ACATATTCAACTCAATTAAAAATTAACTTAAATTCAAAAT
1 ACATATTCAACTCAAATAAAAATTAACTTAAATTCAAAAT
1037989 TATTCAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (44 bp):
ACATATTCAACTCAAATAAAAATTAACTTAAATTCAAAATAAAT
Found at i:1039891 original size:79 final size:79
Alignment explanation
Indices: 1039760--1039958 Score: 204
Period size: 79 Copynumber: 2.5 Consensus size: 79
1039750 AATAACAGGG
* * ** * *
1039760 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTA
*
1039823 GAAAAAAAAATCGGGA
64 GAAAAAAAAACCGGGA
* * *
1039839 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
* * * *
1039904 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* ** *
1039918 TTGGAGTATCCCCTCGGCAGTAACGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1039959 GATGAAATAA
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 7 0.07
79 92 0.93
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:1039969 original size:28 final size:28
Alignment explanation
Indices: 1039913--1039989 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1039903 GGAATAAAGC
*** * *
1039913 CGGGGTTGGAGTATCCCCTCGGCAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1039941 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1039969 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1039990 TGTGAAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1040042 original size:52 final size:51
Alignment explanation
Indices: 1039973--1040309 Score: 167
Period size: 52 Copynumber: 6.4 Consensus size: 51
1039963 AAATAACGAG
*
1039973 GTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAA-TTGGTATTTTTGGAAATAAAATCGGA
** * *
1040025 GTTGGAGTATCCCCGATTAAAG-GAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT---GTGAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
1040078 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-G-AAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
1040129 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTG-AA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
1040184 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-A-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
1040238 GTTAGAGTATCCCCGATTATAGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAATTGGTATTTTTGGAAATAAAATCGGA
* *
1040289 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1040310 GAGAATTGAT
Statistics
Matches: 218, Mismatches: 37, Indels: 62
0.69 0.12 0.20
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 3 0.01
51 38 0.17
52 78 0.36
53 27 0.12
54 33 0.15
55 20 0.09
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:1040157 original size:212 final size:212
Alignment explanation
Indices: 1039906--1040311 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
1039896 TATTTTGGGA
* * * *
1039906 ATAAAGCCGGGGTTGGAGTATCCCCTCGGCAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACG
* * *
1039971 AGGTTGGAGTATCCTCGATTGTGAA-AATTTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTA
65 AGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTA
* *
1040034 TCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTG
130 TCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTG
1040098 GAAAAATTAGTGTTTTAGCG
193 GAAAAATTAGTGTTTTAGCG
* *
1040118 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGA
*
1040183 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTAT
66 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTAT
* * * *
1040248 CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGGA
131 CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1040312 GAATTGATAA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 32 0.18
212 104 0.59
213 39 0.22
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGA
GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTAT
CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:1040169 original size:28 final size:27
Alignment explanation
Indices: 1040129--1040199 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
1040119 TAAAACCGGA
**
1040129 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
1040157 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
1040184 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
1040200 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:1040212 original size:107 final size:105
Alignment explanation
Indices: 1039859--1040251 Score: 314
Period size: 107 Copynumber: 3.7 Consensus size: 105
1039849 CCTTCGAAAA
** * * * * * * *
1039859 TAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
1039924 TATCCCCTCGGCAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTCGG-AATAACGGGGTTGGAGTATCCCCGATG-AT
* * * * *
1039966 TAACGAGGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
1040031 GTAT-CCC-C-GATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGGAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
1040068 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
1040132 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCGG-AATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
1040177 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
1040242 GAGTATCCCC
63 GAGTATCCCC
1040252 GATTATAGAA
Statistics
Matches: 217, Mismatches: 51, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 46 0.21
105 19 0.09
106 18 0.08
107 70 0.32
108 32 0.15
109 27 0.12
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGGAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:1040284 original size:51 final size:53
Alignment explanation
Indices: 1040188--1040306 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
1040178 AACGGGGTTG
* * *
1040188 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1040242 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
1040293 GAATATCCTCGATT
1 GAGTATCCCCGATT
1040307 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1042690 original size:13 final size:13
Alignment explanation
Indices: 1042672--1042697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1042662 ACAAAGATCC
1042672 ATGTATCGATACA
1 ATGTATCGATACA
1042685 ATGTATCGATACA
1 ATGTATCGATACA
1042698 CAGAAAAATG
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:1042697 original size:33 final size:33
Alignment explanation
Indices: 1042655--1042717 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1042645 TTTCCAAATA
***
1042655 TATCGATACAAAGATCCATGTATCGATACAATG
1 TATCGATACAAAGAAAAATGTATCGATACAATG
*
1042688 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
1042718 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (33 bp):
TATCGATACAAAGAAAAATGTATCGATACAATG
Found at i:1042761 original size:19 final size:18
Alignment explanation
Indices: 1042737--1042804 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1042727 CAGTAGCTAA
1042737 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1042756 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1042771 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1042788 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1042805 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1042777 original size:13 final size:13
Alignment explanation
Indices: 1042759--1042783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1042749 ACAATACTTA
1042759 TGTATCGATACAT
1 TGTATCGATACAT
1042772 TGTATCGATACA
1 TGTATCGATACA
1042784 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1042781 original size:32 final size:32
Alignment explanation
Indices: 1042740--1042802 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1042730 TAGCTAATTA
*
1042740 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1042772 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1042803 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1043668 original size:55 final size:55
Alignment explanation
Indices: 1043573--1044382 Score: 928
Period size: 55 Copynumber: 14.4 Consensus size: 55
1043563 ATAAAGTGTA
* * * * * * *
1043573 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1043628 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* **
1043683 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGACAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
1043744 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
1043803 TCCCGCTATTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * * *
1043863 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTCGGCTTTTAAAAAAAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC-TTT------GAAAGGTG
* *
1043924 TCCCGCTCTTTGAGGATTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
1043978 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1044033 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * * * *
1044087 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTAGGCTTTGAAAAGAG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1044142 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
1044196 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1044251 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1044306 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1044361 TCCTGCTCTTTGGGGACTGAAA
1 TCCTGCTCTTTGAGGACTGAAA
1044383 AGCGGACGGA
Statistics
Matches: 679, Mismatches: 46, Indels: 61
0.86 0.06 0.08
Matches are distributed among these distances:
53 10 0.01
54 113 0.17
55 334 0.49
56 14 0.02
57 2 0.00
59 41 0.06
60 89 0.13
61 66 0.10
62 4 0.01
64 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:1043707 original size:26 final size:26
Alignment explanation
Indices: 1043619--1043708 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1043609 GTGTGGGCTT
* *
1043619 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1043645 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
1043672 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1043700 TGAAAGGTG
1 TGAAAGGTG
1043709 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1043732 original size:29 final size:29
Alignment explanation
Indices: 1043645--1043733 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
1043635 CTTTGAGGAC
1043645 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
1043674 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
1043700 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1043729 TGAAA
1 TGAAA
1043734 AGACAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:1044059 original size:109 final size:110
Alignment explanation
Indices: 1043596--1044381 Score: 962
Period size: 109 Copynumber: 7.0 Consensus size: 110
1043586 GGAGTAAAAA
* * * *
1043596 GTGCCACCAACTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACC
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACC
*
1043659 AACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACTGAAAG
65 AACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTG-AAG
* ** *
1043706 GTGCCACCAACTTGTGTGGGCTTTGAAAAGACAAAGCATCCTGCTCTTTGAGGACT--AAAGGTG
1 GTGCCACCAACTTGTGTGGGCTTT--AAAG---AGGTGTCCTGCTCTTTGAGGACTGGAAA-ATG
* * * *
1043769 CCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTATTTGAGGACTGAAAG
60 CCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGGACTG-AAG
* * **
1043826 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCGCTCTTTGAGGACT-GAAGGTGCC
1 GTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCC
* * * * *
1043890 ACCAACTTGTGTCGGCTTTTAAAAAAAAAATGTGTCCCGCTCTTTGAGGATTGAAG
62 ACCAACTTGTGTGGGC-TTT------GAAAGGTGTCCTGCTCTTTGAGGACTGAAG
*
1043946 GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTCTGAGGACTGGAAAATGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
*
1044010 ACTTGTGTGGGCTTTGAAAGGAGTCCTGCTCTTTGAGGACTGAAG
66 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAG
*
1044055 GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTCTGAGGACTGGAAAATGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
* * *
1044119 ACTTGTGTAGGCTTTGAAAAGAGTCCTGCTCTTTGAGGACTGAAG
66 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAG
*
1044164 GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTCTGAGGACTGGAAAATGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
*
1044228 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA
66 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAG
* *
1044274 ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
*
1044338 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAA
66 ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAA
1044382 AAGCGGACGG
Statistics
Matches: 615, Mismatches: 42, Indels: 39
0.88 0.06 0.06
Matches are distributed among these distances:
109 237 0.39
110 125 0.20
111 2 0.00
112 2 0.00
115 50 0.08
116 43 0.07
118 3 0.00
119 45 0.07
120 80 0.13
121 24 0.04
122 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (110 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCA
ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAG
Found at i:1044273 original size:27 final size:27
Alignment explanation
Indices: 1044243--1044328 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1044233 TGTGGGCTTT
1044243 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1044270 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1044298 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1044325 GAAA
1 GAAA
1044329 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1045356 original size:1 final size:1
Alignment explanation
Indices: 1045346--1045418 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
1045336 CTTAAGCAGA
* * * * * * * **
1045346 TTTTTCTTTTTTTTTTTTCTCTTTTTCTTTGTTTTGTTTTTTTTTTGTTTTTTTTTTTTTTGCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1045411 TTTTTTTT
1 TTTTTTTT
1045419 GAAGAGAAGG
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:1045386 original size:16 final size:15
Alignment explanation
Indices: 1045346--1045418 Score: 85
Period size: 16 Copynumber: 4.7 Consensus size: 15
1045336 CTTAAGCAGA
1045346 TTTTTCTTTTTTTTT-
1 TTTTT-TTTTTTTTTG
* *
1045361 TTTCTCTTTTTCTTTG
1 TTT-TTTTTTTTTTTG
1045377 TTTTGTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
1045393 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
1045408 CTTTTTTTTTT
1 -TTTTTTTTTT
1045419 GAAGAGAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
15 23 0.46
16 27 0.54
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:1045418 original size:27 final size:28
Alignment explanation
Indices: 1045354--1045419 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
1045344 GATTTTTCTT
*
1045354 TTTTTTTTTTCTCTTTTTCTTTGTTTTG
1 TTTTTTTTTTGTCTTTTTCTTTGTTTTG
*
1045382 TTTTTTTTTTGT-TTTTT-TTTTTTTTG
1 TTTTTTTTTTGTCTTTTTCTTTGTTTTG
1045408 CTTTTTTTTTTG
1 -TTTTTTTTTTG
1045420 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 8 0.23
27 16 0.46
28 11 0.31
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (28 bp):
TTTTTTTTTTGTCTTTTTCTTTGTTTTG
Found at i:1054515 original size:2 final size:2
Alignment explanation
Indices: 1054508--1054538 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1054498 TGGATATTCC
1054508 CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1054539 AAAAGCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Done.