Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold385
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: 1395621
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 10
Found at i:1326969 original size:59 final size:58
Alignment explanation
Indices: 1326848--1326969 Score: 129
Period size: 59 Copynumber: 2.1 Consensus size: 58
1326838 TTTTTTGTTT
* * **** ** **
1326848 TTTTTTTTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTCCTTTTTTTTGTTTTGT
1 TTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTCCATTGCCATGTCATCA
1326906 TTTTTTCTTTTTCCTTTTTTTTTGTTTTGTTTTTTTCTTTTTCCAATTGCCATG-CATCA
1 TTTTTTCTTTTTCC-TTTTTTTTGTTTTGTTTTTTTCTTTTTCC-ATTGCCATGTCATCA
1326965 TTTTT
1 TTTTT
1326970 CCTCTTGTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 13 0.25
59 35 0.67
60 4 0.08
ACGTcount: A:0.04, C:0.12, G:0.07, T:0.77
Consensus pattern (58 bp):
TTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTCCATTGCCATGTCATCA
Found at i:1338200 original size:53 final size:53
Alignment explanation
Indices: 1338126--1338302 Score: 230
Period size: 53 Copynumber: 3.3 Consensus size: 53
1338116 TTTTCACCTT
* *
1338126 TTCCCTACTCGCCACCAAGGCGTTGCCTCACTAAATGACACCAAGTCACTATC
1 TTCCATACTCGCCACCAAGGCGTCGCCTCACTAAATGACACCAAGTCACTATC
* * * * *
1338179 TTCCTTACTCACCACTAAGGCGTCGCCTCACTAAATGACACCAAGTTACTATT
1 TTCCATACTCGCCACCAAGGCGTCGCCTCACTAAATGACACCAAGTCACTATC
* * *
1338232 TTCCATGCTCGCCACCAAGGCGTCACCTCACTAAGTGACACCAAGTCACTAT-
1 TTCCATACTCGCCACCAAGGCGTCGCCTCACTAAATGACACCAAGTCACTATC
* *
1338284 TCTCCCTAATCGCCACCAA
1 T-TCCATACTCGCCACCAA
1338303 TGGTGTCACT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 106 0.99
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (53 bp):
TTCCATACTCGCCACCAAGGCGTCGCCTCACTAAATGACACCAAGTCACTATC
Found at i:1338378 original size:53 final size:53
Alignment explanation
Indices: 1338307--1338456 Score: 183
Period size: 53 Copynumber: 2.8 Consensus size: 53
1338297 CACCAATGGT
* * *
1338307 GTCACTATTCACCATGATCGCCACTAAGACGTTGCCTCACTAAGTGACACCAA
1 GTCACTATTCTCCCTGATCGCCACCAAGACGTTGCCTCACTAAGTGACACCAA
* * * * *
1338360 GTCACTATCCTCCCTGATCACCACCAAAACGTCGCCTCATTAAGTGACACCAA
1 GTCACTATTCTCCCTGATCGCCACCAAGACGTTGCCTCACTAAGTGACACCAA
* * * * *
1338413 GTCATTATTCTCCCTAATCGCCACCAAGGCATTGTCTCACTAAG
1 GTCACTATTCTCCCTGATCGCCACCAAGACGTTGCCTCACTAAG
1338457 CATCACCAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
53 79 1.00
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (53 bp):
GTCACTATTCTCCCTGATCGCCACCAAGACGTTGCCTCACTAAGTGACACCAA
Found at i:1338416 original size:137 final size:137
Alignment explanation
Indices: 1338190--1338439 Score: 374
Period size: 137 Copynumber: 1.8 Consensus size: 137
1338180 TCCTTACTCA
* * ** * * **
1338190 CCACTAAGGCGTCGCCTCACTAAATGACACCAAGTTACTATTTTCCATGCTCGCCACCAAGGCGT
1 CCACTAAGACGTCGCCTCACTAAATGACACCAAGTCACTATCCTCCATGATCACCACCAAAACGT
1338255 CACCTCACTAAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAATGGTGTCACTATTCACC
66 CACCTCACTAAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAATGGTGTCACTATTCACC
1338320 ATGATCG
131 ATGATCG
* * *
1338327 CCACTAAGACGTTGCCTCACTAAGTGACACCAAGTCACTATCCTCCCTGATCACCACCAAAACGT
1 CCACTAAGACGTCGCCTCACTAAATGACACCAAGTCACTATCCTCCATGATCACCACCAAAACGT
* * *
1338392 CGCCTCATTAAGTGACACCAAGTCATTATTCTCCCTAATCGCCACCAA
66 CACCTCACTAAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAA
1338440 GGCATTGTCT
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
137 99 1.00
ACGTcount: A:0.28, C:0.35, G:0.13, T:0.23
Consensus pattern (137 bp):
CCACTAAGACGTCGCCTCACTAAATGACACCAAGTCACTATCCTCCATGATCACCACCAAAACGT
CACCTCACTAAGTGACACCAAGTCACTATTCTCCCTAATCGCCACCAATGGTGTCACTATTCACC
ATGATCG
Found at i:1341224 original size:32 final size:33
Alignment explanation
Indices: 1341166--1341227 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1341156 AGAAAATGTA
* *
1341166 TCGATATATTAATTAATGTATTGATACATTGTG
1 TCGATACATTAATTAATGTATCGATACATTGTG
*
1341199 TCGATACATT-ATTATTGTATCGATACATT
1 TCGATACATTAATTAATGTATCGATACATT
1341228 TGAGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (33 bp):
TCGATACATTAATTAATGTATCGATACATTGTG
Found at i:1344177 original size:21 final size:21
Alignment explanation
Indices: 1344151--1344199 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1344141 TTAATGTTAC
* *
1344151 GAGTTTCGTAGCTCAAAATAT
1 GAGTTTCGTAACTCAAAACAT
1344172 GAGTTTCGTAACTCAAAACAT
1 GAGTTTCGTAACTCAAAACAT
*
1344193 GGGTTTC
1 GAGTTTC
1344200 AATAGGTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (21 bp):
GAGTTTCGTAACTCAAAACAT
Found at i:1346852 original size:2 final size:2
Alignment explanation
Indices: 1346845--1346886 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1346835 AATTTTCATG
1346845 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1346887 TCAACCAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1347679 original size:3 final size:3
Alignment explanation
Indices: 1347648--1347691 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1347638 AATTCCATGG
* * * *
1347648 GCA GTA GCA GTA GCA GTA GCA GTA GCA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
1347692 TGCACCTGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.34, T:0.09
Consensus pattern (3 bp):
GCA
Found at i:1347691 original size:6 final size:6
Alignment explanation
Indices: 1347648--1347687 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1347638 AATTCCATGG
* *
1347648 GCAGTA GCAGTA GCAGTA GCAGTA GCAGCA GCAGCA GCAG
1 GCAGTA GCAGTA GCAGTA GCAGTA GCAGTA GCAGTA GCAG
1347688 CAGCTGCACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.10
Consensus pattern (6 bp):
GCAGTA
Found at i:1349748 original size:2 final size:2
Alignment explanation
Indices: 1349743--1349786 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1349733 TTAGTGTGTG
1349743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1349785 TA
1 TA
1349787 GTACATTCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1350575 original size:2 final size:2
Alignment explanation
Indices: 1350568--1350599 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1350558 TGTATATGAC
*
1350568 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1350600 GGATCTGAAG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1355896 original size:25 final size:25
Alignment explanation
Indices: 1355832--1355897 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 25
1355822 TAGCCACAAA
* *
1355832 TTTTGACAAATAAACAAGCCTCCAT
1 TTTTGACAAACAAACAAACCTCCAT
* *
1355857 ATTTGACAAATACAAAGAAACCAT-CAT
1 TTTTGAC-AA-ACAAACAAACC-TCCAT
1355884 TTTTGACAAACAAA
1 TTTTGACAAACAAA
1355898 TGAGTGGCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
25 11 0.33
26 4 0.12
27 17 0.52
28 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.26
Consensus pattern (25 bp):
TTTTGACAAACAAACAAACCTCCAT
Found at i:1357819 original size:21 final size:22
Alignment explanation
Indices: 1357781--1357826 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1357771 ATCTGTTGAA
* **
1357781 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1357802 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1357824 ACT
1 ACT
1357827 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1359080 original size:13 final size:13
Alignment explanation
Indices: 1359062--1359087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1359052 CAATTTTTTG
1359062 TGTATCGATACAT
1 TGTATCGATACAT
1359075 TGTATCGATACAT
1 TGTATCGATACAT
1359088 ACTTTGTGTA
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:1359099 original size:32 final size:33
Alignment explanation
Indices: 1359042--1359105 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1359032 TACAAGCCAA
**
1359042 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1359075 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1359106 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1359775 original size:39 final size:38
Alignment explanation
Indices: 1359719--1359807 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 38
1359709 TTTTCTTTCT
1359719 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATT--TACATTCTCC
*
1359759 CCCTTAA-T-AAGATAATTTTAGCAAATTTACATTCTCC
1 CCCTTAATTAAAG-TAATTTTAACAAATTTACATTCTCC
* *
1359796 CCTTTTATTAAA
1 CCCTTAATTAAA
1359808 AAATCTCCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 15 0.35
38 4 0.09
39 17 0.40
40 7 0.16
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.39
Consensus pattern (38 bp):
CCCTTAATTAAAGTAATTTTAACAAATTTACATTCTCC
Found at i:1360015 original size:23 final size:21
Alignment explanation
Indices: 1359983--1360025 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1359973 TTATAGATTA
*
1359983 AAAATTCAAAGTACAATGCAAAT
1 AAAATACAAAGT-CAA-GCAAAT
1360006 AAAATACAAAGTCAAGCAAA
1 AAAATACAAAGTCAAGCAAA
1360026 AACATTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAATACAAAGTCAAGCAAAT
Found at i:1361192 original size:21 final size:20
Alignment explanation
Indices: 1361163--1361205 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1361153 GGCTAGTGTG
* *
1361163 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1361184 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1361204 GG
1 GG
1361206 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1361664 original size:13 final size:13
Alignment explanation
Indices: 1361646--1361681 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1361636 ATAATCCCCC
*
1361646 TGTATCGATACAG
1 TGTATCGATACAA
1361659 TGTATCGATACAA
1 TGTATCGATACAA
1361672 TGTATCGATA
1 TGTATCGATA
1361682 TAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1363785 original size:15 final size:15
Alignment explanation
Indices: 1363765--1363795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1363755 ATTTCGTTTG
*
1363765 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1363780 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1363795 G
1 G
1363796 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1369807 original size:15 final size:15
Alignment explanation
Indices: 1369789--1369819 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1369779 GAAGATGTTG
1369789 ATGTTGCTGATGTCA
1 ATGTTGCTGATGTCA
1369804 ATGTTGCTGATGTCA
1 ATGTTGCTGATGTCA
1369819 A
1 A
1369820 ACTCATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
ATGTTGCTGATGTCA
Found at i:1370275 original size:27 final size:25
Alignment explanation
Indices: 1370216--1370277 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 25
1370206 TAGCCACAAA
* *
1370216 TTTTGACAAATAAACAAGCCTCCAT
1 TTTTGACAAATAAACAAACCACCAT
* *
1370241 ATTTGACAAATACAAAGAAACCACCAT
1 TTTTGACAAAT--AAACAAACCACCAT
1370268 TTTTGACAAA
1 TTTTGACAAA
1370278 CAAATGGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.33
27 20 0.67
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (25 bp):
TTTTGACAAATAAACAAACCACCAT
Found at i:1374979 original size:2 final size:2
Alignment explanation
Indices: 1374972--1375003 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1374962 TAACCCATAA
1374972 AT 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 AT
1375004 TTGTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1380949 original size:18 final size:18
Alignment explanation
Indices: 1380917--1380955 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1380907 AGTTAAAATC
*
1380917 AAAAGTTAACGATAAGTA
1 AAAAGTTAACGATAAGCA
**
1380935 AAAAGTTAATTATAAGCA
1 AAAAGTTAACGATAAGCA
1380953 AAA
1 AAA
1380956 TTAACTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (18 bp):
AAAAGTTAACGATAAGCA
Found at i:1388190 original size:35 final size:36
Alignment explanation
Indices: 1388145--1388215 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1388135 AGATATAAAC
* **
1388145 CTCCCTATC-TTTTCACGGGCTAAGATAGAACCTCT
1 CTCCCAATCTTTTTCAAAGGCTAAGATAGAACCTCT
1388180 CTCCCAATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CTCCCAATCTTTTTCAAAGGCTAAGATAGAACCTCT
1388216 TAATCACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.31
Consensus pattern (36 bp):
CTCCCAATCTTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:1389749 original size:21 final size:21
Alignment explanation
Indices: 1389725--1389782 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1389715 TTTATTAGTT
1389725 AACTCA-TCATTTTCATTTTGC
1 AACTCATTCATTTTC-TTTTGC
*
1389746 AACTCATTTC-TTTTCTTTTTC
1 AACTCA-TTCATTTTCTTTTGC
1389767 AACTCATTCATTTTCT
1 AACTCATTCATTTTCT
1389783 CCTCTAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 23 0.70
22 5 0.15
23 2 0.06
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.53
Consensus pattern (21 bp):
AACTCATTCATTTTCTTTTGC
Found at i:1391409 original size:32 final size:35
Alignment explanation
Indices: 1391364--1391455 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 35
1391354 CAACACTATC
1391364 TTTC-AAGGCTAAGATAGAAACCTC-CCT-ATC-T
1 TTTCAAAGGCTAAGATAGAAACCTCTCCTAATCTT
** * *
1391395 TTTCACGGGCTAAGACAGAACCTCTCTCCTAATCTT
1 TTTCAAAGGCTAAGATAGAAAC-CTCTCCTAATCTT
*
1391431 TTTCAAAGGTTAAGATAG-AACCTCT
1 TTTCAAAGGCTAAGATAGAAACCTCT
1391456 TAATCATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
31 4 0.09
32 13 0.28
33 3 0.06
34 7 0.15
35 5 0.11
36 15 0.32
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTCAAAGGCTAAGATAGAAACCTCTCCTAATCTT
Found at i:1391925 original size:63 final size:63
Alignment explanation
Indices: 1391846--1391971 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
1391836 ATTCATAATT
*
1391846 TATCGATACAAGCATTTGAAATTATAGCCGTTAGG-CTCAATACTATGCACATGAACAGTGATG
1 TATCGATACAAGCATTTGAAATTATAGCCATT-GGACTCAATACTATGCACATGAACAGTGATG
* * *
1391909 TATCGATACATGCATTTGAAATTATAGCCATTGGACTCAATACTATTCATATGAACAGTGATG
1 TATCGATACAAGCATTTGAAATTATAGCCATTGGACTCAATACTATGCACATGAACAGTGATG
1391972 CTTCTGTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 2 0.03
63 56 0.97
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (63 bp):
TATCGATACAAGCATTTGAAATTATAGCCATTGGACTCAATACTATGCACATGAACAGTGATG
Found at i:1394837 original size:51 final size:53
Alignment explanation
Indices: 1394777--1394963 Score: 168
Period size: 50 Copynumber: 3.6 Consensus size: 53
1394767 TAACTAGATG
* * * *
1394777 TATCGATACATTGAAGAATGTATCGATACATTTGGGTCAA-AA-CCAAAAATT
1 TATCGATACAATAAAAAATGTATCGATACATTTGGGTCAATAATCCAAAAATA
* * * * *
1394828 TATCGATACAATAAATAATGTATCGATATATTTAGGTCAATAATCCCATAATA
1 TATCGATACAATAAAAAATGTATCGATACATTTGGGTCAATAATCCAAAAATA
* * * ** * *
1394881 TATCGATACAATAAAAAATATATCGATACACTT-GG--ATTAATCTTAGAATG
1 TATCGATACAATAAAAAATGTATCGATACATTTGGGTCAATAATCCAAAAATA
* * *
1394931 TATCGATATAATAAAAAAAGTATCGATATATTT
1 TATCGATACAATAAAAAATGTATCGATACATTT
1394964 TCTTTCTAGA
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
50 38 0.34
51 35 0.31
52 4 0.04
53 35 0.31
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (53 bp):
TATCGATACAATAAAAAATGTATCGATACATTTGGGTCAATAATCCAAAAATA
Done.