Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1037
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: 37885
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:836 original size:86 final size:88
Alignment explanation
Indices: 670--837 Score: 220
Period size: 86 Copynumber: 1.9 Consensus size: 88
660 TTGATTTTAG
* *
670 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATATA
1 TAAATTCATATAAGAACA--TTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATATA
* *
735 TATTTATATTAATTATTAAATTGTA
64 TATTAATAATAATTATTAAATTGTA
760 TAAATTCATATAAGAA-A-TATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAAT-TA
1 TAAATTCATATAAGAACATTATTATCAAGAATTTTATGAAATTAT-ATA-TAATTATTAAATATA
821 TATGTAATAAT-ATTATT
64 TAT-TAATAATAATTATT
838 TTAAATTATA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
85 1 0.01
86 37 0.52
87 16 0.23
89 1 0.01
90 16 0.23
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (88 bp):
TAAATTCATATAAGAACATTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATATATA
TTAATAATAATTATTAAATTGTA
Found at i:911 original size:15 final size:16
Alignment explanation
Indices: 893--943 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
883 TTTATTAATC
893 ATTAT-TTTAAATAAA
1 ATTATATTTAAATAAA
*
908 ATTATATATTAATTAAA
1 ATTATAT-TTAAATAAA
925 A-TATATTT-AATAAA
1 ATTATATTTAAATAAA
939 ATTAT
1 ATTAT
944 GTATTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 10 0.32
16 6 0.19
17 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATTTAAATAAA
Found at i:924 original size:17 final size:16
Alignment explanation
Indices: 902--948 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
892 CATTATTTTA
902 AATAAAATTATATATT
1 AATAAAATTATATATT
918 AATTAAAA-TATAT-TT
1 AA-TAAAATTATATATT
*
933 AATAAAATTATGTATT
1 AATAAAATTATATATT
949 TATATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 9 0.33
17 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AATAAAATTATATATT
Found at i:950 original size:17 final size:16
Alignment explanation
Indices: 893--950 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 16
883 TTTATTAATC
*
893 ATTATT-TTAAATAAA
1 ATTATTATTTAATAAA
908 ATTA-TATATTAATTAAA
1 ATTATTAT-TTAA-TAAA
925 A-TA-TATTTAATAAA
1 ATTATTATTTAATAAA
939 ATTATGTATTTA
1 ATTAT-TATTTA
951 TATTTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 6 0.17
15 11 0.31
16 8 0.22
17 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTATTATTTAATAAA
Found at i:953 original size:23 final size:23
Alignment explanation
Indices: 926--1006 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 23
916 TTAATTAAAA
926 TATATTTAATAAAATTATGTATT
1 TATATTTAATAAAATTATGTATT
* * *
949 TATATTTATTAATATTATTTATT
1 TATATTTAATAAAATTATGTATT
*
972 AAATATATTAATAATAATTATGTTAATT
1 -TATAT-TTAATAA-AATTATG-T-ATT
1000 TATATTT
1 TATATTT
1007 TACAGATCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
23 20 0.44
24 4 0.09
25 6 0.13
26 7 0.16
27 5 0.11
28 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTTAATAAAATTATGTATT
Found at i:978 original size:26 final size:26
Alignment explanation
Indices: 882--980 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 26
872 TAATTATTAA
*
882 ATTTATTAATCATTA-TT-TTAAATAA
1 ATTTATTAAT-ATTATTTATTAAATAT
* *
907 AATTA-T-ATATTAATTA--AAATAT
1 ATTTATTAATATTATTTATTAAATAT
* * *
929 ATTTAATAAAATTATGTATT---TAT
1 ATTTATTAATATTATTTATTAAATAT
952 ATTTATTAATATTATTTATTAAATAT
1 ATTTATTAATATTATTTATTAAATAT
978 ATT
1 ATT
981 AATAATAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
22 13 0.23
23 25 0.45
24 8 0.14
25 4 0.07
26 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
ATTTATTAATATTATTTATTAAATAT
Found at i:983 original size:22 final size:22
Alignment explanation
Indices: 875--984 Score: 66
Period size: 22 Copynumber: 4.8 Consensus size: 22
865 TTAGTTATAA
*
875 TTATTAAATTTATTAATCATTA-
1 TTATTAAATATATTAAT-ATTAT
*
897 TT-TTAAATAAAATT-ATA-TAT
1 TTATTAAAT-ATATTAATATTAT
*
917 TAATTAAAATATATTTAATAAAATTAT
1 TTATT-AAATATA-TTAAT---ATTAT
* * *
944 GTATTTATATTTATTAATATTAT
1 TTA-TTAAATATATTAATATTAT
967 TTATTAAATATATTAATA
1 TTATTAAATATATTAATA
985 ATAATTATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
19 2 0.03
20 2 0.03
21 12 0.18
22 24 0.36
23 9 0.14
26 6 0.09
27 9 0.14
28 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (22 bp):
TTATTAAATATATTAATATTAT
Found at i:1091 original size:18 final size:17
Alignment explanation
Indices: 1063--1097 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1053 ATTATTAAGA
*
1063 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1080 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1098 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1340 original size:44 final size:44
Alignment explanation
Indices: 1262--1351 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
1252 ACCTCTATTC
* * *
1262 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
***
1306 CATTCAACCAAACAGTTGATTTACTA-TACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
1350 CA
1 CA
1352 CCTCTAATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 33 0.85
45 6 0.15
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:1352 original size:16 final size:16
Alignment explanation
Indices: 1331--1367 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1321 TTGATTTACT
1331 ATACACCTCTAATCCA
1 ATACACCTCTAATCCA
1347 ATACACCTCTAATCCA
1 ATACACCTCTAATCCA
1363 ATACA
1 ATACA
1368 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (16 bp):
ATACACCTCTAATCCA
Found at i:7136 original size:28 final size:29
Alignment explanation
Indices: 7081--7144 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 29
7071 CGCCTCATTA
7081 AAAACCTTACCAGGAAAACCCAATGGGAC
1 AAAACCTTACCAGGAAAACCCAATGGGAC
*
7110 AAAACCTTACTAGG-AAACCCAATGGGAC
1 AAAACCTTACCAGGAAAACCCAATGGGAC
7138 AAAACCT
1 AAAACCT
7145 CGGTTAAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.12
Consensus pattern (29 bp):
AAAACCTTACCAGGAAAACCCAATGGGAC
Found at i:7958 original size:43 final size:43
Alignment explanation
Indices: 7884--7993 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
7874 CATTTGCGGA
* * * *
7884 GCTTTTCCCACAAACGCCGTTATAGACCATGACCTTTAACGGC
1 GCTTTTACCACAAACGCCGCTAAAGAACATGACCTTTAACGGC
* *
7927 GCTTTTACCACAAATGCCGCTAAAGAACATGACCTTTAGCGGC
1 GCTTTTACCACAAACGCCGCTAAAGAACATGACCTTTAACGGC
7970 GC-TTTACCCACAAACGCCGCTAAA
1 GCTTTTA-CCACAAACGCCGCTAAA
7994 AGTACGTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 4 0.07
43 55 0.93
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (43 bp):
GCTTTTACCACAAACGCCGCTAAAGAACATGACCTTTAACGGC
Found at i:18168 original size:25 final size:26
Alignment explanation
Indices: 18121--18176 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
18111 TAATTATAAA
18121 TCATTTGCTAAATGAATTCCATTTCTC
1 TCATTTGCTAAATGAATTCCA-TTCTC
18148 TCATTT-CTAAATG-ATTCCATTCTC
1 TCATTTGCTAAATGAATTCCATTCTC
18172 T-ATTT
1 TCATTT
18177 TTATTTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.14
24 6 0.21
25 6 0.21
26 7 0.24
27 6 0.21
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.48
Consensus pattern (26 bp):
TCATTTGCTAAATGAATTCCATTCTC
Found at i:19535 original size:23 final size:23
Alignment explanation
Indices: 19509--19552 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19499 ATATTTCATA
* *
19509 AATAGATATAGATACAAATGCTT
1 AATAGATACAAATACAAATGCTT
19532 AATAGATACAAATACAAATGC
1 AATAGATACAAATACAAATGC
19553 ATAACAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (23 bp):
AATAGATACAAATACAAATGCTT
Found at i:19563 original size:23 final size:23
Alignment explanation
Indices: 19520--19564 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19510 ATAGATATAG
* * *
19520 ATACAAATGCTTAATAGATACAA
1 ATACAAATGCATAACAAATACAA
19543 ATACAAATGCATAACAAATACA
1 ATACAAATGCATAACAAATACA
19565 TAACAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.22
Consensus pattern (23 bp):
ATACAAATGCATAACAAATACAA
Found at i:30939 original size:12 final size:13
Alignment explanation
Indices: 30917--30945 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30907 GATTCATTCT
30917 ATAATTATAAAAA
1 ATAATTATAAAAA
30930 ATAA-TATAAAAA
1 ATAATTATAAAAA
30942 ATAA
1 ATAA
30946 AAAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAATTATAAAAA
Found at i:32588 original size:161 final size:161
Alignment explanation
Indices: 32318--32724 Score: 699
Period size: 161 Copynumber: 2.5 Consensus size: 161
32308 AGGTCGCACG
* * *
32318 AGTCAAATATTCAGTCATTTCAAAAAAAACAAAAGCATTAATTTTGTATTTTATTTTTCCGTTTC
1 AGTCAAATATTCAGCCATTTC--ATAAAACAAAAGCATTAATTTTGTATTTGATTTTT-CGTTTC
* *
32383 TTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCAAGAAAATATCAATG
63 TTTTAGTCATTAAATTTGGAATAATTATTAAACCGCCATTGCTTAAATGCAAGAAAATATCAATG
32448 TAATGTTTCAAAATGACATGAAAAGAAAGAGAAA
128 TAATGTTTCAAAATGACATGAAAAGAAAGAGAAA
*
32482 AGTCAAATATTCACCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
*
32547 TAGTCATTAAATTTGGAATAATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAA
66 TAGTCATTAAATTTGGAATAATTATTAAACCGCCATTGCTTAAATGCAAGAAAATATCAATGTAA
32612 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
131 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
*
32643 AGTCAAATATTCAGCCATTTCATATAACAAAAGCATTAATTTTGTATTTGATTTTTTC-TTTCTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGA-TTTTTCGTTTCTT
32707 TTAGTCATTAAATTTGGA
65 TTAGTCATTAAATTTGGA
32725 TTATTTTTTT
Statistics
Matches: 233, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
161 175 0.75
162 39 0.17
164 19 0.08
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (161 bp):
AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
TAGTCATTAAATTTGGAATAATTATTAAACCGCCATTGCTTAAATGCAAGAAAATATCAATGTAA
TGTTTCAAAATGACATGAAAAGAAAGAGAAA
Found at i:33537 original size:161 final size:161
Alignment explanation
Indices: 33269--33676 Score: 726
Period size: 161 Copynumber: 2.5 Consensus size: 161
33259 AGGTTGCACG
* * *
33269 AGTCAAATATTCAGTCATTTCAAAAAAACAAAAGCATTAATTTTGTATTTTATTTTTCGTTTCTT
1 AGTCAAATATTCAGCCATTTC-ATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTT
** *
33334 TTAGTCATTAAATTTGGATTAACTATTAAACCGCTCTTGCTTAAATGCAAGGAAATATCAATGTA
65 TTAGTCATTAAATTTGGATTAACTATTAAACCGCAATTGCTTAAATGCAAGAAAATATCAATGTA
33399 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
130 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
33431 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
* *
33496 TAGTCATTAAATTTGGATTAATTATTAAACCGCAATTGCTTAAATGCTAGAAAATATCAATGTAA
66 TAGTCATTAAATTTGGATTAACTATTAAACCGCAATTGCTTAAATGCAAGAAAATATCAATGTAA
33561 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
131 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
*
33592 AGTCAAATATTCAGCCATTCCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
33657 TAGTCATTAAATTTGGATTA
66 TAGTCATTAAATTTGGATTA
33677 TTTTTTCTGA
Statistics
Matches: 237, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
161 217 0.92
162 20 0.08
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (161 bp):
AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
TAGTCATTAAATTTGGATTAACTATTAAACCGCAATTGCTTAAATGCAAGAAAATATCAATGTAA
TGTTTCAAAATGACATGAAAAGAAAGAGAAA
Found at i:34342 original size:938 final size:938
Alignment explanation
Indices: 31783--34613 Score: 5003
Period size: 937 Copynumber: 3.0 Consensus size: 938
31773 AAAATTTTTG
* *
31783 TTATTTTTTCTGATTCAAACCTTATCCCTATTGGGTGGGCTTATACTATATTATTTGTAAACTTA
1 TTATTTTTTCTGATTCAAACCTTATCCATATTGGGTGGGCTTATAGTATATTATTTGTAAACTTA
* *
31848 TATCAAAATGAGTTTGTTGGTTCAAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAAT
66 TATCAAAATGAGTTTGCTGGTTCGAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAAT
* * * *
31913 CCTCACACGAGCATGGATGTTAATTTTTGTCTTGAATGTTTAATAGAATTTCGGTAAAGCTGAAA
131 CCTCACGCGAGCATGGATGTTAATTTTTGTCTTGAATGTCTAATAGAGTTTCGGTAGAGCTGAAA
*
31978 TTCTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAATTTTTATAGGATATGTTGTCATATTCTTTA
196 TTTTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAA--TTTATAGGATATGTTGTCATATTCTTTA
*
32043 CCTTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACATTTTCC
259 CCTTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCC
*
32108 CTTCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATTCTGGACACGGCCATGTGAT
324 CTTCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATTTTGGACACGGCCATGTGAT
* * *
32173 GGCGTGAGTGTGGCCGTGTGGGCCCACATGGGCATGTAGATTTTGGGCCAAGCCCTGTGGACCAC
389 GGCGTGAGTGTGGCCGTGTGGGCCCACATGGGCGTGTAGATTTTGGGCCAGGCCGTGTGGACCAC
* *
32238 ACGAGCAAGGCCAATTTGGGCGTGTGGGCCCACACGGCCATGTGGGCCCATAATTTTAAAATTTT
454 ACGAGCAAGGCCAATTTCGGCGTTTGGGCCCACACGGCCATGTGGGCCCATAATTTTAAAATTTT
32303 CCCTAAGGTCGCACGAGTCAAATATTCAGTCATTTCAAAAAAAACAAAAGCATTAATTTTGTATT
519 CCCTAAGGTCGCACGAGTCAAATATTCAGTCATTTC-AAAAAAACAAAAGCATTAATTTTGTATT
32368 TTATTTTTCCGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGC
583 TTATTTTT-CGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGC
*
32433 AAGAAAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCACCC
647 AAGAAAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCAGCC
32498 ATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGG
712 ATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGG
*
32563 AATAATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGTTTCAAAATGACAT
777 ATTAATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGTTTCAAAATGACAT
*
32628 GAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTTCATATAACAAAAGCATTAATTTTGTATTTG
842 GAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTG
32693 ATTTTTTC-TTTCTTTTAGTCATTAAATTTGGA
907 A-TTTTTCGTTTCTTTTAGTCATTAAATTTGGA
32725 TTATTTTTT-TGATTCAAACCTTATCCCA-ATTGGGTGGGCTTATAG--TA-TA-TTGTAAACTT
1 TTATTTTTTCTGATTCAAACCTTAT-CCATATTGGGTGGGCTTATAGTATATTATTTGTAAACTT
* *
32784 ATATCAAAATGAGTTTCCTGGTTCGAGTGGTAAGGAGTTAACTTGTTGGAGGTCTTGTGTTTAAA
65 ATATCAAAATGAGTTTGCTGGTTCGAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAA
* *
32849 TCCTCACGCGAGCATGGATGTAAATTTTTGTCTTGAATGTCTAATAGAGTTTCAGTAGAGCTGAA
130 TCCTCACGCGAGCATGGATGTTAATTTTTGTCTTGAATGTCTAATAGAGTTTCGGTAGAGCTGAA
* *
32914 ATTTTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAATTTATAAGATACGTTGTCATATTCTTTAC
195 ATTTTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAATTTATAGGATATGTTGTCATATTCTTTAC
*
32979 CTTTTATTTTTATTCTTTTAACTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCCC
260 CTTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCCC
* *
33044 TTCATGTCAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATCTCTTGCCTTTTGAATTCTGG
325 TTCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAA------------T---TT-TGG
* * * *
33109 ACACGGCCATGTGACGACGTGAGCGTGGCCGTGTGGGCCCACATTGGCGTGTAGATTTTGGGCCA
374 ACACGGCCATGTGATGGCGTGAGTGTGGCCGTGTGGGCCCACATGGGCGTGTAGATTTTGGGCCA
33174 GGCCGTGTGGACCACACGAGCAAGGCCAATTTCGGCGTTTGGGCCCACACGGCCATGTGGGCCCA
439 GGCCGTGTGGACCACACGAGCAAGGCCAATTTCGGCGTTTGGGCCCACACGGCCATGTGGGCCCA
*
33239 TAATTTTAAAATTTTCCCTAAGGTTGCACGAGTCAAATATTCAGTCATTTCAAAAAAACAAAAGC
504 TAATTTTAAAATTTTCCCTAAGGTCGCACGAGTCAAATATTCAGTCATTTCAAAAAAACAAAAGC
* *
33304 ATTAATTTTGTATTTTATTTTTCGTTTCTTTTAGTCATTAAATTTGGATTAACTATTAAACCGCT
569 ATTAATTTTGTATTTTATTTTTCGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCC
*
33369 CTTGCTTAAATGCAAGGAAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGT
634 CTTGCTTAAATGCAAGAAAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGT
33434 CAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAG
699 CAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAG
*
33499 TCATTAAATTTGGATTAATTATTAAACCGCAATTGCTTAAATGCTAGAAAATATCAATGTAATGT
764 TCATTAAATTTGGATTAATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGT
*
33564 TTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTCCATAAAACAAAAGCATT
829 TTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTTCATAAAACAAAAGCATT
33629 AATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGGA
894 AATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGGA
33674 TTATTTTTTCTGATTCAAACCTTATCCATATTGGGTGGGCTTATAGTATATTATTTGTAAACTTA
1 TTATTTTTTCTGATTCAAACCTTATCCATATTGGGTGGGCTTATAGTATATTATTTGTAAACTTA
*
33739 TATCAAAATGATTTTGCTGGTTCGAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAAT
66 TATCAAAATGAGTTTGCTGGTTCGAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAAT
*
33804 CCTCATGCGAGCATGGATGTTAATTTTTGTCTTGAATGTCTAATAGAGTTTCGGTAGAGCTGAAA
131 CCTCACGCGAGCATGGATGTTAATTTTTGTCTTGAATGTCTAATAGAGTTTCGGTAGAGCTGAAA
*
33869 TTTTGAATTTTTAGAAGGTTAGAGGGGAGAGGAAATTTATAGGATATGTTGTCATATTCTTTACC
196 TTTTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAATTTATAGGATATGTTGTCATATTCTTTACC
33934 TTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCCCT
261 TTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCCCT
33999 TCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATTTTGGACACGGCCATGTGATGG
326 TCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATTTTGGACACGGCCATGTGATGG
34064 CGTGAGTGTGGCCGTGTGGGCCCACATGGGCGTGTAGATTTTGGGCCAGGCCGTGTGGACCACAC
391 CGTGAGTGTGGCCGTGTGGGCCCACATGGGCGTGTAGATTTTGGGCCAGGCCGTGTGGACCACAC
*
34129 GAGCAAGGCCAATTTCGGCATTTGGGCCCACACGGCCATGTGGGCCCATAATTTTAAAATTTTCC
456 GAGCAAGGCCAATTTCGGCGTTTGGGCCCACACGGCCATGTGGGCCCATAATTTTAAAATTTTCC
*
34194 CTAGGGTCGCACGAGTCAAATATTCAGTCATTTCAAAAAAACAAAAGCATTAATTTTGTATTTTA
521 CTAAGGTCGCACGAGTCAAATATTCAGTCATTTCAAAAAAACAAAAGCATTAATTTTGTATTTTA
34259 TTTTTCGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCAAGA
586 TTTTTCGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCAAGA
* *
34324 AAATATCAATGTAATGTTTAAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTTAGCCATTT
651 AAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTT
34389 CATAAAAC-AAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGGATTA
716 CATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGGATTA
34453 ATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGTTTCAAAATGACATGAAA
781 ATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGTTTCAAAATGACATGAAA
34518 AGAAAGAGAAAAGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTT
846 AGAAAGAGAAAAGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTT
34583 TTCGTTTCTTTTAGTCATTAAATTTGGA
911 TTCGTTTCTTTTAGTCATTAAATTTGGA
34611 TTA
1 TTA
34614 ATTATTAAAC
Statistics
Matches: 1801, Mismatches: 64, Indels: 53
0.94 0.03 0.03
Matches are distributed among these distances:
935 131 0.07
937 380 0.21
938 343 0.19
939 4 0.00
941 31 0.02
942 12 0.01
947 1 0.00
948 6 0.00
949 345 0.19
950 69 0.04
951 174 0.10
952 2 0.00
953 2 0.00
954 301 0.17
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (938 bp):
TTATTTTTTCTGATTCAAACCTTATCCATATTGGGTGGGCTTATAGTATATTATTTGTAAACTTA
TATCAAAATGAGTTTGCTGGTTCGAGTGGTAAGGAGTTAGCTTGTTGGAGGTCTTGTGTTTAAAT
CCTCACGCGAGCATGGATGTTAATTTTTGTCTTGAATGTCTAATAGAGTTTCGGTAGAGCTGAAA
TTTTGAATTGTTAGAAGGTTAGAGGGGAGAGGAAATTTATAGGATATGTTGTCATATTCTTTACC
TTTTATTTTTATTCTTTTATCTTTTTCTCTCACCTTTAAAAATCCCTAAATTTGACGTTTTCCCT
TCATATTAATTGGCACAATCCCTTTTTCCCTTGCCTTTTGAATTTTGGACACGGCCATGTGATGG
CGTGAGTGTGGCCGTGTGGGCCCACATGGGCGTGTAGATTTTGGGCCAGGCCGTGTGGACCACAC
GAGCAAGGCCAATTTCGGCGTTTGGGCCCACACGGCCATGTGGGCCCATAATTTTAAAATTTTCC
CTAAGGTCGCACGAGTCAAATATTCAGTCATTTCAAAAAAACAAAAGCATTAATTTTGTATTTTA
TTTTTCGTTTCTTTTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCAAGA
AAATATCAATGTAATGTTTCAAAATGACATGAAAAGAAAGAGAAAAGTCAAATATTCAGCCATTT
CATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTTTAGTCATTAAATTTGGATTA
ATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAATGTTTCAAAATGACATGAAA
AGAAAGAGAAAAGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTT
TTCGTTTCTTTTAGTCATTAAATTTGGA
Found at i:34639 original size:161 final size:161
Alignment explanation
Indices: 34207--35252 Score: 1598
Period size: 161 Copynumber: 6.6 Consensus size: 161
34197 GGGTCGCACG
* * *
34207 AGTCAAATATTCAGTCATTTCAAAAAAACAAAAGCATTAATTTTGTATTTTATTTTTCGTTTCTT
1 AGTCAAATATTCAGCCATTTC-ATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTT
*
34272 TTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCAAGAAAATATCAATGTA
65 TTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTA
*
34337 ATGTTTAAAAATGACATGAAAAGAAAGAGAAA
130 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
*
34369 AGTCAAATATTTAGCCATTTCATAAAAC-AAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
*
34433 TAGTCATTAAATTTGGATTAATTATTAAACCGCCATTGCTTAAATGCTAGAAAATATCAATGTAA
66 TAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTAA
34498 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
131 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
34529 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
**
34594 TAGTCATTAAATTTGGATTAATTATTAAACCGCTATTGCTTAAATGCTAGAAAATATCAATGTAA
66 TAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTAA
*
34659 TGTTTCAAAATAACATGAAAAGAAAGAGAAA
131 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
* ** *
34690 AGTCATATATTCAGCCATTTCA-AAAATTGAAAGCATTAATTTTGTATTTGATTTTTCATTTCTT
1 AGTCAAATATTCAGCCATTTCATAAAA-CAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTT
* * *
34754 TTAGTCATTAAATTTGGACTAATTATTAAACCGCCCTTGCTTAAATGCTGGAAAATATGAATGTA
65 TTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTA
34819 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
130 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
* * *
34851 AGTCAAACATTCAGCAATTTCA-AAAACAAAAGCATTAATTTTTGTGTTTGATTTTTCGTTTCTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAA-TTTTGTATTTGATTTTTCGTTTCTT
34915 TTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTA
65 TTAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTA
34980 ATGTTTCAAAATGACATGAAAAGAAAGAG-AA
130 ATGTTTCAAAATGACATGAAAAGAAAGAGAAA
* * *
35011 AGTCAAATATTCTGTCA-TT--T-AAA-AAAA-CATTAATTTTGTATTTGATTTTCCGTTTCTTT
1 AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
* * * * *
35070 TAGTCATTAAATTTAGATTAAGTATTAAATCTCCCTTGTTTAAATGCTAGAAAATATCAATGTAA
66 TAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTAA
*
35135 TG-TTAAAAATGACATGAAAAGAAAGAGAAA
131 TGTTTCAAAATGACATGAAAAGAAAGAGAAA
* * * * ** * *
35165 AGTCAAATA-TCAACCATTTCAAAAAATATATA-TTTTACTTTTGTATTTGATTTTT-GTTTCTC
1 AGTCAAATATTCAGCCATTTCATAAAACA-AAAGCATTAATTTTGTATTTGATTTTTCGTTTCTT
* * *
35227 TTAGACATTAAATTTGCATTGATTAT
65 TTAGTCATTAAATTTGGATTAATTAT
35253 CAAATCACCT
Statistics
Matches: 816, Mismatches: 57, Indels: 26
0.91 0.06 0.03
Matches are distributed among these distances:
153 28 0.03
154 99 0.12
155 6 0.01
156 4 0.00
157 6 0.01
158 28 0.03
159 23 0.03
160 184 0.23
161 419 0.51
162 19 0.02
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (161 bp):
AGTCAAATATTCAGCCATTTCATAAAACAAAAGCATTAATTTTGTATTTGATTTTTCGTTTCTTT
TAGTCATTAAATTTGGATTAATTATTAAACCGCCCTTGCTTAAATGCTAGAAAATATCAATGTAA
TGTTTCAAAATGACATGAAAAGAAAGAGAAA
Done.