Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 136 of 136
Found at i:47383842 original size:23 final size:23
Alignment explanation
Indices: 47383816--47383863 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
47383806 TAAAAGTATC
47383816 TTAAATTTTTTTATTATTTTACT
1 TTAAATTTTTTTATTATTTTACT
47383839 TTAAATTTTTTTATTATTTTACT
1 TTAAATTTTTTTATTATTTTACT
47383862 TT
1 TT
47383864 GAAAAAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTAAATTTTTTTATTATTTTACT
Found at i:47390917 original size:170 final size:170
Alignment explanation
Indices: 47390635--47390945 Score: 405
Period size: 170 Copynumber: 1.8 Consensus size: 170
47390625 TTAGGTCTTT
47390635 CCTCTGAAAAGCTGGTCCCGAATCCTCATTTGAACATAAATGCTTTAGGTGGCTGATTTATCAAA
1 CCTCTGAAAAGCTGGTCCCGAATCCTCATTTGAACATAAATGCTTTAGGTGGCTGATTTATCAAA
** ** *
47390700 CCAATTAAGCTATCCAGACGCAACATTTATTTCCTTCTCAGTATATATAAACTTTTATTTTTGTT
66 CCAACCAAGCTATCCAGACGCAACATTTATACCCTTCTCAGTATATAT-AACTTTTATTCTTGTT
*
47390765 T-ACTATAATGTTGCTCTGTACCCCCCAATTGTTTTTTTCC
130 TAACCATAATGTTGCTCTGTACCCCCCAATTGTTTTTTTCC
** *
47390805 CCTCTGAAAAGCTGGTCCCGAATCCTCATTTGGGCATGAAATATGGTTTAGGT-G-T-ATTTATC
1 CCTCTGAAAAGCTGGTCCCGAATCCTCATTTGAACAT--AA-ATGCTTTAGGTGGCTGATTTATC
* * ** * * * *
47390867 AAACCAACCAAGTTTTCCTTACGGAACTTTTATACCCTTTTCCGTATATATAACTTTTATTCTTG
63 AAACCAACCAAGCTATCCAGACGCAACATTTATACCCTTCTCAGTATATATAACTTTTATTCTTG
47390932 TTTAACCATAATGT
128 TTTAACCATAATGT
47390946 CGTCTTTATT
Statistics
Matches: 120, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
169 16 0.13
170 90 0.75
171 1 0.01
172 3 0.03
173 10 0.08
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (170 bp):
CCTCTGAAAAGCTGGTCCCGAATCCTCATTTGAACATAAATGCTTTAGGTGGCTGATTTATCAAA
CCAACCAAGCTATCCAGACGCAACATTTATACCCTTCTCAGTATATATAACTTTTATTCTTGTTT
AACCATAATGTTGCTCTGTACCCCCCAATTGTTTTTTTCC
Found at i:47391723 original size:28 final size:27
Alignment explanation
Indices: 47391661--47391723 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 27
47391651 TTTAAGTAAT
*
47391661 TAATAAAATTATTTTTAAAAATTGATGA
1 TAAT-AAATTATTTTTAAAAATTAATGA
47391689 TATATAAATTATTTTTAAAAAGTTAAAT-A
1 TA-ATAAATTATTTTTAAAAA-TT-AATGA
47391718 TAATAA
1 TAATAA
47391724 TATATAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
28 22 0.71
29 7 0.23
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
TAATAAATTATTTTTAAAAATTAATGA
Found at i:47393568 original size:28 final size:29
Alignment explanation
Indices: 47393532--47393586 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
47393522 TTTAAGATTC
*
47393532 AGGATTCA-GGATTTAGGATTGGGGGTTCG
1 AGGATTCAGGGA-TTAGGATTCGGGGTTCG
*
47393561 AGGA-TCAGGGATTAGGGTTCGGGGTT
1 AGGATTCAGGGATTAGGATTCGGGGTT
47393587 TGGAGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.20, C:0.07, G:0.44, T:0.29
Consensus pattern (29 bp):
AGGATTCAGGGATTAGGATTCGGGGTTCG
Found at i:47393634 original size:13 final size:13
Alignment explanation
Indices: 47393616--47393640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47393606 GGTTCGGGGT
47393616 TTGGGGCTTGGGC
1 TTGGGGCTTGGGC
47393629 TTGGGGCTTGGG
1 TTGGGGCTTGGG
47393641 GTTTAGGGTT
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:0.00, C:0.12, G:0.56, T:0.32
Consensus pattern (13 bp):
TTGGGGCTTGGGC
Found at i:47393846 original size:33 final size:34
Alignment explanation
Indices: 47393794--47393860 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
47393784 CGTCTCGAGC
47393794 TTCTGTATCTTCAATTGGATCTGTTCCCGCTCCT
1 TTCTGTATCTTCAATTGGATCTGTTCCCGCTCCT
47393828 TTCTGTATC-TCAATTGGATCTGTTCCCGCTCCT
1 TTCTGTATCTTCAATTGGATCTGTTCCCGCTCCT
47393861 AATGAAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.73
34 9 0.27
ACGTcount: A:0.12, C:0.30, G:0.15, T:0.43
Consensus pattern (34 bp):
TTCTGTATCTTCAATTGGATCTGTTCCCGCTCCT
Found at i:47397133 original size:21 final size:21
Alignment explanation
Indices: 47397107--47397148 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
47397097 TCTACTTTGG
47397107 GGATATCCCGTCATATCCTAA
1 GGATATCCCGTCATATCCTAA
47397128 GGATATCCCGTCATATCCTAA
1 GGATATCCCGTCATATCCTAA
47397149 TCGGGATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
GGATATCCCGTCATATCCTAA
Found at i:47399528 original size:24 final size:24
Alignment explanation
Indices: 47399496--47399545 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
47399486 ATTGGAGCTG
47399496 AGCACATCATGATAGTAATATTTA
1 AGCACATCATGATAGTAATATTTA
47399520 AGCACATCATGATAGTAATATTTA
1 AGCACATCATGATAGTAATATTTA
47399544 AG
1 AG
47399546 AAATGATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (24 bp):
AGCACATCATGATAGTAATATTTA
Found at i:47426231 original size:15 final size:15
Alignment explanation
Indices: 47426211--47426239 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47426201 GTGATTAAAA
47426211 TGTAAGTATTCATGC
1 TGTAAGTATTCATGC
47426226 TGTAAGTATTCATG
1 TGTAAGTATTCATG
47426240 TTGTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
TGTAAGTATTCATGC
Found at i:47427027 original size:23 final size:23
Alignment explanation
Indices: 47426752--47427027 Score: 168
Period size: 23 Copynumber: 12.0 Consensus size: 23
47426742 AATTGAAGAA
* *
47426752 TTTAAATGCTGTGAATTGAAGTG
1 TTTAAATGCTGTAAATTGAGGTG
* * *
47426775 -TTAACGTGCTGCAAATTGAAGTG
1 TTTAA-ATGCTGTAAATTGAGGTG
* *
47426798 TTTAAATGTTGTAAATTGAAGTG
1 TTTAAATGCTGTAAATTGAGGTG
* ** * **
47426821 TTTTAAGTATTGCAAATTGAATTG
1 -TTTAAATGCTGTAAATTGAGGTG
** * * *
47426845 TTTAGTTGTTGGAAATTGAGATG
1 TTTAAATGCTGTAAATTGAGGTG
47426868 TTT--ATCGCTGT-AATTGAGGTG
1 TTTAAAT-GCTGTAAATTGAGGTG
* * *
47426889 TATAAATGTTGTTAATTG-GGATG
1 TTTAAATGCTGTAAATTGAGG-TG
* *
47426912 -TTAAAGTGTTGTAAGTTGAGGTG
1 TTTAAA-TGCTGTAAATTGAGGTG
*
47426935 TTTAAATGCTGTAAATTGAAGTG
1 TTTAAATGCTGTAAATTGAGGTG
* *
47426958 TTTAATTGCTGTAAATTAAGGTG
1 TTTAAATGCTGTAAATTGAGGTG
* * * *
47426981 CTCAAATGATGTAAATTGAAGTG
1 TTTAAATGCTGTAAATTGAGGTG
* * *
47427004 TTTAAGTGCTGCAAATTGTGGTG
1 TTTAAATGCTGTAAATTGAGGTG
47427027 T
1 T
47427028 ACAAATGAGT
Statistics
Matches: 198, Mismatches: 44, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
21 12 0.06
22 17 0.09
23 139 0.70
24 30 0.15
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (23 bp):
TTTAAATGCTGTAAATTGAGGTG
Found at i:47427035 original size:46 final size:46
Alignment explanation
Indices: 47426729--47427027 Score: 241
Period size: 46 Copynumber: 6.5 Consensus size: 46
47426719 TAAAGCCCTA
* * ** * *
47426729 TTTAAGTGTTGCAAATTGAAGAATTTAAATGCTGTGAATTGAAGTG
1 TTTAAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTG
*
47426775 -TTAACGTGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTG
1 TTTAA-GTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTG
** ** ** *
47426821 TTTTAAGTATTGCAAATTGAATTGTTTAGTTGTTGGAAATTG-AGATG
1 -TTTAAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAG-TG
* * * *
47426868 TTT-A-TCGCTG-TAATTGAGGTGTATAAATGTTGTTAATTG-GGATG
1 TTTAAGT-GCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAG-TG
* * * * *
47426912 TTAAAGTGTTGTAAGTTGAGGTGTTTAAATGCTGTAAATTGAAGTG
1 TTTAAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTG
* * * * * *
47426958 TTTAATTGCTGTAAATTAAGGTGCTCAAATGATGTAAATTGAAGTG
1 TTTAAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTG
*
47427004 TTTAAGTGCTGCAAATTGTGGTGT
1 TTTAAGTGCTGCAAATTGAGGTGT
47427028 ACAAATGAGT
Statistics
Matches: 201, Mismatches: 43, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
44 28 0.14
45 11 0.05
46 125 0.62
47 33 0.16
48 4 0.02
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (46 bp):
TTTAAGTGCTGCAAATTGAGGTGTTTAAATGTTGTAAATTGAAGTG
Done.