Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1651
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: 39213
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:815 original size:17 final size:19
Alignment explanation
Indices: 775--816 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
765 ATAAATGGGT
*
775 CATTACGCATTTTATATCA
1 CATTAAGCATTTTATATCA
794 CATTAAGCA-TTTATAT-A
1 CATTAAGCATTTTATATCA
811 CATTAA
1 CATTAA
817 TTTACATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 8 0.36
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (19 bp):
CATTAAGCATTTTATATCA
Found at i:3686 original size:22 final size:22
Alignment explanation
Indices: 3658--3700 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3648 GTGTTTTGTT
*
3658 GAGAAAATCAAGGAGAGGATTG
1 GAGAAAAGCAAGGAGAGGATTG
3680 GAGAAAAGCAAGGAGAGGATT
1 GAGAAAAGCAAGGAGAGGATT
3701 ATGGAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.37, T:0.12
Consensus pattern (22 bp):
GAGAAAAGCAAGGAGAGGATTG
Found at i:5813 original size:40 final size:40
Alignment explanation
Indices: 5758--5973 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
5748 CGGATGGTAA
* *
5758 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
5798 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
5837 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
5877 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
5917 CCGGGCTAAGTCCCGAAGGCATTTGAG-GAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
5956 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
5974 TACTTGGTTT
Statistics
Matches: 170, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
38 17 0.10
39 47 0.28
40 106 0.62
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:5889 original size:79 final size:80
Alignment explanation
Indices: 5758--5973 Score: 343
Period size: 79 Copynumber: 2.7 Consensus size: 80
5748 CGGATGGTAA
* *
5758 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
5822 GTGC-AGTTACTATAT
65 GTGCGAGTTACTATAT
5837 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
5902 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
* *
5917 CCGGGCTAAGTCCCGAAGGCATTTGAG-GAG-TAGCTATATCC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
5974 TACTTGGTTT
Statistics
Matches: 130, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
78 17 0.13
79 75 0.58
80 38 0.29
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:14006 original size:40 final size:40
Alignment explanation
Indices: 13912--14092 Score: 176
Period size: 40 Copynumber: 4.5 Consensus size: 40
13902 TATTCGAATG
*
13912 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* * *
13953 ATAAT-CGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTG-CT
1 AT-ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAG-TGACT
* *
13993 ATATCTGGGCTAAGTCCCGAAGGCATTTTTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
14033 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CT
*
14072 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
14093 ATTACTTGAG
Statistics
Matches: 116, Mismatches: 17, Indels: 17
0.77 0.11 0.11
Matches are distributed among these distances:
38 14 0.12
39 20 0.17
40 52 0.45
41 27 0.23
42 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:17040 original size:40 final size:40
Alignment explanation
Indices: 16983--17160 Score: 247
Period size: 40 Copynumber: 4.5 Consensus size: 40
16973 CGGATGGTAA
*
16983 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATA-T
*
17023 CTGGGCTAAGTCCCGAAGGCATTTGTG-TAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAT
*
17063 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
* *
17103 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CTATAT
*
17143 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
17161 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
39 18 0.14
40 109 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
Found at i:18986 original size:26 final size:27
Alignment explanation
Indices: 18956--19033 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 27
18946 GCCAATAAAC
*
18956 CAATATCGCAGTAAAACTGCCAGTAAT
1 CAATATCGCAGCAAAACTGCCAGTAAT
* *
18983 -AATATCGCAGCAAAGCTGCTAGT-AT
1 CAATATCGCAGCAAAACTGCCAGTAAT
* *
19008 CAGTAACGCAGCAAAACTGCCAGTAA
1 CAATATCGCAGCAAAACTGCCAGTAA
19034 CAAAATATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 39 0.93
27 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (27 bp):
CAATATCGCAGCAAAACTGCCAGTAAT
Found at i:27059 original size:37 final size:36
Alignment explanation
Indices: 26999--27090 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
26989 TCCCCACGCG
*
26999 TAGTTATCGGGTCTTACCTGGACAAAATCTCCACACA
1 TAGTCATCGGGTCTTACC-GGACAAAATCTCCACACA
* * **
27036 TAGTCATCGGGTCTTACTCGGACATAATCTCCTCATG
1 TAGTCATCGGGTCTTAC-CGGACAAAATCTCCACACA
27073 TAGTCATCGGGTCTTACC
1 TAGTCATCGGGTCTTACC
27091 CGGAATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.02
37 47 0.96
38 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (36 bp):
TAGTCATCGGGTCTTACCGGACAAAATCTCCACACA
Found at i:27293 original size:48 final size:48
Alignment explanation
Indices: 27231--27990 Score: 1226
Period size: 48 Copynumber: 15.9 Consensus size: 48
27221 CACAATATAC
* * *
27231 ACATATCTCCTACATATTTCACACTAGTCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27279 ACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
* * *
27327 ACATATCTCATTCATATTTCACACTAGCCATTCAGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
* * *
27375 ACATATCTTATATATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27423 ACATATCTCATACATATTTCACAGTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27471 ACATATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27519 ACATATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
* *
27567 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACGTAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27615 ACATA--T-AT--ATATTTCACATTAGCCATTCGGCTTTACCACGTAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
* *
27658 ACATATCTTATACATATTTCACATTAACCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27706 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
* *
27754 ACATATCTCATATATATTTCACACTAGCCATTCGG-TCTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCT-TTACCACATAT
** *
27802 ACATATCTCCCACATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27850 ACATATCTCAGACATATTTCACATTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27898 ACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
*
27946 ACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACA
1 ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
27991 CACATATATA
Statistics
Matches: 673, Mismatches: 32, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
43 40 0.06
45 3 0.00
46 3 0.00
47 1 0.00
48 625 0.93
49 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATAT
Found at i:29659 original size:27 final size:27
Alignment explanation
Indices: 29620--29797 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29610 CCATTGAGTC
* * * *
29620 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29647 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29674 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29702 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29729 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29756 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29783 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29798 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29759 original size:82 final size:81
Alignment explanation
Indices: 29641--29796 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29631 TGCTATATAA
* *
29641 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29706 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29723 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29787 CACTTAGTGC
65 CACTTAGTGC
29797 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:33574 original size:17 final size:18
Alignment explanation
Indices: 33541--33575 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33531 GAAAAGAATG
*
33541 AAAGGGCTTTTAGGGTTT
1 AAAGGGCTTTTAAGGTTT
33559 AAAGGG-TTTTAAGGTTT
1 AAAGGGCTTTTAAGGTTT
33576 TTGAGAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.40
Consensus pattern (18 bp):
AAAGGGCTTTTAAGGTTT
Found at i:38299 original size:26 final size:26
Alignment explanation
Indices: 38270--38359 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 26
38260 CCCCAAAATA
38270 GGTAAAATGATCGTAATACCCTGTAG
1 GGTAAAATGATCGTAATACCCTGTAG
* * * *
38296 GGTAAAATAATTGTAATGCCCCGGTAG
1 GGTAAAATGATCGTAAT-ACCCTGTAG
* * **
38323 GGTAAAATGACCGAAATACCCATGTTT
1 GGTAAAATGATCGTAATACCC-TGTAG
38350 GGTAAAATGA
1 GGTAAAATGA
38360 AGATTATGCC
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
26 18 0.36
27 32 0.64
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (26 bp):
GGTAAAATGATCGTAATACCCTGTAG
Found at i:38329 original size:27 final size:26
Alignment explanation
Indices: 38270--38330 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
38260 CCCCAAAATA
* *
38270 GGTAAAATGATCGTAATACCCTGTAG
1 GGTAAAATAATCGTAATACCCGGTAG
* *
38296 GGTAAAATAATTGTAATGCCCCGGTAG
1 GGTAAAATAATCGTAAT-ACCCGGTAG
38323 GGTAAAAT
1 GGTAAAAT
38331 GACCGAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (26 bp):
GGTAAAATAATCGTAATACCCGGTAG
Found at i:38805 original size:33 final size:33
Alignment explanation
Indices: 38762--38827 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
38752 CTTAGCCCAC
*
38762 ACTGTTACTGTATAGGGCTAAAGCCCAGACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAGACTGT
38795 ACTGATACTGTATAGGGCTAAAGCCCAGACTGT
1 ACTGATACTGTATAGGGCTAAAGCCCAGACTGT
38828 GTTATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (33 bp):
ACTGATACTGTATAGGGCTAAAGCCCAGACTGT
Done.