Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold8123.1
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: 5523
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:936 original size:39 final size:39
Alignment explanation
Indices: 882--964 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
872 AGGTAGGTAT
*
882 CCAAGACAGAGGAGGTGAGCCATGAAGGTTGCCTAAGTA
1 CCAAGACAGAGGAGGTGAGCCATGAAGGCTGCCTAAGTA
921 CCAAGACAGAGGAGGTGAGCCATGAAGGCTGCCTAAGTA
1 CCAAGACAGAGGAGGTGAGCCATGAAGGCTGCCTAAGTA
960 CCAAG
1 CCAAG
965 CTCTTTGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.33, T:0.13
Consensus pattern (39 bp):
CCAAGACAGAGGAGGTGAGCCATGAAGGCTGCCTAAGTA
Found at i:1523 original size:31 final size:31
Alignment explanation
Indices: 1482--1545 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1472 CCTTTTCATA
*
1482 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
1513 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
1544 TT
1 TT
1546 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:1842 original size:23 final size:24
Alignment explanation
Indices: 1753--1857 Score: 167
Period size: 24 Copynumber: 4.4 Consensus size: 24
1743 CTGGAGGCCT
*
1753 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
1778 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
1802 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
1826 AGCCC-TTTAATAACTGGGGCCTA
1 AGCCCTTTTAATAACTGGGGCATA
1849 AGCCCTTTT
1 AGCCCTTTT
1858 GCACTTCCTC
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 21 0.28
24 50 0.67
25 4 0.05
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:1853 original size:47 final size:48
Alignment explanation
Indices: 1743--1858 Score: 173
Period size: 47 Copynumber: 2.4 Consensus size: 48
1733 TATCATATAT
*
1743 CTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAA
1 CTGG-GGCCTAAGCC-CTTTTGATAACTGGGGCAAAAGCCCTTTTAATAA
* *
1792 CTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAA
1 CTGGGGCCTAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTAATAA
1839 CTGGGGCCTAAGCCCTTTTG
1 CTGGGGCCTAAGCCCTTTTG
1859 CACTTCCTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
47 27 0.44
48 27 0.44
49 8 0.13
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
CTGGGGCCTAAGCCCTTTTGATAACTGGGGCAAAAGCCCTTTTAATAA
Found at i:1929 original size:9 final size:9
Alignment explanation
Indices: 1915--1971 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
1905 ATCTCATGTT
1915 CATATCATA
1 CATATCATA
*
1924 CATATCATGTG
1 CATATCA--TA
1935 CATATCATA
1 CATATCATA
* *
1944 CATGTCATGTG
1 CATATCA--TA
1955 CATATCATA
1 CATATCATA
1964 CATATCAT
1 CATATCAT
1972 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:1931 original size:20 final size:20
Alignment explanation
Indices: 1903--1973 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1893 GCATTTATGA
* *
1903 ACATCTCATGTTCATATCAT
1 ACATATCATGTGCATATCAT
1923 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
1943 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
1963 ACATATCATGT
1 ACATATCATGT
1974 TTATCAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:3524 original size:27 final size:27
Alignment explanation
Indices: 3286--3524 Score: 169
Period size: 27 Copynumber: 8.8 Consensus size: 27
3276 TTTCATCCTA
* * * *
3286 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
* * **
3313 CAAAGGTATTTCAGTAATTTTTTAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
* * *
3340 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTACAAA-C
* * ** *
3369 CAAGGCTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTACAAAC
* *
3396 C-AGGGCTATTTTAGTAATTTCACAAAT
1 CAAGGG-TATTTTAGTAATTTTACAAAC
** ** *
3423 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
*
3450 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
* * *
3477 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAAC
3504 CAAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTTAGTAATTTT
3525 GTAAATCGAG
Statistics
Matches: 169, Mismatches: 36, Indels: 14
0.77 0.16 0.06
Matches are distributed among these distances:
26 4 0.02
27 133 0.79
28 18 0.11
29 14 0.08
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTACAAAC
Found at i:3524 original size:54 final size:54
Alignment explanation
Indices: 3397--3538 Score: 187
Period size: 54 Copynumber: 2.6 Consensus size: 54
3387 TTTGTAAATC
* *
3397 AGGGCTATTTTAGTAATTTCACAAATTGAGGGTATTTCGGTAATTTCACAAACCA
1 AGGG-TATTTTAGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCA
* * *
3452 AGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTTACAAACCA
1 AGGGTATTTTAGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTTCACAAACCA
** *
3506 AGGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 AGGGTATTTTAGTAATTTTACAAATAGAGGGTA
3539 AAACAGTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 68 0.89
55 6 0.08
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCA
Found at i:3536 original size:27 final size:27
Alignment explanation
Indices: 3317--3592 Score: 146
Period size: 27 Copynumber: 10.1 Consensus size: 27
3307 ACAAACCAAA
* * * *
3317 GGTATTTCAGTAATTTTTTAAACCAAT
1 GGTATTTTAGTAATTTTATAAATCAAG
*
3344 GGTATTTCTA-TAATTTTTAGAAAGTCAAG
1 GGTATTT-TAGTAA-TTTTATAAA-TCAAG
* * *
3373 GCTATTTCT-GTAACTTTGTAAATC-AG
1 GGTATTT-TAGTAATTTTATAAATCAAG
* * **
3399 GGCTATTTTAGTAATTTCACAAATTGAG
1 GG-TATTTTAGTAATTTTATAAATCAAG
** * * *
3427 GGTATTTCGGTAATTTCACAAACCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
* * *
3454 GGTATTTTGGTAATTTTACAAA-CTAGG
1 GGTATTTTAGTAATTTTATAAATC-AAG
* * *
3481 GGTATTTTGGTAATTTTACAAACCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
* *
3508 GGTATTTTAGTAATTTTGTAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
**** * *
3535 GGTAAAACAGTAATTCTGTAAATCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
*** * *
3562 GGTAAAATAGTAATTCTATAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
3589 GGTA
1 GGTA
3593 AAACGGTAAT
Statistics
Matches: 202, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
26 5 0.02
27 164 0.81
28 19 0.09
29 14 0.07
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTATAAATCAAG
Found at i:3548 original size:54 final size:54
Alignment explanation
Indices: 3489--3711 Score: 205
Period size: 54 Copynumber: 4.1 Consensus size: 54
3479 GGGGTATTTT
*** *
3489 GGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTTTACAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAAC
* * ** * *
3543 AGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAAC
1 GGTAATTTTACAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAAC
* * * * *
3597 GGTAATTTTGCAAATCAAGGGTAAAACAGTAATTTTGTAAGTCGAGGGTAAAAC
1 GGTAATTTTACAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAAC
* * ** * * * * * *
3651 GATAATTATGTAAATCAGGGGTAAAA-CGATAATTATGTAAATCGGGGGTAAAAC
1 GGTAATTTTACAAACCAAGGGTAAAATAG-TAATTTTATAAATCGAGGGTAAAAC
3705 GGTAATT
1 GGTAATT
3712 CTGTAAATCG
Statistics
Matches: 142, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 1 0.01
54 141 0.99
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (54 bp):
GGTAATTTTACAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAAC
Found at i:3565 original size:81 final size:81
Alignment explanation
Indices: 3488--3781 Score: 232
Period size: 81 Copynumber: 3.6 Consensus size: 81
3478 AGGGGTATTT
** *
3488 TGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTG
1 TGGTAATTTTACAAACCAAGGGTATTACAGTAATTTTGCAAATCGAGGGTAAAACAGTAATTCTG
*
3553 TAAATCAAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * * * * ** * * *
3569 TAGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGCAAATCAAGGGTAAAACAGTAATTTTG
1 TGGTAATTTTACAAACCAAGGGTATTACAGTAATTTTGCAAATCGAGGGTAAAACAGTAATTCTG
*
3634 TAAGTCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * * ** * * ** * * * *
3650 CGATAATTATGTAAATCAGGGGTAAAAC-GATAATTATGTAAATCGGGGGTAAAACGGTAATTCT
1 TGGTAATTTTACAAACCAAGGGTATTACAG-TAATTTTGCAAATCGAGGGTAAAACAGTAATTCT
* ***
3714 GTAAATCGGGGGTACTT
65 GTAAATCGAGGGTAAAA
* * * *
3731 TGGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTACAAATCGAGGGTA
1 TGGTAATTTTACAA-ACCAAGGGTATTACAGTAATTTTGCAAATCGAGGGTA
3782 TTTCAGTATT
Statistics
Matches: 161, Mismatches: 49, Indels: 6
0.75 0.23 0.03
Matches are distributed among these distances:
80 1 0.01
81 158 0.98
82 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (81 bp):
TGGTAATTTTACAAACCAAGGGTATTACAGTAATTTTGCAAATCGAGGGTAAAACAGTAATTCTG
TAAATCGAGGGTAAAA
Found at i:3593 original size:27 final size:27
Alignment explanation
Indices: 3516--3727 Score: 241
Period size: 27 Copynumber: 7.9 Consensus size: 27
3506 AGGGTATTTT
*
3516 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
3543 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
3570 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * * *
3597 GGTAATTTTGCAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
3624 AGTAATTTTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
3651 -GATAATTATGTAAATC-AGGGGTAAAAC
1 AG-TAATTCTGTAAATCGA-GGGTAAAAC
* *
3678 -GATAATTATGTAAATCGGGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* *
3705 GGTAATTCTGTAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
3728 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 2 0.01
27 159 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:3727 original size:54 final size:54
Alignment explanation
Indices: 3516--3720 Score: 286
Period size: 54 Copynumber: 3.8 Consensus size: 54
3506 AGGGTATTTT
* *
3516 AGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
* * * *
3570 AGTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGCAAATCAAGGGTAAAAC
1 AGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
* * * *
3624 AGTAATTTTGTAAGTCGAGGGTAAAACGATAATTATGTAAATCAGGGGTAAAAC
1 AGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
* *
3678 -GATAATTATGTAAATCGGGGGTAAAACGGTAATTCTGTAAATC
1 AG-TAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC
3721 GGGGGTACTT
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.01
54 131 0.99
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
AGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAAC
Found at i:3754 original size:27 final size:27
Alignment explanation
Indices: 3733--3822 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
3723 GGGTACTTTG
*
3733 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
3760 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* *
3787 GTATTTTTAC-AATCTAAGGGTATTTCA
1 GTAATTTTACAAATCGAA-GGTATTTCA
*
3814 TTAATTTTA
1 GTAATTTTA
3823 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 5 0.09
27 50 0.91
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:3764 original size:54 final size:54
Alignment explanation
Indices: 3706--3819 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 54
3696 GGGTAAAACG
** * *
3706 GTAATTCTGTAAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTTCA
1 GTAATTCTACAAATCGAGGGTA-TTTCAGTAATTTTACAA-TCGAAGGGTATTTCA
* * *
3760 GTAATTTTACAAATCGAGGGTATTTCAGTATTTTTACAATCTAAGGGTATTTCA
1 GTAATTCTACAAATCGAGGGTATTTCAGTAATTTTACAATCGAAGGGTATTTCA
*
3814 TTAATT
1 GTAATT
3820 TTAGTAAACT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 7 0.14
54 43 0.86
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (54 bp):
GTAATTCTACAAATCGAGGGTATTTCAGTAATTTTACAATCGAAGGGTATTTCA
Done.