Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2023
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: 44133
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1394 original size:93 final size:93
Alignment explanation
Indices: 1281--1452 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
1271 CCCCCATAAG
* *
1281 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1346 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
1374 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1439 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
1453 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:1449 original size:46 final size:46
Alignment explanation
Indices: 1274--1449 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
1264 CATTAACCCC
* * *
1274 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
1320 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
1370 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
1413 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
1450 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:8906 original size:91 final size:92
Alignment explanation
Indices: 8794--8962 Score: 304
Period size: 91 Copynumber: 1.8 Consensus size: 92
8784 GCCCATAAGT
* *
8794 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACT-AA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
8858 CGAGTTCGGATGCCTAGTTACATTCAC
66 CGAGTTCGGATGCCTAGTTACATTCAC
*
8885 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
8950 CGAGTTCGGATGC
66 CGAGTTCGGATGC
8963 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 59 0.80
92 15 0.20
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTCAC
Found at i:8959 original size:46 final size:46
Alignment explanation
Indices: 8786--8959 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
8776 TGTAACCCGC
* * *
8786 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
8832 CCATAAGTGAACTCGGACTCAACT-AACGAGTTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* * *
8877 ACATTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
8923 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
8960 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
45 31 0.28
46 69 0.63
48 4 0.04
49 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:8978 original size:46 final size:46
Alignment explanation
Indices: 8791--8978 Score: 142
Period size: 46 Copynumber: 4.1 Consensus size: 46
8781 CCCGCCCATA
* ** * *
8791 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCC-T
*
8836 AAGTGAACTCGGACTCAACT-AACGAGTTCGGATGC-CTAGTTA-CATTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCCT
* * * * *
8883 A-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCCT
8928 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
8974 AGTGA
1 AGTGA
8979 CATGTCACTT
Statistics
Matches: 114, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
44 10 0.09
45 28 0.25
46 67 0.59
48 4 0.04
49 5 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:10737 original size:40 final size:40
Alignment explanation
Indices: 10682--10903 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
10672 TATTCGGATG
*
10682 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
10722 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCGACTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
10762 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
10802 ATATCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
10842 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCAAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* *
10882 ATATCC-GGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
10904 TACTTGGTTT
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 17 0.10
40 150 0.90
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:12977 original size:14 final size:15
Alignment explanation
Indices: 12951--12981 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12941 TTCTTTATAC
12951 TATATACCATATTCT
1 TATATACCATATTCT
12966 TATATA-CATATTCT
1 TATATACCATATTCT
12980 TA
1 TA
12982 ATAGTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATACCATATTCT
Found at i:15702 original size:21 final size:21
Alignment explanation
Indices: 15662--15700 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15652 GATGATGTTG
15662 ATGTAGAGTTTTTCAGAAATC
1 ATGTAGAGTTTTTCAGAAATC
15683 ATGTCAGA-TTTTT-AGAAA
1 ATGT-AGAGTTTTTCAGAAA
15701 ATTTTCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
ATGTAGAGTTTTTCAGAAATC
Found at i:19717 original size:18 final size:18
Alignment explanation
Indices: 19691--19743 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
19681 CAATTTCTCG
*
19691 TAATTATAATGAAAATAA
1 TAATAATAATGAAAATAA
** *
19709 TAATAATAATTCAAGTAA
1 TAATAATAATGAAAATAA
19727 TAATAACTTAATGAAAA
1 TAATAA--TAATGAAAA
19744 CCTTGTTACA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 20 0.77
20 6 0.23
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (18 bp):
TAATAATAATGAAAATAA
Found at i:20930 original size:24 final size:23
Alignment explanation
Indices: 20889--20943 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
20879 TACCGTAGCC
*
20889 CAACTTTTGGCTTTTTGGCATTT
1 CAACTTTTAGCTTTTTGGCATTT
20912 CAACTTTTCAGCTTTTTGGCATTT
1 CAACTTTT-AGCTTTTTGGCATTT
*
20936 CAGCTTTT
1 CAACTTTT
20944 GCCGATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.51
Consensus pattern (23 bp):
CAACTTTTAGCTTTTTGGCATTT
Found at i:22753 original size:69 final size:69
Alignment explanation
Indices: 22642--22776 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 69
22632 AAGGAGAGAC
*
22642 CTTAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATGCTTAAGGTCAGCATATGACT
1 CTTAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAGCATATGACT
22707 TTTG
66 TTTG
* *
22711 CTTAAGGAAAACTAAGTCCTCCACTGCAAACTCTATTTCTTGATACTTAAGGTTAGCATATGACT
1 CTTAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAGCATATGACT
22776 T
66 T
22777 CTGCCTATCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (69 bp):
CTTAAGGAAAACTAAGTCCCCCACTGCAAACTCTATTTCTTGATACTTAAGGTCAGCATATGACT
TTTG
Found at i:27151 original size:47 final size:47
Alignment explanation
Indices: 27097--27450 Score: 600
Period size: 47 Copynumber: 7.5 Consensus size: 47
27087 TATTTGAATA
27097 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27144 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
27193 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27240 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
27287 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27334 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
27381 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
27428 GATGTGAAAGTGTATAAATGTGA
1 AATGTGAAAGTGTATATATGTGA
27451 GAAGTCCCGA
Statistics
Matches: 296, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 249 0.84
49 47 0.16
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29229 original size:40 final size:40
Alignment explanation
Indices: 28866--29217 Score: 526
Period size: 40 Copynumber: 8.8 Consensus size: 40
28856 GAGAATTGAG
28866 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
28906 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
28946 AGTGATGTATCCAGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
28986 AGTGATGTATCCGGGCTAAG-CCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCT
**
29026 AGTGATGTATCCGGGCTAAGTCTTGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
29066 AGTGATGTATCCGGGCTAAGTCTCGAAGAGAATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
29106 AGTGATGTATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * **
29146 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * **
29186 GGTGTTATATCCGGGCTTGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
29218 ATCATGCTGG
Statistics
Matches: 285, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 1 0.00
40 283 0.99
41 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:33358 original size:47 final size:47
Alignment explanation
Indices: 33229--33581 Score: 591
Period size: 47 Copynumber: 7.5 Consensus size: 47
33219 TATTTGAATA
33229 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
33276 -ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
33324 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
33371 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
33418 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
33465 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
33512 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
33559 GATGTGAAAGTGTATAAATGTGA
1 AATGTGAAAGTGTATATATGTGA
33582 GAAGTCCCGA
Statistics
Matches: 294, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
46 11 0.04
47 238 0.81
48 34 0.12
49 11 0.04
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:36720 original size:31 final size:31
Alignment explanation
Indices: 36685--36747 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
36675 ATTATTTAGC
*
36685 TATGTGAATGTAATACTTTAGTTAAAGCCGA
1 TATGTGAATGTAATACTTTAGTCAAAGCCGA
36716 TATGTGAATGTAATACTTTAGTCAAAGCCGA
1 TATGTGAATGTAATACTTTAGTCAAAGCCGA
36747 T
1 T
36748 TTCATTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (31 bp):
TATGTGAATGTAATACTTTAGTCAAAGCCGA
Done.