Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2145
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: 11381
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1280 original size:20 final size:19
Alignment explanation
Indices: 1255--1325 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
1245 CCCTTATTTT
1255 TATCGATACACATGAAAATG
1 TATCGATACACATG-AAATG
* * *
1275 TATCGACACAAATTGCAATG
1 TATCGATACACA-TGAAATG
* *
1295 TATTGATACATCATGTGAATG
1 TATCGATACA-CATG-AAATG
1316 TATCGATACA
1 TATCGATACA
1326 AGTCATTGGC
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
20 24 0.60
21 16 0.40
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (19 bp):
TATCGATACACATGAAATG
Found at i:2359 original size:20 final size:20
Alignment explanation
Indices: 2334--2403 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
2324 ACTAGTGACT
2334 TGTATCGATACATTCACATA
1 TGTATCGATACATTCACATA
* *
2354 TGTATCGATACAATGCA-TTA
1 TGTATCGATAC-ATTCACATA
* ** *
2374 TTTATCGATACATTTTCATG
1 TGTATCGATACATTCACATA
2394 TGTATCGATA
1 TGTATCGATA
2404 GAAATAAGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.05
20 33 0.85
21 4 0.10
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACATA
Found at i:2741 original size:30 final size:30
Alignment explanation
Indices: 2688--3089 Score: 201
Period size: 30 Copynumber: 13.4 Consensus size: 30
2678 CAAATTTTAC
* **
2688 CCTCAGTTGACTGTATTTAGTCAAGTCTTT
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
* * * *
2718 CCTCATTTGATTGTACTCGGTCAAATCTTA
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
* * * * *
2748 CC-CCTCTTGATTGTATTCGATCAAGACCTT
1 CCTCAT-TTGACTGTATTCGGTCAAGTCTTT
* * * *
2778 CCTCATTTGACTGTATTTGATCAAAT-TTGAC
1 CCTCATTTGACTGTATTCGGTCAAGTCTT--T
* **
2809 CCTCGTTTGACTGTATTCATTCAAGTCTTT
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
* * *
2839 CCTCATTGGACTGTACTCGGTCAAATCTTAT
1 CCTCATTTGACTGTATTCGGTCAAGTCTT-T
* * ** *
2870 CC-C-TCTTGACTATATTCAGTCAAAACTAT
1 CCTCAT-TTGACTGTATTCGGTCAAGTCTTT
* * * * * *
2899 CCTTATTTGACTATACTCGATTGAA-TCTTA
1 CCTCATTTGACTGTATTCG-GTCAAGTCTTT
* * *
2929 CCTC-TCCTGACTGTATTCGGTCAAGACTAT
1 CCTCAT-TTGACTGTATTCGGTCAAGTCTTT
* * * *
2959 CCTTATTTGATTGTATTCGGTAAAGTCTTA
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
2989 CC-C-TGCTTGACTGTATTCGGTCAAGTC-TT
1 CCTCAT--TTGACTGTATTCGGTCAAGTCTTT
* * * * *
3018 CTTCATTTGACTGTACTCGATCAAATCTTA
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
* * * * *
3048 CCCCATTTAACTATATTCGGTTAAGTTTTT
1 CCTCATTTGACTGTATTCGGTCAAGTCTTT
*
3078 CTTCATTTGACT
1 CCTCATTTGACT
3090 ATACTTGTTC
Statistics
Matches: 269, Mismatches: 85, Indels: 36
0.69 0.22 0.09
Matches are distributed among these distances:
28 1 0.00
29 31 0.12
30 203 0.75
31 32 0.12
32 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (30 bp):
CCTCATTTGACTGTATTCGGTCAAGTCTTT
Found at i:2783 original size:60 final size:60
Alignment explanation
Indices: 2677--3109 Score: 296
Period size: 60 Copynumber: 7.2 Consensus size: 60
2667 TTGTATTTAG
* * * * * *
2677 TCAAATTTTA-CCCTCAGTTGACTGTATT-TAGTCAAGTCTTTCCTCATTTGATTGTACTCGG
1 TCAAATCTTACCCCTC--TTGACTGTATTCGA-TCAAGACCTTCCTCATTTGACTGTACTCGA
* * *
2738 TCAAATCTTACCCCTCTTGATTGTATTCGATCAAGACCTTCCTCATTTGACTGTATTTGA
1 TCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACCTTCCTCATTTGACTGTACTCGA
* * * *
2798 TCAAAT-TTGA-CCCTCGTTTGACTGTATTC-ATTCAAGTCTTTCCTCATTGGACTGTACTCGG
1 TCAAATCTT-ACCCCTC--TTGACTGTATTCGA-TCAAGACCTTCCTCATTTGACTGTACTCGA
* * * * *
2859 TCAAATCTTATCCCTCTTGACTATATTC-AGTCAA-AACTATCCTTATTTGACTATACTCGA
1 TCAAATCTTACCCCTCTTGACTGTATTCGA-TCAAGACCT-TCCTCATTTGACTGTACTCGA
** * * * * * * *
2919 TTGAATCTTACCTCTCCTGACTGTATTCGGTCAAGA-CTATCCTTATTTGATTGTATTCGG
1 TCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACCT-TCCTCATTTGACTGTACTCGA
* * *
2979 T-AAAGTCTTA-CCCTGCTTGACTGTATTCGGTCAAG-TCTTCTTCATTTGACTGTACTCGA
1 TCAAA-TCTTACCCCT-CTTGACTGTATTCGATCAAGACCTTCCTCATTTGACTGTACTCGA
* * * * *** * * * *
3038 TCAAATCTTACCCCAT-TTAACTATATTCGGTTAAGTTTTTCTTCATTTGACTATACTTGT
1 TCAAATCTTACCCC-TCTTGACTGTATTCGATCAAGACCTTCCTCATTTGACTGTACTCGA
3098 TCAAATCTTACC
1 TCAAATCTTACC
3110 TTGATTGATT
Statistics
Matches: 303, Mismatches: 51, Indels: 37
0.77 0.13 0.09
Matches are distributed among these distances:
59 51 0.17
60 186 0.61
61 54 0.18
62 12 0.04
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (60 bp):
TCAAATCTTACCCCTCTTGACTGTATTCGATCAAGACCTTCCTCATTTGACTGTACTCGA
Found at i:2886 original size:121 final size:119
Alignment explanation
Indices: 2677--3109 Score: 405
Period size: 121 Copynumber: 3.6 Consensus size: 119
2667 TTGTATTTAG
*
2677 TCAAATTTTACCCTCAG-TTGACTGTATTTAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCA
1 TCAAA-TTTACCCTC-GTTTGACTGTATTCAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCA
* * * *
2741 AATCTTACCCCTCTTGATTGTATTCGATCAAGACCTTCCTCATTTGACTGTATTTGA
64 AATCTTA-CCCTCTTGACTGTATTCGATCAAGAACTTCCTCATTTGACTGTACTCGA
* * *
2798 TCAAATTTGACCCTCGTTTGACTGTATTCATTCAAGTCTTTCCTCATTGGACTGTACTCGGTCAA
1 TCAAATTT-ACCCTCGTTTGACTGTATTCAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCAA
* * *
2863 ATCTTATCCCTCTTGACTATATTC-AGTCAA-AACTATCCTTATTTGACTATACTCGA
65 ATCTTA-CCCTCTTGACTGTATTCGA-TCAAGAACT-TCCTCATTTGACTGTACTCGA
** * * * * * *
2919 TTGAATCTTA-CCTC-TCCTGACTGTATTCGGTCAAGACTATCCTTATTTGATTGTATTCGGT-A
1 TCAAAT-TTACCCTCGT-TTGACTGTATTCAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCA
* * *
2981 AAGTCTTACCCTGCTTGACTGTATTCGGTCAAG-TCTTCTTCATTTGACTGTACTCGA
64 AA-TCTTACCCT-CTTGACTGTATTCGATCAAGAACTTCCTCATTTGACTGTACTCGA
* * * * * * * * * * *
3038 TCAAATCTTACCC-CATTTAACTATATTCGGTTAAGTTTTTCTTCATTTGACTATACTTGTTCAA
1 TCAAAT-TTACCCTCGTTTGACTGTATTCAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCAA
3102 ATCTTACC
65 ATCTTACC
3110 TTGATTGATT
Statistics
Matches: 254, Mismatches: 45, Indels: 28
0.78 0.14 0.09
Matches are distributed among these distances:
119 73 0.29
120 77 0.30
121 102 0.40
122 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (119 bp):
TCAAATTTACCCTCGTTTGACTGTATTCAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCAAA
TCTTACCCTCTTGACTGTATTCGATCAAGAACTTCCTCATTTGACTGTACTCGA
Found at i:3903 original size:33 final size:33
Alignment explanation
Indices: 3861--3942 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
3851 GTCGTTGGGC
3861 ACAATGTATCGATACAATTCTTCATATATCGA-T
1 ACAATGTATCGATACAATTCTTCATATATC-ATT
*
3894 ACAATGTATCGATACAATTCTTCATGTATCATT
1 ACAATGTATCGATACAATTCTTCATATATCATT
3927 ACAATGTATCGATACA
1 ACAATGTATCGATACA
3943 TTACCTTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (33 bp):
ACAATGTATCGATACAATTCTTCATATATCATT
Found at i:3905 original size:13 final size:13
Alignment explanation
Indices: 3887--3911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3877 ATTCTTCATA
3887 TATCGATACAATG
1 TATCGATACAATG
3900 TATCGATACAAT
1 TATCGATACAAT
3912 TCTTCATGTA
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:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:3922 original size:20 final size:20
Alignment explanation
Indices: 3864--3923 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
3854 GTTGGGCACA
3864 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
*
3884 ATATATCGATAC-A------
1 ATGTATCGATACAATTCTTC
3897 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
3917 ATGTATC
1 ATGTATC
3924 ATTACAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
19 1 0.03
20 18 0.58
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTC
Found at i:4049 original size:13 final size:13
Alignment explanation
Indices: 4031--4057 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4021 TACAATGAAC
4031 ATGTATCGATACA
1 ATGTATCGATACA
4044 ATGTATCGATACA
1 ATGTATCGATACA
4057 A
1 A
4058 GGCATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4710 original size:21 final size:22
Alignment explanation
Indices: 4681--4738 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
4671 CAATTTTTAA
* *
4681 CTCCGTTTT-AATAAAACATTT
1 CTCCTTTTTAAATAAAAAATTT
*
4702 CTCCTTTTTTAAAAAAAAAATTT
1 CTCC-TTTTTAAATAAAAAATTT
*
4725 C-CCTTTTTGAATAA
1 CTCCTTTTTAAATAA
4739 TCCCCCCCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 13 0.43
22 6 0.20
23 11 0.37
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.43
Consensus pattern (22 bp):
CTCCTTTTTAAATAAAAAATTT
Found at i:6854 original size:15 final size:15
Alignment explanation
Indices: 6834--6863 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6824 CAGATTAAAC
6834 AACAAATTCTCAAGA
1 AACAAATTCTCAAGA
6849 AACAAATTCTCAAGA
1 AACAAATTCTCAAGA
6864 GCGCAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (15 bp):
AACAAATTCTCAAGA
Found at i:8286 original size:79 final size:79
Alignment explanation
Indices: 8182--8351 Score: 259
Period size: 79 Copynumber: 2.2 Consensus size: 79
8172 GATAAAGACG
* * * * * *
8182 GGGTTGGAGTAGCCCCTCAAAAATAATGGGGCTGGAGTATCCCCGATTATGAAAAATTAATGTTC
1 GGGTTGGAGTATCCACTCAAAAATAACGAGGCTGGAGTATCCCCGAGTATGAAAAATCAATGTTC
8247 TAGAAATAAAATCA
66 TAGAAATAAAATCA
* * *
8261 GGGTTGGGGTATCCACTCGAAAATAACGAGGTTGGAGTATCCCCGAGTATGAAAAATCAATGTTC
1 GGGTTGGAGTATCCACTCAAAAATAACGAGGCTGGAGTATCCCCGAGTATGAAAAATCAATGTTC
8326 TAGAAATAAAATCA
66 TAGAAATAAAATCA
8340 GGGTTGGAGTAT
1 GGGTTGGAGTAT
8352 TCCCAATGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCACTCAAAAATAACGAGGCTGGAGTATCCCCGAGTATGAAAAATCAATGTTC
TAGAAATAAAATCA
Found at i:8375 original size:130 final size:130
Alignment explanation
Indices: 8241--8484 Score: 285
Period size: 130 Copynumber: 1.9 Consensus size: 130
8231 TGAAAAATTA
* * *
8241 ATGTTCTAGAAATAAAATCAGGGTTGGGGTATCCACTCGA-AAATAACGAGGTTGGAGTATCCCC
1 ATGTTCTAGAAATAAAACCAGGGTTAGAGTATCCACT-GAGAAATAACGAGGTTGGAGTATCCCC
* * *
8305 GAGTATGAAAAATCAATGTTCTAGAAATAAAA-TCAGGGTTGGAGTATTCCCAATGGTAGAAAAT
65 AAGTATGAAAAATCAATATTCTAAAAATAAAACT-AGGGTTGGAGTATTCCCAATGGTAGAAAAT
8369 CG
129 CG
* * ** * * * * *
8371 ATGTTTTAGAAATAAAACCGGGGTTAGAGTATCTTCTTAGAAATAACGGGGTTTGAGTCTCTCCA
1 ATGTTCTAGAAATAAAACCAGGGTTAGAGTATCCACTGAGAAATAACGAGGTTGGAGTATCCCCA
* * * *
8436 ATTGTGAAAAATCGATATTTTAAAAATAAAACTAGGGTTGGAGTATTCC
66 AGTATGAAAAATCAATATTCTAAAAATAAAACTAGGGTTGGAGTATTCC
8485 TTCGAAAATA
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
129 1 0.01
130 91 0.98
131 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (130 bp):
ATGTTCTAGAAATAAAACCAGGGTTAGAGTATCCACTGAGAAATAACGAGGTTGGAGTATCCCCA
AGTATGAAAAATCAATATTCTAAAAATAAAACTAGGGTTGGAGTATTCCCAATGGTAGAAAATCG
Found at i:8583 original size:28 final size:28
Alignment explanation
Indices: 8550--8618 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
8540 ATAAAATCGA
8550 GGTTGGAGTATCCCCTC-AGAAATAACGG
1 GGTTGGAGTATCCCCTCGA-AAATAACGG
*
8578 GGTTGGAGTATCCCCTCGAAAATAATGG
1 GGTTGGAGTATCCCCTCGAAAATAACGG
8606 GGTTGGAGTATCC
1 GGTTGGAGTATCC
8619 TTGATTGTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCGAAAATAACGG
Found at i:8589 original size:79 final size:77
Alignment explanation
Indices: 8340--8592 Score: 260
Period size: 79 Copynumber: 3.2 Consensus size: 77
8330 AATAAAATCA
* * *
8340 GGGTTGGAGTATTCCCAATGGTA-G-AAAATCGATGTTTTAGAAATAAAACCGGGGTTAGAGTAT
1 GGGTTGGAGTATCCCCAAT--TATGAAAAATCGATGTTTTA-AAATAAAA-CGAGGTTGGAGTAT
** *
8403 CTTCTTAGAAATAACG
62 CCCCTCAGAAATAACG
* * * * * * *
8419 GGGTTTGAGTCTCTCCAATTGTGAAAAATCGATATTTTAAAAATAAAACTAGGGTTGGAGTATTC
1 GGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTT-AAAATAAAACGA-GGTTGGAGTATCC
*
8484 CTTC-GAAAATAACG
64 CCTCAG-AAATAACG
* *
8498 AGATTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTT-AAAATAAAA-CGAGGTTGGAGTATCC
8563 CCTCAGAAATAACG
64 CCTCAGAAATAACG
8577 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
8593 TCGAAAATAA
Statistics
Matches: 140, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
77 1 0.01
78 3 0.02
79 132 0.94
80 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTAAAATAAAACGAGGTTGGAGTATCCCC
TCAGAAATAACG
Found at i:8598 original size:107 final size:107
Alignment explanation
Indices: 8470--8805 Score: 431
Period size: 107 Copynumber: 3.1 Consensus size: 107
8460 AATAAAACTA
* * * * * * * *
8470 GGGTTGGAGTATTCCTTCGAAAATAACGAGATTGGAGTATCCCCAATTATGAAAAATCGATGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTT
* * * *
8535 TGAAAATAAAATCGAGGTTGGAGTATCCCCTCAGAAATAACG
66 TGGAAATAAAACCGAGGTTGGAGTATCCCCTTAGAAATAATG
* * * *
8577 GGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCTTGATTGTGGAAATTTGATGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTT
* * * *
8642 TGGAAACAAAACCGGGGTTGGAGTATTCCCTTAGAAATAATA
66 TGGAAATAAAACCGAGGTTGGAGTATCCCCTTAGAAATAATG
* * *
8684 GGGTTTGAGTATCCCCCCAAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTT
* *
8749 TGGAAATAAAACCAAGGTTGGAGTATCCCCTTGGAAATAATG
66 TGGAAATAAAACCGAGGTTGGAGTATCCCCTTAGAAATAATG
*
8791 GGGTTTGAGTA-CCCC
1 GGGTTGGAGTATCCCC
8806 GATTGTGGGA
Statistics
Matches: 196, Mismatches: 33, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
106 4 0.02
107 192 0.98
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (107 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTT
TGGAAATAAAACCGAGGTTGGAGTATCCCCTTAGAAATAATG
Done.