Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1429
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: 34142
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:1220 original size:42 final size:40
Alignment explanation
Indices: 1136--1678 Score: 518
Period size: 42 Copynumber: 12.9 Consensus size: 40
1126 AGGTCTCGAC
*
1136 GATG-ATCCGGGCTAACGTCCGGAAGGAGCATTTC-TGCTAGT
1 GATGTATCCGGGCTAA-GTCCCGAA-GAGCA-TTCGTGCTAGT
*
1177 GATGTATCCGGGCTAAGTCCCGAAAGAGCATTCATGCTAAGT
1 GATGTATCCGGGCTAAGTCCCG-AAGAGCATTCGTGCT-AGT
* *
1219 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCGTGTTAGTT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAG-T
*
1260 GATGTATCCGGGCTATAAAGGCTAAGTCCCGAAGAGCATTCATGTAG-AAGCT
1 GATGTATCC--G-------GGCTAAGTCCCGAAGAGCATTC--GT-GCTAG-T
* *
1312 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCCTGCTAG-
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
1351 GATGTACCCGGGCTAAGTTCCCGAAGAGCATTCGTGCTAAGT
1 GATGTATCCGGGCTAAG-TCCCGAAGAGCATTCGTGCT-AGT
*
1393 GATGTATCCGGGTCTAAGTCCCGAAGAAGCA-TC-TGCTACT
1 GATGTATCCGGG-CTAAGTCCCGAAG-AGCATTCGTGCTAGT
* * *
1433 GATGTATCCGGGCTATAGTTCCCGAAAAGAATTCATGCTACGT
1 GATGTATCCGGGCTA-AG-TCCCGAAGAGCATTCGTGCTA-GT
1476 GATGTATCCGGGGCTAAGTCCCGAAGAGCATTCGTGCCTAGT
1 GATGTATCC-GGGCTAAGTCCCGAAGAGCATTCGTG-CTAGT
*
1518 GATG-ACCCGGGCTAAGTCCCGAAGAGCA-TCGTTG-TAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCG-TGCTAGT
1556 GATAGTA-CCGGGCTAAAGTCCCGAAGAGCATTCGTTGCTAGT
1 GAT-GTATCCGGGCT-AAGTCCCGAAGAGCATTCG-TGCTAGT
1598 GA-GTATTCCGGGCTAAGTTCTCCGAAGAGC-TTCGCTGCTAGT
1 GATGTA-TCCGGGCTAAG-TC-CCGAAGAGCATTCG-TGCTAGT
*
1640 GATGTAGT-CGGGCTGATAGTCTCGAAGAGCATTCGTGCT
1 GATGTA-TCCGGGCT-A-AGTCCCGAAGAGCATTCGTGCT
1679 TAGTATTGAC
Statistics
Matches: 433, Mismatches: 25, Indels: 87
0.79 0.05 0.16
Matches are distributed among these distances:
38 7 0.02
39 30 0.07
40 84 0.19
41 70 0.16
42 130 0.30
43 66 0.15
44 8 0.02
50 23 0.05
52 14 0.03
53 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:1455 original size:83 final size:82
Alignment explanation
Indices: 1279--1678 Score: 434
Period size: 83 Copynumber: 4.8 Consensus size: 82
1269 GGGCTATAAA
* *
1279 GGCTAAG-TCCCGAAGAGCATTCATG-TAGAAGCTGATGTATCCGGGCTAAGTCTCGAAGAGCAT
1 GGCTAAGTTCCCGAAGAGCATTCGTGCT--AAG-TGATGTATCCGGGCTAAGTCCCGAAGAGCAT
*
1342 TCCTGCTAG-GATGTACCCG
63 TCGTGCTAGTGATGTACCCG
1361 GGCTAAGTTCCCGAAGAGCATTCGTGCTAAGTGATGTATCCGGGTCTAAGTCCCGAAGAAGCA-T
1 GGCTAAGTTCCCGAAGAGCATTCGTGCTAAGTGATGTATCCGGG-CTAAGTCCCGAAG-AGCATT
* *
1425 C-TGCTACTGATGTATCCG
64 CGTGCTAGTGATGTACCCG
* * * *
1443 GGCTATAGTTCCCGAAAAGAATTCATGCTACGTGATGTATCCGGGGCTAAGTCCCGAAGAGCATT
1 GGCTA-AGTTCCCGAAGAGCATTCGTGCTAAGTGATGTATCC-GGGCTAAGTCCCGAAGAGCATT
1508 CGTGCCTAGTGATG-ACCCG
64 CGTG-CTAGTGATGTACCCG
1527 GGCTAAG-TCCCGAAGAGCA-TCGTTG-T-AGTGATAGTA-CCGGGCTAAAGTCCCGAAGAGCAT
1 GGCTAAGTTCCCGAAGAGCATTCG-TGCTAAGTGAT-GTATCCGGGCT-AAGTCCCGAAGAGCAT
*
1587 TCGTTGCTAGTGA-GTATTCCG
63 TCG-TGCTAGTGATGTA-CCCG
*
1608 GGCTAAGTTCTCCGAAGAGC-TTCGCTGCT-AGTGATGTAGT-CGGGCTGATAGTCTCGAAGAGC
1 GGCTAAGTTC-CCGAAGAGCATTCG-TGCTAAGTGATGTA-TCCGGGCT-A-AGTCCCGAAGAGC
1670 ATTCGTGCT
61 ATTCGTGCT
1679 TAGTATTGAC
Statistics
Matches: 277, Mismatches: 18, Indels: 44
0.82 0.05 0.13
Matches are distributed among these distances:
79 6 0.02
80 34 0.12
81 36 0.13
82 56 0.20
83 87 0.31
84 33 0.12
85 25 0.09
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (82 bp):
GGCTAAGTTCCCGAAGAGCATTCGTGCTAAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCG
TGCTAGTGATGTACCCG
Found at i:1542 original size:165 final size:161
Alignment explanation
Indices: 1136--1678 Score: 563
Period size: 165 Copynumber: 3.2 Consensus size: 161
1126 AGGTCTCGAC
* *
1136 GATG-ATCCGGGCTAACGTCCGGAAGGAGCATTTC-TGCTAGTGATGTATCCGGGCTAAGTCCCG
1 GATGTATCCGGGCTAA-GTCCCGAA-GAGCA-TTCGTGCTAGTGATGTACCCGGGCTAAGTCCCG
* * *
1199 AAAGAGCATTCATGCTAAGTGATGTACCCGGGCTAAGTCCCGAAGAGCATTCGTGTTAGTTGATG
63 -AAGAGCATTCGTGCTAAGTGATGTA-CCGGGCTAAGTCCCGAAGAGCATTCGTGCTA-CTGATG
1264 TATCCGGGCTATAAAGGCTAAGTCCCGAAGAGCATTCATG-TAGAAGCT
125 TATCCGGGCTAT--A-G-T---TCCCGAAGAG-ATTCATGCT---AG-T
* *
1312 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCCTGCTAG-GATGTACCCGGGCTAAGTTCCCGAA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTACCCGGGCTAAG-TCCCGAA
1376 GAGCATTCGTGCTAAGTGATGTATCCGGGTCTAAGTCCCGAAGAAGCA-TC-TGCTACTGATGTA
65 GAGCATTCGTGCTAAGTGATGTA-CCGGG-CTAAGTCCCGAAG-AGCATTCGTGCTACTGATGTA
*
1439 TCCGGGCTATAGTTCCCGAAAAGAATTCATGCTACGT
127 TCCGGGCTATAGTTCCCGAAGAG-ATTCATGCTA-GT
1476 GATGTATCCGGGGCTAAGTCCCGAAGAGCATTCGTGCCTAGTGATG-ACCCGGGCTAAGTCCCGA
1 GATGTATCC-GGGCTAAGTCCCGAAGAGCATTCGTG-CTAGTGATGTACCCGGGCTAAGTCCCGA
*
1540 AGAGCA-TCGTTG-T-AGTGATAGTACCGGGCTAAAGTCCCGAAGAGCATTCGTTGCTAGTGA-G
64 AGAGCATTCG-TGCTAAGTGAT-GTACCGGGCT-AAGTCCCGAAGAGCATTCG-TGCTACTGATG
* *
1601 TATTCCGGGCTA-AGTTCTCCGAAGAGCTTCGCTGCTAGT
125 TA-TCCGGGCTATAGTTC-CCGAAGAGATTC-ATGCTAGT
*
1640 GATGTAGT-CGGGCTGATAGTCTCGAAGAGCATTCGTGCT
1 GATGTA-TCCGGGCT-A-AGTCCCGAAGAGCATTCGTGCT
1679 TAGTATTGAC
Statistics
Matches: 329, Mismatches: 16, Indels: 56
0.82 0.04 0.14
Matches are distributed among these distances:
162 6 0.02
163 29 0.09
164 41 0.12
165 88 0.27
166 32 0.10
167 5 0.02
169 1 0.00
170 1 0.00
171 1 0.00
173 17 0.05
174 52 0.16
175 31 0.09
176 14 0.04
177 11 0.03
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (161 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTACCCGGGCTAAGTCCCGAAG
AGCATTCGTGCTAAGTGATGTACCGGGCTAAGTCCCGAAGAGCATTCGTGCTACTGATGTATCCG
GGCTATAGTTCCCGAAGAGATTCATGCTAGT
Found at i:4378 original size:47 final size:47
Alignment explanation
Indices: 4300--4749 Score: 708
Period size: 47 Copynumber: 9.6 Consensus size: 47
4290 CCCTTCGGGA
* * * * * *
4300 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
4347 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4394 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4441 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4490 CTCATCACATATATACAC-TTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4536 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4582 CTTATCACATATATATACACTTTCACATTCATCACATTGG-CATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4630 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4677 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4724 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
4750 CACAATTATC
Statistics
Matches: 374, Mismatches: 22, Indels: 14
0.91 0.05 0.03
Matches are distributed among these distances:
45 15 0.04
46 85 0.23
47 184 0.49
48 15 0.04
49 75 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11378 original size:50 final size:48
Alignment explanation
Indices: 11211--11535 Score: 232
Period size: 48 Copynumber: 6.8 Consensus size: 48
11201 TAGGGTATAA
* * * * *
11211 TGCCGTTGCCATGTCCCAGACATGGTCCTACACTTGCTCATCT-ATCAAG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC-TCTCAT-ATG
* * * *
11260 T--CGATGCTATGTCCCAGACATGGTCTTACACT-G-AATATCGAAATCG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCTC-ATAT-G
* * * *
11306 AGGCCGATGCCATGTCCCAGACATCGTCTTACACTAGCTCTCACATATTTG
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCTCATA--TG
* *
11357 TGCCGATGCCATGTCCCAGACATGGTGTTACACT-GACAC-CTCTATAGG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CACTCTC-ATATG
* *
11405 TGCCCATGCCATGTCCC-GAACATGGTCTTACACTAACACATCTCATA--
1 TGCCGATGCCATGTCCCAG-ACATGGTCTTACACTAGCAC-TCTCATATG
* *
11452 -GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTTGTCTCA-A--
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC---TCTCATATG
*
11497 TACCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
11536 ACAAATGACC
Statistics
Matches: 221, Mismatches: 33, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
44 15 0.07
45 14 0.06
46 20 0.09
47 42 0.19
48 48 0.22
49 36 0.16
50 42 0.19
51 3 0.01
52 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCTCATATG
Found at i:20720 original size:79 final size:81
Alignment explanation
Indices: 20584--20768 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
20574 TTGAATGATG
* *
20584 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
20648 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
20663 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20725 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
20743 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20769 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:20782 original size:40 final size:40
Alignment explanation
Indices: 20585--20768 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
20575 TGAATGATGT
* * * *
20585 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20625 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
20665 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
20703 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20744 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20769 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20790 original size:79 final size:79
Alignment explanation
Indices: 20637--20801 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
20627 GGACTAAGAT
* * **
20637 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20702 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20716 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20779 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20795 CCGAAGG
1 CCGAAGG
20802 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.