Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1456
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: 19675
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:8220 original size:46 final size:46
Alignment explanation
Indices: 8153--8320 Score: 218
Period size: 46 Copynumber: 3.6 Consensus size: 46
8143 TATTTGGGCA
8153 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
8199 TCCGAACTCGTTGAGTTGAGTCTGAGTTCA-TGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
*
8244 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
8292 TCTGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
8321 GTGAGGTGTA
Statistics
Matches: 106, Mismatches: 7, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 58 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:8266 original size:47 final size:47
Alignment explanation
Indices: 8202--8349 Score: 162
Period size: 47 Copynumber: 3.2 Consensus size: 47
8192 GCGAACGTCC
*
8202 GAACTCGTTGAGTTGAGTCTGAGTTCATGAGATGTAACTAGGCATCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAGGCATCT
* *
8249 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATG-TAACTAGGCATCT
* * *
8295 GAACTCGTTGAGTTGAGTCCGAGTTCGTGAGGTGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAGGCATCT
*
8342 GAGCTCGT
1 GAACTCGT
8350 GAGATGTAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
42 3 0.04
43 3 0.04
45 3 0.04
46 29 0.35
47 35 0.42
48 3 0.04
50 4 0.05
51 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (47 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAGGCATCT
Found at i:8308 original size:93 final size:93
Alignment explanation
Indices: 8149--8349 Score: 348
Period size: 93 Copynumber: 2.2 Consensus size: 93
8139 CGGATATTTG
8149 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
8214 TTGAGTCTGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
* *
8242 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
* *
8307 TTGAGTCCGAGTTCGTGAGGTGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
*
8335 GGCATCCGAGCTCGT
1 GGCATCCGAACTCGT
8350 GAGATGTAAC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 101 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:8350 original size:27 final size:27
Alignment explanation
Indices: 8312--8376 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
8302 TTGAGTTGAG
* *
8312 TCCGAGTTCGTGAGGTGTAACTAGGCA
1 TCCGAGCTCGTGAGATGTAACTAGGCA
8339 TCCGAGCTCGTGAGATGTAACTAGGCA
1 TCCGAGCTCGTGAGATGTAACTAGGCA
8366 TCCGAGCTCGT
1 TCCGAGCTCGT
8377 TGAGTTGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.25
Consensus pattern (27 bp):
TCCGAGCTCGTGAGATGTAACTAGGCA
Found at i:13326 original size:49 final size:47
Alignment explanation
Indices: 13001--13596 Score: 857
Period size: 47 Copynumber: 12.6 Consensus size: 47
12991 CCCTTCGGGA
* * *
13001 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
13047 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
13094 CTTATCTCATATATGCA-TGTTCACA-TCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
13140 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
13187 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
13234 CTTATCACACA-ATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAC-T-TTCACATTCATCACATTGGCCATTCGGC
13282 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
13331 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
13378 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
13427 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
13474 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
13522 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
13571 CTTATCACATATATA-ACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
13597 TATTCAAATA
Statistics
Matches: 523, Mismatches: 14, Indels: 26
0.93 0.02 0.05
Matches are distributed among these distances:
46 101 0.19
47 200 0.38
48 85 0.16
49 128 0.24
50 3 0.01
51 6 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:13387 original size:96 final size:96
Alignment explanation
Indices: 13001--13596 Score: 864
Period size: 96 Copynumber: 6.3 Consensus size: 96
12991 CCCTTCGGGA
* *
13001 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGG-CTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
13063 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
13094 CTTATCTC--ATATATGCA-TGTTCACA-TCATCACATTGGCCATTCGGCCTTATCACACATACA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
13155 CA-TGTTCACATTCATCACATTGGCCATTCGGC
65 CACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
13187 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACA-ATA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
13248 CACATGTTCACATTCATCACATTGGCCATTCGGC
65 CAC-T-TTCACATTCATCACATTGGCCATTCGGC
13282 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
13347 ACTTTCACATTCATCACATCGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* *
13378 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
13443 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* *
13474 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
*
13538 ACACTTTCACATTCATCACATTGGCCATTAGGC
64 ACACTTTCACATTCATCACATTGGCCATTCGGC
13571 CTTATCAC--ATATATA-ACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
13597 TATTCAAATA
Statistics
Matches: 470, Mismatches: 19, Indels: 27
0.91 0.04 0.05
Matches are distributed among these distances:
92 22 0.05
93 85 0.18
94 43 0.09
95 53 0.11
96 168 0.36
97 92 0.20
98 7 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:16274 original size:39 final size:39
Alignment explanation
Indices: 16172--16538 Score: 508
Period size: 39 Copynumber: 9.4 Consensus size: 39
16162 CTAGGCACGA
* * * * *
16172 AGCCCGAATACACGTCACCAGCATGATTGCTCTTCGGGACCT
1 AGCCCGGATACA--TCACTAGCACGAATGCTCTTC-GGACTT
* * * **
16214 AGCCCGGATATAACACCAGCACGAATGCTCTTCGGGTTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
* *
16253 AGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGG-ACTT
*
16293 AGCCC-GATACATCACTAGCATGAATGCTCTTCGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
16331 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
16370 AG-CCGGATACATCACTAGCACGAATGCTCTTCGGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTC-GGACTT
*
16409 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
*
16448 AGCCCGGATACATCACTAGCATGAATGCT-TTCGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
*
16486 AGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTT
1 AGCCCGGATACATCACTAGCACGAATGCTCTTC-GGACTT
16526 AGCCCGGAT-CATC
1 AGCCCGGATACATC
16539 GTCGAGACCT
Statistics
Matches: 301, Mismatches: 18, Indels: 15
0.90 0.05 0.04
Matches are distributed among these distances:
38 77 0.26
39 146 0.49
40 68 0.23
42 10 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
AGCCCGGATACATCACTAGCACGAATGCTCTTCGGACTT
Found at i:16661 original size:38 final size:38
Alignment explanation
Indices: 16592--16666 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
16582 GAATTTTAAT
*
16592 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
16630 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
16667 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:19277 original size:47 final size:46
Alignment explanation
Indices: 19086--19675 Score: 728
Period size: 47 Copynumber: 12.6 Consensus size: 46
19076 TGCCCTTGGA
* * *
19086 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
19133 CTTATCACATATATACACATTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATAT--ACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
19182 CTTATCTCA-ATATGCATGTTCACATTCA-CACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
19227 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
19274 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
19321 CTTATCTCATTATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACA-TATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
19369 CTTATCACACATACACATTTCACAATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACATTTCAC-ATTCATCACATTGGCCATTCGGC
* * *
19415 CTTATCACATAGTAT-TA-TACACATTTATCACA-TGGCCATTCGGC
1 CTTATCACATA-TATACATTTCACATTCATCACATTGGCCATTCGGC
* *
19459 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
* * *
19506 CTTATCACATATATAACACTTTCACATTCATCACATCGGCATATTAGGC
1 CTTATCACATATAT-ACA-TTTCACATTCATCACATTGGC-CATTCGGC
* * *
19555 CTTATCACATAATATACACTTTCACATTCATCACATCGCGCTATTAGGC
1 CTTATCACAT-ATATACA-TTTCACATTCATCACATTG-GCCATTCGGC
19604 CTTA-CACATATATACACTTTCACATTCATCACATTGGCCATT-GGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
19649 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACA-TTTCACATT
Statistics
Matches: 496, Mismatches: 30, Indels: 35
0.88 0.05 0.06
Matches are distributed among these distances:
43 3 0.01
44 33 0.07
45 37 0.07
46 97 0.20
47 153 0.31
48 77 0.16
49 90 0.18
50 6 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (46 bp):
CTTATCACATATATACATTTCACATTCATCACATTGGCCATTCGGC
Found at i:19423 original size:21 final size:21
Alignment explanation
Indices: 19397--19468 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
19387 TTCACAATTC
19397 ATCACATGGCCATTCGGCCTT
1 ATCACATGGCCATTCGGCCTT
* * ***
19418 ATCACATAG-TATTATACACATTT
1 ATCACATGGCCATTCGGC-C--TT
19441 ATCACATGGCCATTCGGCCTT
1 ATCACATGGCCATTCGGCCTT
19462 ATCACAT
1 ATCACAT
19469 ATATACACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
20 4 0.11
21 18 0.49
23 11 0.30
24 4 0.11
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (21 bp):
ATCACATGGCCATTCGGCCTT
Done.