Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2972
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: 28990
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1268 original size:26 final size:28
Alignment explanation
Indices: 1237--1386 Score: 184
Period size: 26 Copynumber: 5.5 Consensus size: 28
1227 ATATTAAGTC
*
1237 CGCACACTCAGTGCTATATAATC-AA-T
1 CGCACACTTAGTGCTATATAATCAAACT
*
1263 CGCACACTTAGTGCTAAATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
1291 TGCACACTTAGTGCTATAT-ATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
1317 CACACACTTAGTGCT-TATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1344 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1373 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1387 CAATCTCATG
Statistics
Matches: 108, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
25 3 0.03
26 41 0.38
27 23 0.21
28 22 0.20
29 19 0.18
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:1343 original size:53 final size:54
Alignment explanation
Indices: 1237--1358 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
1227 ATATTAAGTC
* *
1237 CGCACACTCAGTGCTATATAATCAATCGCACACTTAGTGCTAAATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAATCACACACTTAGTGCTAAATAATCAAACT
* *
1291 TGCACACTTAGTGCTATAT-ATCAACTCACACACTTAGTGCT-TATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAA-TCACACACTTAGTGCTAAATAATCAAACT
1344 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1359 GTACAATTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
53 30 0.48
54 32 0.52
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (54 bp):
CGCACACTTAGTGCTATATAATCAATCACACACTTAGTGCTAAATAATCAAACT
Found at i:9432 original size:28 final size:28
Alignment explanation
Indices: 9369--9522 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
9359 ATATTAAGTC
*
9369 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
9396 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
9424 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
9452 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
9480 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
9509 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9523 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.18
28 76 0.66
29 19 0.16
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:14369 original size:42 final size:43
Alignment explanation
Indices: 14248--14388 Score: 110
Period size: 44 Copynumber: 3.3 Consensus size: 43
14238 CATAGGATTC
* ** * **
14248 CGATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTG-GCAT
1 CGATATTTGATTTCGTGTAAGACCATATCTAGGAC-ACGAGCAT
* * * *
14291 CGAT-TTGAGACTTACGTGTAAGACCATGTCTGGGACATCGA-CAT
1 CGATATT-TGA-TTTCGTGTAAGACCATATCTAGGACA-CGAGCAT
* *
14335 CG-TATTTGATTTCGTGTAAGACCCTATCTAGGACACTAGCAT
1 CGATATTTGATTTCGTGTAAGACCATATCTAGGACACGAGCAT
14377 CGATATTTGATT
1 CGATATTTGATT
14389 ACATGTAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
41 2 0.03
42 28 0.35
43 18 0.23
44 31 0.39
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCATATCTAGGACACGAGCAT
Found at i:14408 original size:43 final size:42
Alignment explanation
Indices: 14248--14410 Score: 134
Period size: 43 Copynumber: 3.8 Consensus size: 42
14238 CATAGGATTC
* * * * *
14248 CGATATGTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTACGTGTAAGACCACGTCTAGGAC-ATAGCAT
* * * *
14291 CGAT-TTGAGACTTACGTGTAAGACCATGTCTGGGACATCGACAT
1 CGATATT-TGA-TTACGTGTAAGACCACGTCTAGGACATAG-CAT
* *
14335 CG-TATTTGATTTCGTGTAAGACC-CTATCTAGGACACTAGCAT
1 CGATATTTGATTACGTGTAAGACCAC-GTCTAGGACA-TAGCAT
* *
14377 CGATATTTGATTACATGTAAAACCACGTCTAGGA
1 CGATATTTGATTACGTGTAAGACCACGTCTAGGA
14411 TGTTGGCATT
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
42 27 0.28
43 38 0.40
44 31 0.32
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (42 bp):
CGATATTTGATTACGTGTAAGACCACGTCTAGGACATAGCAT
Found at i:15646 original size:18 final size:18
Alignment explanation
Indices: 15623--15660 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15613 GTGACCTTTG
*
15623 TAACTTAGAAAAATTGTT
1 TAACTTAGAAAAATTATT
*
15641 TAACTTTGAAAAATTATT
1 TAACTTAGAAAAATTATT
15659 TA
1 TA
15661 TGTGTTCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TAACTTAGAAAAATTATT
Found at i:23846 original size:22 final size:22
Alignment explanation
Indices: 23725--23846 Score: 68
Period size: 22 Copynumber: 5.3 Consensus size: 22
23715 CATGCATATG
* *
23725 TGTGAAAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATTGCCAA
* * *
23747 TGTGATGAATG-TGAATATGCATATA
1 TGTGAT-AAGGCCGAAT-TGC-CA-A
*
23772 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATTGCCAA
* * * *
23794 TGTGATGAATG-TGAACATGCATATA
1 TGTGAT-AAGGCCGAA-TTGC-CA-A
23819 TGTGATAAGGCCGAATTGCCAA
1 TGTGATAAGGCCGAATTGCCAA
23841 TGTGAT
1 TGTGAT
23847 GAACGTGGAT
Statistics
Matches: 72, Mismatches: 18, Indels: 20
0.65 0.16 0.18
Matches are distributed among these distances:
22 26 0.36
23 12 0.17
24 13 0.18
25 21 0.29
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (22 bp):
TGTGATAAGGCCGAATTGCCAA
Found at i:23881 original size:47 final size:47
Alignment explanation
Indices: 23467--23849 Score: 676
Period size: 47 Copynumber: 8.1 Consensus size: 47
23457 GGATTTTATA
* *
23467 TGATGAATGTGAATATGCATATATGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
*
23514 TGATGAATGTGAACATGAATATGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
*
23561 TGATGAATGTGAATATGCATATGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
23608 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
23655 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
* *
23702 TGAAGAATGTGAACATGCATATGTGTGAAAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
* *
23749 TGATGAATGTGAATATGCATATATGTGATAAGGCCGAATGGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
* *
23796 TGATGAATGTGAACATGCATATATGTGATAAGGCCGAATTGCCAATG
1 TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
23843 TGATGAA
1 TGATGAA
23850 CGTGGATGTG
Statistics
Matches: 322, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 322 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
TGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATG
Found at i:23919 original size:46 final size:46
Alignment explanation
Indices: 23863--24012 Score: 273
Period size: 46 Copynumber: 3.3 Consensus size: 46
23853 GGATGTGTAT
* *
23863 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
23909 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
23955 ATATGAGGTAAAGCCGAATGGCTAATGTGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
24001 ATATGAGGTAAA
1 ATATGAGGTAAA
24013 TGAATTACAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 101 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
Found at i:25859 original size:40 final size:40
Alignment explanation
Indices: 25424--25858 Score: 692
Period size: 40 Copynumber: 10.9 Consensus size: 40
25414 TGAGAGTTAT
25424 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
25464 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
25504 ATATATAC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
25543 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGGTAATG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
25583 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
25623 ATATATCTGAGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
25663 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
25703 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCAAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
25743 ATATATCCAGGCTAAGTCCCGAAGAGCATACGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
25783 TTATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
25823 TTATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
25859 GATGATGTGT
Statistics
Matches: 363, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
39 36 0.10
40 327 0.90
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:28543 original size:47 final size:47
Alignment explanation
Indices: 28426--28785 Score: 498
Period size: 47 Copynumber: 7.6 Consensus size: 47
28416 CCCTTCGGGA
* * * * *
28426 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28473 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28519 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28566 CTTATCACATATATATACACTTTCACATTCATCACATCGG-CATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28614 CTTATCACATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28660 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-C
* *
28708 CTATAATCACATATATATAACATCTTTCACATTCATCAACATTGGCCATT-CGC
1 CT-T-ATCAC--ATATAT-ACA-CTTTCACATTCATC-ACATCGGCCATTAGGC
28761 CTTATCAC--ATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28786 ACCAACCCTT
Statistics
Matches: 287, Mismatches: 13, Indels: 28
0.88 0.04 0.09
Matches are distributed among these distances:
45 29 0.10
46 78 0.27
47 82 0.29
48 18 0.06
49 31 0.11
50 5 0.02
51 5 0.02
52 7 0.02
53 6 0.02
54 15 0.05
55 11 0.04
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28692 original size:141 final size:144
Alignment explanation
Indices: 28426--28785 Score: 567
Period size: 141 Copynumber: 2.5 Consensus size: 144
28416 CCCTTCGGGA
* * *
28426 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCATTCGGCC-TGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
28488 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
28553 TCGGCCATTAGG-C
131 TCGGCCATTAGGCC
*
28566 CTTATCACATATATATACACTTTCACATTCATCACATCGG-CATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
28630 AC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
28694 TCGGCCATTAGGCC
131 TCGGCCATTAGGCC
28708 CTATAATCACATATATATAACATCTTTCACATTCATCAACATTGGCCATTC-GCCTTATCAC--A
1 CT-T-ATCACATATATAT-ACA-CTTTCACATTCATC-ACATTGGCCATTCGGCCTTATCACATA
28770 TATACACTTTCACATT
61 TATACACTTTCACATT
28786 ACCAACCCTT
Statistics
Matches: 203, Mismatches: 6, Indels: 16
0.90 0.03 0.07
Matches are distributed among these distances:
140 10 0.05
141 83 0.41
142 42 0.21
143 1 0.00
144 13 0.06
145 11 0.05
146 22 0.11
147 16 0.08
148 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (144 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCC
Done.