Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2635
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: 98194
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:804 original size:24 final size:24
Alignment explanation
Indices: 772--819 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
762 GCTTTACAAA
772 GAAATTTTTAAATTTCGTTTCTTT
1 GAAATTTTTAAATTTCGTTTCTTT
796 GAAATTTTTAAATTTCGTTTCTTT
1 GAAATTTTTAAATTTCGTTTCTTT
820 CTCAAAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (24 bp):
GAAATTTTTAAATTTCGTTTCTTT
Found at i:1581 original size:12 final size:12
Alignment explanation
Indices: 1566--1590 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1556 TTCATCTGAG
1566 TCAACATCTTCA
1 TCAACATCTTCA
1578 TCAACATCTTCA
1 TCAACATCTTCA
1590 T
1 T
1591 AATCTTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAACATCTTCA
Found at i:3059 original size:13 final size:13
Alignment explanation
Indices: 3041--3066 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3031 CATTTTATGG
3041 TGTATCGATACAA
1 TGTATCGATACAA
3054 TGTATCGATACAA
1 TGTATCGATACAA
3067 GTTTGGCTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3806 original size:13 final size:13
Alignment explanation
Indices: 3788--3814 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3778 ACATCATGCT
3788 TTGTATCGATACA
1 TTGTATCGATACA
3801 TTGTATCGATACA
1 TTGTATCGATACA
3814 T
1 T
3815 GCTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3823 original size:19 final size:19
Alignment explanation
Indices: 3799--3854 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
3789 TGTATCGATA
3799 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCT
*
3818 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
*
3837 CAATTGTAACGATACATG
1 C-ATTGTATCGATACATG
3855 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:27077 original size:20 final size:20
Alignment explanation
Indices: 27052--27177 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
27042 TTTTTAACCA
27052 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
27072 AATGTATTGATACATTCTATCTTTTACCC
1 AATGTATCGAT--A--C-AT-TTTT---C
*
27101 ATATGTATCGATATATTTTTC
1 A-ATGTATCGATACATTTTTC
* * *
27122 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
27142 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
27162 AATGTATTGATACATT
1 AATGTATCGATACATT
27178 CTGGCTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
20 56 0.67
21 2 0.02
22 1 0.01
24 5 0.06
25 4 0.05
26 4 0.05
28 1 0.01
29 2 0.02
30 9 0.11
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:28126 original size:20 final size:22
Alignment explanation
Indices: 28086--28126 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28076 TAGCCTTTGA
*
28086 CCATGCATTTCTTTACTATGTT
1 CCATGCATTTCTTAACTATGTT
28108 CCATGCATTT-TTAAC-ATGT
1 CCATGCATTTCTTAACTATGT
28127 CTAGCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (22 bp):
CCATGCATTTCTTAACTATGTT
Found at i:29482 original size:20 final size:20
Alignment explanation
Indices: 29457--29507 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29447 ACCCTGAAAA
*
29457 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
29477 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
29497 GTATCGATACA
1 GTATCGATACA
29508 TGAAAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:29598 original size:13 final size:13
Alignment explanation
Indices: 29580--29604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29570 ACACACAGTA
29580 TGTATCGATACAT
1 TGTATCGATACAT
29593 TGTATCGATACA
1 TGTATCGATACA
29605 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:38239 original size:20 final size:20
Alignment explanation
Indices: 38214--38264 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38204 ACCCTGAAAA
*
38214 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
38234 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
38254 GTATCGATACA
1 GTATCGATACA
38265 TGAAAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:38355 original size:13 final size:13
Alignment explanation
Indices: 38337--38361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38327 ACACACAGTA
38337 TGTATCGATACAT
1 TGTATCGATACAT
38350 TGTATCGATACA
1 TGTATCGATACA
38362 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:38358 original size:32 final size:33
Alignment explanation
Indices: 38317--38384 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
38307 GTAGCCAAAC
**
38317 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
38349 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
38382 TTG
1 TTG
38385 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:49545 original size:13 final size:13
Alignment explanation
Indices: 49527--49551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49517 ATTCATCATG
49527 TATCGATACATTA
1 TATCGATACATTA
49540 TATCGATACATT
1 TATCGATACATT
49552 GTGCCATGTA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:57813 original size:28 final size:28
Alignment explanation
Indices: 57777--58378 Score: 683
Period size: 28 Copynumber: 21.1 Consensus size: 28
57767 ATATGACCCT
57777 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
57805 TTTCAAAGCCTACAAGCCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
57833 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
57861 TGTCACACCCCATAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
57889 TTTCAAAGCCCACAAGTC-GATGGCACCC
1 TTTCAAAGCCCACAAGTCAG-TGGCATCC
* * * * *
57917 TGTCAAACCCCACAAGACAATGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
57945 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
57973 TTTCAAATCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
58001 TTTTCAAAGCACACAAGTTAGTGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
58032 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
58059 TTTTCAAAGCCCACAAGTCAATGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
58088 TTTCAAAGCTCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
58116 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
58144 TTTGAAAGCCCACAAGTTAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
58172 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
58199 ATTTCAAAGCCCACAAGTCAATGGCATCA
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
58228 TTTCAAAGCCCATAAGTCAGTGGCTTCTT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
*
58257 TTTCAAAGCCAACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
58284 ATTTCAAAACCCACAAGTCAATGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
*
58315 TTTCAAAGCTCACACAAGTCAGTGGCAACGC
1 TTTCAAAGC-C-CACAAGTCAGTGGCATC-C
*
58346 TTTTCAAAGCCCACACAAGTTAGTGGCA-CC
1 -TTTCAAAG-CC-CACAAGTCAGTGGCATCC
58376 TTT
1 TTT
58379 TTTTAAAGCC
Statistics
Matches: 486, Mismatches: 69, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.01
28 354 0.73
29 49 0.10
30 33 0.07
31 7 0.01
32 38 0.08
33 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:59410 original size:20 final size:21
Alignment explanation
Indices: 59385--59464 Score: 103
Period size: 20 Copynumber: 4.0 Consensus size: 21
59375 TTTTACCCAG
59385 ATGTATCGATACATT-TATCA
1 ATGTATCGATACATTATATCA
* *
59405 ATGTATCGATACA-TGTATGA
1 ATGTATCGATACATTATATCA
* *
59425 ATGTATGGATACATTCT-TCA
1 ATGTATCGATACATTATATCA
59445 ATGTATCGATACATTATATC
1 ATGTATCGATACATTATATC
59465 TTTTTACCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 46 0.90
21 4 0.08
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTATATCA
Found at i:62775 original size:22 final size:21
Alignment explanation
Indices: 62747--62796 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
62737 ATTTTTACTT
62747 AAAAACATTTGATTTA-AAGCTC
1 AAAAACATTTG-TTTATAA-CTC
62769 AAAAACATTTGTTTATAACTC
1 AAAAACATTTGTTTATAACTC
62790 AAAAACA
1 AAAAACA
62797 GTTATTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAAACATTTGTTTATAACTC
Found at i:62946 original size:13 final size:13
Alignment explanation
Indices: 62928--62952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62918 GATCCTAACA
62928 GTATCGATACAAT
1 GTATCGATACAAT
62941 GTATCGATACAA
1 GTATCGATACAA
62953 AGCATAATGT
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:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:63420 original size:49 final size:49
Alignment explanation
Indices: 63346--63445 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
63336 AAGGGATATG
*
63346 ATTAGGAATGTACGAGGTTAGGATGGTTTTGCCCTGAAGTTCTTGGGTT
1 ATTAGGAATGTACGAGGTTAAGATGGTTTTGCCCTGAAGTTCTTGGGTT
* *
63395 ATTAGGAATGTGCGAGGTTAAGATGGTTTTGCCCTGGAGTTCTTGGGTT
1 ATTAGGAATGTACGAGGTTAAGATGGTTTTGCCCTGAAGTTCTTGGGTT
63444 AT
1 AT
63446 AAAGTCAAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (49 bp):
ATTAGGAATGTACGAGGTTAAGATGGTTTTGCCCTGAAGTTCTTGGGTT
Found at i:70385 original size:20 final size:19
Alignment explanation
Indices: 70338--70423 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
70328 GCCAATCACC
*
70338 TGTATCGATACATTCTTTGTA
1 TGTATCGATACA-T-TTGGTA
*
70359 AGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGGT-A
70379 TGTATCGATACA------A
1 TGTATCGATACATTTGGTA
70392 TGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGGT-A
70412 TGTATCGATACA
1 TGTATCGATACA
70424 ATGTATCGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
13 13 0.24
19 4 0.07
20 26 0.48
21 11 0.20
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATTTGGTA
Found at i:70396 original size:13 final size:12
Alignment explanation
Indices: 70377--70434 Score: 61
Period size: 13 Copynumber: 5.0 Consensus size: 12
70367 TACATTTGGT
70377 CATGTATCGATA
1 CATGTATCGATA
70389 CAATGTATCGATA
1 C-ATGTATCGATA
*
70402 CAT-T-T-GGT-
1 CATGTATCGATA
70410 CATGTATCGATA
1 CATGTATCGATA
70422 CAATGTATCGATA
1 C-ATGTATCGATA
70435 TTGTGCATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 4 0.11
13 23 0.61
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:70402 original size:33 final size:33
Alignment explanation
Indices: 70360--70434 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
70350 TTCTTTGTAA
70360 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
70393 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATACATTTGGTCATGTATCGATACAAT
70426 GTATCGATA
1 GTATCGATA
70435 TTGTGCATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (33 bp):
GTATCGATACATTTGGTCATGTATCGATACAAT
Found at i:70448 original size:33 final size:32
Alignment explanation
Indices: 70360--70456 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 32
70350 TTCTTTGTAA
*
70360 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATA-ATTTGATCATGTATCGATACAAT
*
70393 GTATCGATACATTTGGTCATGTATCGATACAAT
1 GTATCGATA-ATTTGATCATGTATCGATACAAT
*
70426 GTATCGAT-ATTGTGCATTATGTATCGATACA
1 GTATCGATAATT-TG-ATCATGTATCGATACA
70457 TCTGAAGGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.05
32 2 0.03
33 55 0.92
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (32 bp):
GTATCGATAATTTGATCATGTATCGATACAAT
Found at i:73567 original size:33 final size:32
Alignment explanation
Indices: 73525--73592 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
73515 CGTTACAAGC
* *
73525 CAATGTATCGATACATTTTAG-GATGTATCGATA
1 CAATGTATCGATAAATATT-GTG-TGTATCGATA
73558 CAATGTATCGATAAATATTGTGTGTATCGATA
1 CAATGTATCGATAAATATTGTGTGTATCGATA
73590 CAA
1 CAA
73593 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATAAATATTGTGTGTATCGATA
Found at i:73680 original size:20 final size:21
Alignment explanation
Indices: 73633--73685 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
73623 GCCAATCACC
*
73633 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
73654 AGTATCGATACATT-TAGT-CA
1 TGTATCGATACATTCT-GTACA
73674 TGTATCGATACA
1 TGTATCGATACA
73686 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:73691 original size:13 final size:13
Alignment explanation
Indices: 73673--73697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73663 ACATTTAGTC
73673 ATGTATCGATACA
1 ATGTATCGATACA
73686 ATGTATCGATAC
1 ATGTATCGATAC
73698 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:74267 original size:66 final size:66
Alignment explanation
Indices: 74192--74322 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
74182 GATCTAATTT
*
74192 CCATAGCTTCAAGAAACACATTAGTAAAGTTCAAATATCAAGATTTTTCATTTTCCTTTTCTCTC
1 CCATAGCTTCAAGAAACACATTAGTAAAATTCAAATATCAAGATTTTTCATTTTCCTTTTCTCTC
74257 C
66 C
*
74258 CCATAGCTTCAAGAAATACATTAGTAAAATTCAAATATCAAGATTTTTCATTTTCCTTTTCTCTC
1 CCATAGCTTCAAGAAACACATTAGTAAAATTCAAATATCAAGATTTTTCATTTTCCTTTTCTCTC
74323 TCCCTTAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (66 bp):
CCATAGCTTCAAGAAACACATTAGTAAAATTCAAATATCAAGATTTTTCATTTTCCTTTTCTCTC
C
Found at i:76209 original size:13 final size:13
Alignment explanation
Indices: 76191--76216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76181 TATAAACCCT
76191 TTGTATCGATACA
1 TTGTATCGATACA
76204 TTGTATCGATACA
1 TTGTATCGATACA
76217 GAGAATGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:76432 original size:8 final size:8
Alignment explanation
Indices: 76419--76444 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
76409 AACACAAAAC
76419 ATCACAAA
1 ATCACAAA
76427 ATCACAAA
1 ATCACAAA
76435 ATCACAAA
1 ATCACAAA
76443 AT
1 AT
76445 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:77634 original size:13 final size:13
Alignment explanation
Indices: 77616--77641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77606 TACACCAAGT
77616 ATGTATCGATACA
1 ATGTATCGATACA
77629 ATGTATCGATACA
1 ATGTATCGATACA
77642 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:77639 original size:32 final size:33
Alignment explanation
Indices: 77598--77661 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
77588 TAGCCAAACT
* **
77598 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
77630 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
77662 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:77869 original size:5 final size:5
Alignment explanation
Indices: 77852--77881 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
77842 TCCATCAGCT
77852 AGAGA AG-GA AGAGA AGAGA AGAGA AGAGA A
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA A
77882 ACAAGTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:78167 original size:34 final size:35
Alignment explanation
Indices: 78104--78170 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
78094 CTAAGTGATT
78104 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
78140 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
78171 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:82856 original size:13 final size:13
Alignment explanation
Indices: 82838--82863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82828 TACACCAAGT
82838 ATGTATCGATACA
1 ATGTATCGATACA
82851 ATGTATCGATACA
1 ATGTATCGATACA
82864 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:82861 original size:32 final size:33
Alignment explanation
Indices: 82820--82883 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
82810 TAGCCAAACT
* **
82820 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
82852 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
82884 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:83091 original size:5 final size:5
Alignment explanation
Indices: 83074--83103 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
83064 TCCATCAGCT
83074 AGAGA AG-GA AGAGA AGAGA AGAGA AGAGA A
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA A
83104 ACAAGTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:83389 original size:34 final size:35
Alignment explanation
Indices: 83326--83392 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
83316 CTAAGTGATT
83326 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
83362 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
83393 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:88804 original size:32 final size:33
Alignment explanation
Indices: 88740--88807 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
88730 CGTTACAAGC
*
88740 CAATGTATCGATACATTTTCGGATGTATCGATA
1 CAATGTATCGATACATATTCGGATGTATCGATA
*
88773 CAATGTATTGATACATATT-GTG-TGTATCGATA
1 CAATGTATCGATACATATTCG-GATGTATCGATA
88805 CAA
1 CAA
88808 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTCGGATGTATCGATA
Found at i:88884 original size:20 final size:21
Alignment explanation
Indices: 88837--88887 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
88827 GCCAATCACC
**
88837 TGTATCGATACATTTTTTACA
1 TGTATCGATACATTTGGTACA
*
88858 AGTATCGATACATTTGGT-CA
1 TGTATCGATACATTTGGTACA
88878 TGTATCGATA
1 TGTATCGATA
88888 TAATGTATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTTGGTACA
Done.