Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 1758877
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
File 12 of 12
Found at i:1725961 original size:48 final size:48
Alignment explanation
Indices: 1725890--1725985 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1725880 ATCTTGGGGT
1725890 AAATTTAGTTTTTCAGGTCTGGAATCATGATTAAAACAAGTCCAAGAC
1 AAATTTAGTTTTTCAGGTCTGGAATCATGATTAAAACAAGTCCAAGAC
1725938 AAATTTAGTTTTTCAGGTCTGGAATCATGATTAAAACAAGTCCAAGAC
1 AAATTTAGTTTTTCAGGTCTGGAATCATGATTAAAACAAGTCCAAGAC
1725986 TCTAATTGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (48 bp):
AAATTTAGTTTTTCAGGTCTGGAATCATGATTAAAACAAGTCCAAGAC
Found at i:1729888 original size:16 final size:16
Alignment explanation
Indices: 1729864--1729895 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1729854 AAAAACTCTA
1729864 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCT
*
1729880 TTTTTTTTTCTTTTCT
1 TTTTCTTTTCTTTTCT
1729896 CCCTCTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCT
Found at i:1729938 original size:15 final size:16
Alignment explanation
Indices: 1729901--1729938 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1729891 TTTCTCCCTC
* *
1729901 TCTCTTTTTCTTTTTA
1 TCTCTTTTTCTGTTAA
1729917 TCTCTTTTTCTGTTAA
1 TCTCTTTTTCTGTTAA
1729933 TC-CTTT
1 TCTCTTT
1729939 AAGAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (16 bp):
TCTCTTTTTCTGTTAA
Found at i:1730022 original size:15 final size:15
Alignment explanation
Indices: 1730002--1730037 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1729992 GCCACGCTAA
1730002 TTTTTTAACCTTT-TT
1 TTTTTTAA-CTTTATT
1730017 TTTTTTAACTTTATT
1 TTTTTTAACTTTATT
1730032 TTTTTT
1 TTTTTT
1730038 TCACTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTAACTTTATT
Found at i:1730033 original size:16 final size:15
Alignment explanation
Indices: 1730002--1730044 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1729992 GCCACGCTAA
*
1730002 TTTTTTAACCTTTTT
1 TTTTTTAACTTTTTT
1730017 TTTTTTAACTTTATTT
1 TTTTTTAACTTT-TTT
*
1730033 TTTTTTCACTTT
1 TTTTTTAACTTT
1730045 CTTTCACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAACTTTTTT
Found at i:1730479 original size:27 final size:27
Alignment explanation
Indices: 1730430--1730490 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
1730420 TAGGAATTTA
* * * *
1730430 ATTAAAAATTTCATAGGTAGAAAGTCTT
1 ATTAAAAATCTCACAAGTAGAAAGT-TG
1730458 ATTAAAAATCTCACAAGT-GAAAGTTG
1 ATTAAAAATCTCACAAGTAGAAAGTTG
1730484 ATTAAAA
1 ATTAAAA
1730491 CTTTACATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.28
27 6 0.21
28 15 0.52
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (27 bp):
ATTAAAAATCTCACAAGTAGAAAGTTG
Found at i:1733065 original size:28 final size:28
Alignment explanation
Indices: 1732977--1733065 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
1732967 AAATTAATTA
*
1732977 TAATATTAGTTATAATACTAATTATTT-TATT
1 TAATA-TAATTATAAT--TAATT-TTTATATT
* * *
1733008 TAATTTAATTGA-AAATAATTTTAAGT-TT
1 TAATATAATT-ATAATTAATTTTTA-TATT
1733036 TAATATAATTATAATTAATTTTTATATT
1 TAATATAATTATAATTAATTTTTATATT
1733064 TA
1 TA
1733066 TAAAAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
27 4 0.09
28 30 0.65
29 1 0.02
30 6 0.13
31 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (28 bp):
TAATATAATTATAATTAATTTTTATATT
Found at i:1733393 original size:13 final size:13
Alignment explanation
Indices: 1733375--1733400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1733365 ACATGCATTA
1733375 TTTTTAAGAATGT
1 TTTTTAAGAATGT
1733388 TTTTTAAGAATGT
1 TTTTTAAGAATGT
1733401 ATTAATTGCG
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTTTAAGAATGT
Found at i:1734417 original size:19 final size:19
Alignment explanation
Indices: 1734393--1734435 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1734383 CTTTCATAAA
1734393 AGGTTTCAATGGATTAGAT
1 AGGTTTCAATGGATTAGAT
1734412 AGGTTTCAATGGATTAGAT
1 AGGTTTCAATGGATTAGAT
1734431 -GGTTT
1 AGGTTT
1734436 TTCAACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (19 bp):
AGGTTTCAATGGATTAGAT
Found at i:1734550 original size:16 final size:16
Alignment explanation
Indices: 1734529--1734564 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1734519 TCAAATTCGA
1734529 AAATAA-CTCGAACTCG
1 AAATAATCT-GAACTCG
1734545 AAATAATCTGAACTCG
1 AAATAATCTGAACTCG
1734561 AAAT
1 AAAT
1734565 GATCCAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (16 bp):
AAATAATCTGAACTCG
Found at i:1738197 original size:16 final size:17
Alignment explanation
Indices: 1738165--1738198 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1738155 TCCGAGTCTT
1738165 AGATCTTTACTTTTACC
1 AGATCTTTACTTTTACC
1738182 AGATCTTTAC-TTTACC
1 AGATCTTTACTTTTACC
1738198 A
1 A
1738199 AATTCTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (17 bp):
AGATCTTTACTTTTACC
Found at i:1738205 original size:17 final size:17
Alignment explanation
Indices: 1738167--1738201 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1738157 CGAGTCTTAG
*
1738167 ATCTTTACTTTTACCAG
1 ATCTTTACTTTTACCAA
1738184 ATCTTTAC-TTTACCAA
1 ATCTTTACTTTTACCAA
1738200 AT
1 AT
1738202 TCTTCAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.46
Consensus pattern (17 bp):
ATCTTTACTTTTACCAA
Found at i:1740568 original size:123 final size:123
Alignment explanation
Indices: 1740414--1740668 Score: 474
Period size: 123 Copynumber: 2.1 Consensus size: 123
1740404 ATTTTTTTTA
*
1740414 TTATGGGTTCGAGGACTTGGATTAGTCGATTAGTCTAATTAAGAGTTAGGATTTGGGTTGGGGGA
1 TTATGGGTTCGAGGACTTGGATTAGTCGATTAGTCTAATTAAGAGTTAGGATTTGGGTCGGGGGA
1740479 GTTATATTAGCCAACTATGCCATTTAGGCTTACGTATTTTGGATTATAGGTTATTGGG
66 GTTATATTAGCCAACTATGCCATTTAGGCTTACGTATTTTGGATTATAGGTTATTGGG
*
1740537 TTATGGGTTGGAGGACTTGGATTAGTCGATTAGTCTAATTAAGAGTTAGGATTTGGGTCGGGGGA
1 TTATGGGTTCGAGGACTTGGATTAGTCGATTAGTCTAATTAAGAGTTAGGATTTGGGTCGGGGGA
* *
1740602 TTTATATTAGCCAATTATGCCATTTAGGCTTACGTATTTTGGATTATAGGTTATTGGG
66 GTTATATTAGCCAACTATGCCATTTAGGCTTACGTATTTTGGATTATAGGTTATTGGG
1740660 TTATGGGTT
1 TTATGGGTT
1740669 TTGATTAAGA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.39
Consensus pattern (123 bp):
TTATGGGTTCGAGGACTTGGATTAGTCGATTAGTCTAATTAAGAGTTAGGATTTGGGTCGGGGGA
GTTATATTAGCCAACTATGCCATTTAGGCTTACGTATTTTGGATTATAGGTTATTGGG
Found at i:1741028 original size:170 final size:169
Alignment explanation
Indices: 1740733--1741072 Score: 427
Period size: 170 Copynumber: 2.0 Consensus size: 169
1740723 ATCATGTTGA
* * * ** *
1740733 TTTGAAAAGTTAAAACAGTAAATCGATTAATTAAATTTACTTAAGTTGAACTACCCTAAATTGAT
1 TTTGAAAAATTAAAACAGCAAATCAATTAATTAAACCTACTTAAATTGAACTACCCTAAATTGAT
* ** *
1740798 TAAGCTAAACTGATAAAACTAACCCGAATAAATTAAACTGAGTCAATTTTGATCGTTTTTCAATT
66 TAAGCAAAACCAATAAAACCAACCCGAATAAATTAAACTGAGTCAATTTTGATCGTTTTTCAATT
* * *
1740863 TA-TCGTAATTTGAGTCACTTAAACTCTATTTTTTGATAG
131 TACTAG-AATTTGAGTCACTCAAACTCCATTTTTTGATAG
*
1740902 TTTGAAAAATTAAAACCA-CAAATCAATTGATTAAACCTACTTAAATTCGAACTACCCTAAATTG
1 TTTGAAAAATTAAAA-CAGCAAATCAATTAATTAAACCTACTTAAATT-GAACTACCCTAAATTG
* * * * *
1740966 ATTAATCAAAACCAACT-AAACCAGCCCGAATAAATTGAATTGAGTC-ATTTTCGATTGTTTTTC
64 ATTAAGCAAAACCAA-TAAAACCAACCCGAATAAATTAAACTGAGTCAATTTT-GATCGTTTTTC
*
1741029 AATTTACTAGAATTTGGGTCACTCAAACTCCATTTTTTGATAG
127 AATTTACTAGAATTTGAGTCACTCAAACTCCATTTTTTGATAG
1741072 T
1 T
1741073 CATTTTTGTT
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
169 42 0.29
170 101 0.69
171 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (169 bp):
TTTGAAAAATTAAAACAGCAAATCAATTAATTAAACCTACTTAAATTGAACTACCCTAAATTGAT
TAAGCAAAACCAATAAAACCAACCCGAATAAATTAAACTGAGTCAATTTTGATCGTTTTTCAATT
TACTAGAATTTGAGTCACTCAAACTCCATTTTTTGATAG
Found at i:1744031 original size:21 final size:21
Alignment explanation
Indices: 1743966--1744041 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1743956 TACATAAGTA
1743966 AATGTATCGATACA-TT-TTG
1 AATGTATCGATACATTTGTTG
* ***
1743985 CAATGTA-CGGATATATTTGGCC
1 -AATGTATC-GATACATTTGTTG
*
1744007 AATGTATGGATACATTTGTTG
1 AATGTATCGATACATTTGTTG
1744028 AATGTATCGATACA
1 AATGTATCGATACA
1744042 ATCTCCAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.02
20 11 0.26
21 30 0.71
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTTG
Found at i:1744589 original size:14 final size:14
Alignment explanation
Indices: 1744570--1744599 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1744560 TACCAAAAGC
1744570 AAAAGTAAAAGAAA
1 AAAAGTAAAAGAAA
*
1744584 AAAAGTAAGAGAAA
1 AAAAGTAAAAGAAA
1744598 AA
1 AA
1744600 TGAAAGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAAGTAAAAGAAA
Found at i:1747427 original size:76 final size:77
Alignment explanation
Indices: 1747326--1747529 Score: 216
Period size: 76 Copynumber: 2.6 Consensus size: 77
1747316 GAGATAATAA
* * * * *
1747326 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
1747390 A-TT-AGAAAAAAT
64 ATTTGAGAAAAAAG
* * **
1747402 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* *
1747467 TTTGGGAATAAAG
65 TTTGAGAAAAAAG
* * *
1747480 CTGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 C-GGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1747530 GAAATAACGA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 7 0.07
76 47 0.45
77 2 0.02
78 7 0.07
79 41 0.39
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (77 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAAAAAAG
Found at i:1747522 original size:28 final size:28
Alignment explanation
Indices: 1747482--1747552 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1747472 GAATAAAGCT
** *
1747482 GGGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
1747510 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
1747538 GAGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
1747553 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:1747610 original size:52 final size:50
Alignment explanation
Indices: 1747541--1747710 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 50
1747531 AAATAACGAG
* *
1747541 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTA-TTTT-GAAATAAAACCGGA
** * *
1747593 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGA-TTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGG-TATTTTG-AAATAAAACC-GGA
* *
1747646 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTGAA--ATAAAACCGGA
1747697 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1747711 TCGAAAATAA
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 78 0.80
53 12 0.12
54 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGAAATAAAACCGGA
Found at i:1747729 original size:28 final size:28
Alignment explanation
Indices: 1747684--1747765 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
1747674 AGTGTTTTAA
* *
1747684 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1747711 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
1747738 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
1747766 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:1750201 original size:13 final size:13
Alignment explanation
Indices: 1750183--1750208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1750173 ACAAAGATCC
1750183 ATGTATCGATACA
1 ATGTATCGATACA
1750196 ATGTATCGATACA
1 ATGTATCGATACA
1750209 CAGAAAAATA
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:1750223 original size:33 final size:33
Alignment explanation
Indices: 1750162--1750228 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1750152 AAAATTTCCA
*** *
1750162 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATATATCGATAC
*
1750195 AATGTATCGATACACAGAAAAATATATCGATAC
1 AATGTATCGATACAAAGAAAAATATATCGATAC
1750228 A
1 A
1750229 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATATATCGATAC
Found at i:1750272 original size:19 final size:18
Alignment explanation
Indices: 1750248--1750315 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1750238 CAGTAGCTAA
1750248 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1750267 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1750282 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1750299 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1750316 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1750288 original size:13 final size:13
Alignment explanation
Indices: 1750270--1750294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1750260 ACAATACTTA
1750270 TGTATCGATACAT
1 TGTATCGATACAT
1750283 TGTATCGATACA
1 TGTATCGATACA
1750295 AAACTTATGT
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:1750292 original size:32 final size:32
Alignment explanation
Indices: 1750251--1750313 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1750241 TAGCTAATTA
*
1750251 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1750283 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1750314 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1750927 original size:55 final size:55
Alignment explanation
Indices: 1750843--1751629 Score: 1145
Period size: 55 Copynumber: 14.3 Consensus size: 55
1750833 ATAAATTGTA
* * * * * *
1750843 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1750898 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1750953 TCCTGCTCTTT-AGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1751008 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1751063 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1751118 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1751173 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1751228 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAA-GTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1751282 TCCTGCTCTTT-AGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1751337 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
1751392 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1751447 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1751502 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1751557 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1751612 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
1751630 AAAAAGCGGA
Statistics
Matches: 687, Mismatches: 29, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
53 3 0.00
54 62 0.09
55 606 0.88
56 16 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:1751138 original size:26 final size:26
Alignment explanation
Indices: 1751109--1751253 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 26
1751099 GTGTGGGCTT
1751109 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
1751135 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
1751162 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
** * * *
1751190 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
*
1751217 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
1751245 TGAAAGGTG
1 TGAAAGGTG
1751254 CCACCCACTT
Statistics
Matches: 85, Mismatches: 24, Indels: 20
0.66 0.19 0.16
Matches are distributed among these distances:
25 6 0.07
26 25 0.29
27 16 0.19
28 16 0.19
29 16 0.19
30 6 0.07
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:1751227 original size:29 final size:29
Alignment explanation
Indices: 1751139--1751227 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1751129 GAGGACTGAA
1751139 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
1751168 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
1751194 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1751223 AGGTG
1 AGGTG
1751228 TCCTGCTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:1751469 original size:27 final size:27
Alignment explanation
Indices: 1751439--1751582 Score: 64
Period size: 27 Copynumber: 5.3 Consensus size: 27
1751429 TGTGGGCTTT
1751439 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1751466 GAAA-ATG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
1751493 TAAAAGGTGTCCTGCTCTTTGAGGACTG
1 GA-AAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1751521 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1751549 GAAAGGTGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1751575 GAAAGGTG
1 GAAAGGTG
1751583 CCACCAACTT
Statistics
Matches: 78, Mismatches: 29, Indels: 21
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 18 0.23
27 19 0.24
28 19 0.24
29 10 0.13
30 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1752615 original size:1 final size:1
Alignment explanation
Indices: 1752611--1752658 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
1752601 CTTTTCTCTC
* * * * *
1752611 TTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1752659 GAAGAGAAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:1752643 original size:12 final size:12
Alignment explanation
Indices: 1752626--1752659 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1752616 CTTTGTTTTG
1752626 TTTTTTTTTGTT
1 TTTTTTTTTGTT
*
1752638 TTTTTTTTTCTT
1 TTTTTTTTTGTT
1752650 TTTTTTTTTG
1 TTTTTTTTTG
1752660 AAGAGAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:1752658 original size:15 final size:15
Alignment explanation
Indices: 1752595--1752658 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
1752585 CTTAAGTAGG
* *
1752595 TTTTTTCTTTTCTCT
1 TTTTTTCTTTTTTTT
*
1752610 CTTTTTCTTTGTTTTGT
1 TTTTTTCTTT-TTTT-T
*
1752627 TTTTTT-TTGTTTTT
1 TTTTTTCTTTTTTTT
1752641 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
1752656 TTT
1 TTT
1752659 GAAGAGAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.17
15 23 0.57
16 4 0.10
17 6 0.15
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Done.