Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3797
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: 92498
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1409 original size:39 final size:40
Alignment explanation
Indices: 1364--1588 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
1354 GCTCCTCGTT
* * * *
1364 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
1404 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
1443 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
1483 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
1523 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
1564 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
1589 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:1597 original size:41 final size:41
Alignment explanation
Indices: 1520--1597 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1510 CTTGTATCTC
* * *
1520 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1561 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1598 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:9016 original size:40 final size:40
Alignment explanation
Indices: 8923--9147 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
8913 GCTCCTCGTT
* * * *
8923 CAAATGCCTTCGGGACATATCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
8963 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
9002 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
9042 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
9082 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
9123 CAAA-GCCTTCGGGGCTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9148 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9156 original size:41 final size:41
Alignment explanation
Indices: 9079--9156 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
9069 CTTGTATCTC
* * * *
9079 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGAGCTTAGCCCGGACACATTCACTTA
*
9120 GCACAAA-GCCTTCGGGGCTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTCGGAGCTTAGCCCGGACA-CATTCA
9157 ATTAATCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 19 0.61
41 12 0.39
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGAGCTTAGCCCGGACACATTCACTTA
Found at i:16934 original size:43 final size:42
Alignment explanation
Indices: 16860--16952 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
16850 GATTTATGTA
* * * *
16860 TAAGACCATGTCTGGGACATTGACATCATATTTGATTTCGTG
1 TAAGACCATGTCTGAGACAGTGACATCATATTTGATTACATG
* * *
16902 TAAGACCCTGTCTGAGATAGTGTCATCGATATTTGATTACATG
1 TAAGACCATGTCTGAGACAGTGACATC-ATATTTGATTACATG
16945 TAAGACCA
1 TAAGACCA
16953 CATCTGGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 22 0.52
43 20 0.48
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (42 bp):
TAAGACCATGTCTGAGACAGTGACATCATATTTGATTACATG
Found at i:35535 original size:177 final size:177
Alignment explanation
Indices: 35237--35657 Score: 643
Period size: 177 Copynumber: 2.4 Consensus size: 177
35227 AGGTTGGCGA
* * * * *
35237 TAGCAAGGAAACAAACTAAAGATTGAAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAG
1 TAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCAAAG
35302 ATGGCGAATCTTATCTCCATGTATCAGCAATGGAGCAGATTTAAGTCCCTAAGCCTTATCTCTCT
66 ATGGCGAATCTTATCTCCATGTATCAGCAATGGAGCAGATTTAAGTCCCTAAGCCTTATCTCTCT
*
35367 GAGGTAGTAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTCCTGAGG
131 GAGGTAGCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTCCTGAGG
*
35414 TAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCGGAA
1 TAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATC-AAA
*
35479 GA-GGCGAATCTTATCTCCATGTATC-GACAATGGAGCAGATTTAAG-CCTTCAAGCCTTATCTC
65 GATGGCGAATCTTATCTCCATGTATCAG-CAATGGAGCAGATTTAAGTCCCT-AAGCCTTATCTC
35541 TCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTCCTGAGG
128 TCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTCCTGAGG
* * * * * *
35591 TAGCAAGGAAGCAGATTGATGATTGTAGATCTTATCTCTCTAAGGTAGC-AGTGCAGCAGATCAA
1 TAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAA-GCA-CTAGTGGAGCAGATCAA
35655 AGA
64 AGA
35658 CGATGAATTC
Statistics
Matches: 224, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
176 4 0.02
177 201 0.90
178 18 0.08
179 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (177 bp):
TAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCACTAGTGGAGCAGATCAAAG
ATGGCGAATCTTATCTCCATGTATCAGCAATGGAGCAGATTTAAGTCCCTAAGCCTTATCTCTCT
GAGGTAGCAAGAGAGCAGGTTGAAGATTGAGTCTTATCTTCCTGAGG
Found at i:35651 original size:45 final size:42
Alignment explanation
Indices: 35356--35640 Score: 170
Period size: 43 Copynumber: 6.5 Consensus size: 42
35346 GTCCCTAAGC
* *
35356 CTTATCTCTCTGAGGTAGTAAGAGAGCAGGTTGAAGATTGAGT
1 CTTATCTCTCTGAGGTAGCAAG-GAGCAGATTGAAGATTGAGT
*
35399 CTTATCT-TCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGAT
1 CTTATCTCT-CTGAGGTAGCAAGG-AGCAGATTGAAGATTG-AG-T
* * * * * ** *
35444 CTTATCTCCCT-AAGCA-CTAGTGGAGCAGATCGGAAGAGGCGAAT
1 CTTATCTCTCTGAGGTAGC-A-AGGAGCAGAT-TGAAGA-TTGAGT
* * * * *
35488 CTTATCTC-CATGTA--TCGACAATGGAGCAGATTTAAGCCTTCAAGC
1 CTTATCTCTC-TG-AGGTAG-CAA-GGAGCAGATTGAAG-ATT-GAGT
*
35533 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAGT
1 CTTATCTCTCTGAGGTAGCAAG-GAGCAGATTGAAGATTGAGT
*
35576 CTTATCT-TCCTGAGGTAGCAAGGAAGCAGATTGATGATTGTAGAT
1 CTTATCTCT-CTGAGGTAGCAAGG-AGCAGATTGAAGATTG-AG-T
*
35621 CTTATCTCTCTAAGGTAGCA
1 CTTATCTCTCTGAGGTAGCA
35641 GTGCAGCAGA
Statistics
Matches: 184, Mismatches: 32, Indels: 50
0.69 0.12 0.19
Matches are distributed among these distances:
42 4 0.02
43 71 0.39
44 31 0.17
45 71 0.39
46 7 0.04
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
CTTATCTCTCTGAGGTAGCAAGGAGCAGATTGAAGATTGAGT
Found at i:41536 original size:10 final size:10
Alignment explanation
Indices: 41521--41583 Score: 72
Period size: 10 Copynumber: 5.9 Consensus size: 10
41511 TGATACTTTA
41521 TAAAATTAAT
1 TAAAATTAAT
*
41531 TAAAATTCAT
1 TAAAATTAAT
*
41541 CAAAATTAATT
1 TAAAATTAA-T
41552 ATAAAATTAATT
1 -TAAAATTAA-T
41564 ATAAAATTAAT
1 -TAAAATTAAT
41575 TAAAATTAA
1 TAAAATTAA
41584 ACATTTTCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
10 25 0.53
11 2 0.04
12 20 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAAATTAAT
Found at i:41559 original size:12 final size:12
Alignment explanation
Indices: 41518--41576 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
41508 CCTTGATACT
41518 TTATAAAATTAA
1 TTATAAAATTAA
*
41530 -T-TAAAATTCA
1 TTATAAAATTAA
*
41540 -T-CAAAATTAA
1 TTATAAAATTAA
41550 TTATAAAATTAA
1 TTATAAAATTAA
41562 TTATAAAATTAA
1 TTATAAAATTAA
41574 TTA
1 TTA
41577 AAATTAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 16 0.39
11 2 0.05
12 23 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
TTATAAAATTAA
Found at i:50074 original size:46 final size:45
Alignment explanation
Indices: 50002--50175 Score: 156
Period size: 46 Copynumber: 3.8 Consensus size: 45
49992 TTTGGGCATT
*
50002 CGAACTCGTTGAGTTGAGTCCCAGTTCACCTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG-C
* **** *
50048 CGAACTCATTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG-GCAA--C
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-ACCTATG-GA-T-GCG-AATGC
* * *
50095 CGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGC
* *
50140 CTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 C-GAACTCGTTGAGTTGAGTCCGAGTTCACCTATGG
50176 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
43 3 0.03
44 2 0.02
45 3 0.03
46 60 0.58
47 29 0.28
48 1 0.01
49 2 0.02
50 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGC
Found at i:65784 original size:39 final size:40
Alignment explanation
Indices: 65683--65865 Score: 184
Period size: 39 Copynumber: 4.7 Consensus size: 40
65673 TTGAATGATG
* *
65683 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
65722 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
65763 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
65802 TCCGGGTTAAGTCCCGAAGGCA-TT-TGCGAGTTACTACA-
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTA-AT
* *
65840 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
65866 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
38 31 0.25
39 40 0.32
40 40 0.32
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:65819 original size:79 final size:79
Alignment explanation
Indices: 65683--65865 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 79
65673 TTGAATGATG
*
65683 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
65747 TGTGCGAGATACTA-A
65 T-TGCGAGATACTACA
* * * **
65762 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
65824 TTTGCGAGTTACTACA
64 TTTGCGAGATACTACA
* *
65840 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
65866 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
77 20 0.22
78 18 0.20
79 34 0.38
80 18 0.20
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGCGAGATACTACA
Found at i:65845 original size:38 final size:39
Alignment explanation
Indices: 65684--65865 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
65674 TGAATGATGT
* * * *
65684 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
65724 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
65764 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
65802 TCCGGGTTAAGTCCCGAAGGCA-TT-TGCGAGTTACTACAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
65841 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
65866 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
38 31 0.25
39 41 0.34
40 42 0.34
41 8 0.07
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:65872 original size:78 final size:78
Alignment explanation
Indices: 65736--65888 Score: 188
Period size: 77 Copynumber: 2.0 Consensus size: 78
65726 GGACTAAGAT
* **
65736 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTA-CTA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAG-TAGCTA
65800 AATCCGGGTTAAGTC
65 AATCC-GGTTAAGTC
* *
65815 CCGAAGGCA-TT-TGCGAGTTACTACA-ACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGATACTA-ATACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTAGCT
*
65877 ATATCCGGTTAA
64 AAATCCGGTTAA
65889 AATTCCGAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
77 28 0.43
78 28 0.43
79 9 0.14
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAA
ATCCGGTTAAGTC
Found at i:65897 original size:78 final size:79
Alignment explanation
Indices: 65735--65899 Score: 187
Period size: 78 Copynumber: 2.1 Consensus size: 79
65725 CGGACTAAGA
* **
65735 TCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
*
65800 AATCCGGGTTAAGT
66 AATCCGGGTTAAAT
* * *
65814 CCCGAAGGCA-TT-TGCGAGTTACTACA-ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCATTTGTGCGAGATACTA-ATACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
65875 CTATATCC-GGTTAAAAT
63 CTAAATCCGGGTT-AAAT
65892 TCCGAAGG
1 TCCGAAGG
65900 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
77 26 0.36
78 38 0.52
79 9 0.12
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTTAAAT
Found at i:67238 original size:65 final size:59
Alignment explanation
Indices: 67157--67278 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 59
67147 AGGGTTTAAA
67157 GTCTGCTAACACCTCGTGTTCGACTCCGGTGTCGGTCTCGGGTTCGGGGTGTTACATTTGATTTG
1 GTCTGCTAACACCTCGTGTTCGACTCC---G-CGGTCTC-GGTTC-GGGTGTTACATTTGATTTG
67222 GTCTGCTAACACCTCGTGTTCGACTCCGCGGTCTCGGTTCGGGTGTTACATTTGATT
1 GTCTGCTAACACCTCGTGTTCGACTCCGCGGTCTCGGTTCGGGTGTTACATTTGATT
67279 GGTATCAAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
59 17 0.30
60 5 0.09
61 7 0.12
62 1 0.02
65 27 0.47
ACGTcount: A:0.11, C:0.25, G:0.29, T:0.35
Consensus pattern (59 bp):
GTCTGCTAACACCTCGTGTTCGACTCCGCGGTCTCGGTTCGGGTGTTACATTTGATTTG
Found at i:73775 original size:40 final size:40
Alignment explanation
Indices: 73691--73875 Score: 166
Period size: 40 Copynumber: 4.7 Consensus size: 40
73681 TTGAATGATG
* * * *
73691 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
73731 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* *
73771 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
73810 TCCGGGTTAA-ATCCCGAAGGCAATTATGCGAGTTACTACAA
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
73851 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGGCTAAGAT-CCGAAGGCATTTG
73876 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 33 0.28
40 75 0.64
41 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:73827 original size:79 final size:79
Alignment explanation
Indices: 73691--73908 Score: 221
Period size: 79 Copynumber: 2.7 Consensus size: 79
73681 TTGAATGATG
* * * * ** *
73691 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATATCCGGGTTAA-ATCCGAAGGCAAT
*
73755 TGTGCGAGATACTA-A
64 TATGCGAGATACTACA
*
73770 TTCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCAAT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAAT-CCGAAGGCAAT
*
73834 TATGCGAGTTACTACA
64 TATGCGAGATACTACA
* * * *
73850 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTAAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTA-CTATATCCGGGTTAAA-TCCGAAGG
73909 TATGTGATTT
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
78 2 0.02
79 70 0.60
80 45 0.38
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAATCCGAAGGCAATTA
TGCGAGATACTACA
Found at i:75259 original size:65 final size:66
Alignment explanation
Indices: 75178--75303 Score: 227
Period size: 65 Copynumber: 1.9 Consensus size: 66
75168 GGGGTTTAAA
*
75178 GTCTGCTAACACCTCGTGTTCGACTCCGGTGTCGGTCTCGGGTTCGGGGTGTTAC-ATTTGATTT
1 GTCTGCTAACACCTCGTGTTCGACTCCGGTGTCGGTCTCGAGTTCGGGGTGTTACAATTTGATTT
75242 G
66 G
*
75243 GTCTGCTAACACCTCGTGTTCGACTCTGGTGTCGGTCTCGAGTTCGGGGTGTTACAATTTG
1 GTCTGCTAACACCTCGTGTTCGACTCCGGTGTCGGTCTCGAGTTCGGGGTGTTACAATTTG
75304 GCTGTCCACA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 53 0.91
66 5 0.09
ACGTcount: A:0.12, C:0.23, G:0.30, T:0.35
Consensus pattern (66 bp):
GTCTGCTAACACCTCGTGTTCGACTCCGGTGTCGGTCTCGAGTTCGGGGTGTTACAATTTGATTT
G
Found at i:77210 original size:22 final size:22
Alignment explanation
Indices: 77184--77228 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
77174 ATTATGTGTA
77184 TTAATTCATGATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
77206 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
77228 T
1 T
77229 GGATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:81723 original size:42 final size:42
Alignment explanation
Indices: 81628--81789 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 42
81618 TTAGGGTTAC
* * *
81628 TGAGA-TTAGTGTAAGACCATAT-TGTGATATGGCATCTATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * *
81668 TAAGGTTTCGTGTAAGACCATATTTGGGATATGGCATCGATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
81710 TGAGATTTTGTGTAAAACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* * *
81753 CGAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGGCAT
81790 TGGTACGGTA
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 3 0.03
41 16 0.16
42 46 0.46
43 35 0.35
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:83792 original size:27 final size:27
Alignment explanation
Indices: 83762--83939 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
83752 ATATTGAGTC
* * * *
83762 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
83789 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
83816 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
83844 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
83871 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
83898 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
83925 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
83940 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:83901 original size:82 final size:81
Alignment explanation
Indices: 83783--83938 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
83773 TGCTATATAA
* *
83783 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
83848 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
83865 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
83929 CACTTAGTGC
65 CACTTAGTGC
83939 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:91973 original size:27 final size:27
Alignment explanation
Indices: 91943--92120 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
91933 ATATTGAGTC
* * * *
91943 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
91970 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
91997 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
92025 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
92052 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
92079 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
92106 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
92121 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:92082 original size:82 final size:81
Alignment explanation
Indices: 91964--92119 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
91954 TGCTATATAA
* *
91964 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
92029 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
92046 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
92110 CACTTAGTGC
65 CACTTAGTGC
92120 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.