Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1359
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: 73978
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:2319 original size:40 final size:39
Alignment explanation
Indices: 2264--2342 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
2254 ATTTGAATGA
2264 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTT-TGCTAGTGATTT
2304 TATCCGGGCTAAGTCCCGAAGGCATTTTGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTTGCTAGTGATTT
2343 CGTAAGTCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (39 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTTGCTAGTGATTT
Found at i:2469 original size:38 final size:40
Alignment explanation
Indices: 2368--2470 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
2358 ATTTTAGTCC
2368 GGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCG
1 GGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCG
*
2408 GGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATA-CCG
1 GGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCG
* *
2447 GGTTAAGA-CCGAAGGCAATTGTGC
1 GGCTAAGACCCGAAGGCATTTGTGC
2471 TTGTGGTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 15 0.25
39 10 0.17
40 35 0.58
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (40 bp):
GGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCG
Found at i:10505 original size:40 final size:40
Alignment explanation
Indices: 10450--10636 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
10440 ATTTGAATGA
10450 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
10490 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
10530 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
* * * *
10570 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTT
*
10610 TATCCGGGCTAAGACCCGAAGGCATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTT
10637 GTGCGAGTTG
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
40 139 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
Found at i:10637 original size:40 final size:40
Alignment explanation
Indices: 10449--10700 Score: 312
Period size: 40 Copynumber: 6.3 Consensus size: 40
10439 CATTTGAATG
*
10449 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
10489 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
10529 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* * *
10569 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * *
10609 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * * * *
10649 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
10689 ATATCC-GGCTAA
1 ATATCCGGGCTAA
10701 ATTCCGAAGA
Statistics
Matches: 196, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 7 0.04
40 186 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
Found at i:18632 original size:40 final size:39
Alignment explanation
Indices: 18442--18625 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
18432 CGAATGATGT
* * * *
18442 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* *
18482 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
18522 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
18560 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
18601 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
18626 AACGAGTAGT
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:20094 original size:26 final size:26
Alignment explanation
Indices: 20059--20110 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20049 AATGTGAAAG
*
20059 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
20085 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
20111 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:20121 original size:103 final size:101
Alignment explanation
Indices: 19981--20343 Score: 597
Period size: 101 Copynumber: 3.6 Consensus size: 101
19971 TGTATATAAA
** * * *
19981 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
20045 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCG
20084 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
20149 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCG
20185 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
20250 TGAAAT-AAAAGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
20286 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCG-GATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
20344 ATAACGGTTA
Statistics
Matches: 250, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
100 31 0.12
101 155 0.62
103 63 0.25
104 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (101 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:20195 original size:26 final size:26
Alignment explanation
Indices: 20160--20211 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
20150 GAAATGAAAG
*
20160 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
20186 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
20212 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:20301 original size:27 final size:27
Alignment explanation
Indices: 20259--20310 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
20249 TTGAAATAAA
*
20259 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
20286 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
20311 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:27671 original size:26 final size:26
Alignment explanation
Indices: 27636--27687 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
27626 AATGTGAAAG
*
27636 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
27662 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
27688 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:27812 original size:104 final size:104
Alignment explanation
Indices: 27558--27924 Score: 618
Period size: 103 Copynumber: 3.6 Consensus size: 104
27548 TGTATATAAA
** * * *
27558 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
27622 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
27661 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
27726 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
27765 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
27830 TGAAA--T-AAAAGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
27866 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
27925 ATAACGGTTA
Statistics
Matches: 254, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
101 86 0.34
102 1 0.00
103 91 0.36
104 76 0.30
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:27881 original size:27 final size:27
Alignment explanation
Indices: 27839--27890 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
27829 TTGAAATAAA
*
27839 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
27866 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
27891 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:35923 original size:47 final size:47
Alignment explanation
Indices: 35854--36270 Score: 708
Period size: 47 Copynumber: 8.8 Consensus size: 47
35844 CCCTTCGGGA
* * * * * *
35854 CTTATCGCATTTATACACTTTCACATCCATCACTTTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35901 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35948 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
35995 CTTATCACATATATAGACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
36042 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
36089 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
36138 CTTATCACATATATATACACTTGCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
36187 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
36234 ATTATCACATATATACACTTTCACATTCATCACATCG
1 CTTATCACATATATACACTTTCACATTCATCACATCG
36271 AATCCTAAAT
Statistics
Matches: 355, Mismatches: 13, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
47 260 0.73
49 95 0.27
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:36201 original size:192 final size:188
Alignment explanation
Indices: 35854--36270 Score: 708
Period size: 192 Copynumber: 2.2 Consensus size: 188
35844 CCCTTCGGGA
* * * * * *
35854 CTTATCGCATTTATACACTTTCACATCCATCACTTTGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
35919 TTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTGCACATTCATCACATC
*
35984 GGCCATTAGGCCTTATCACATATATAGACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
36042 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
36107 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTGCACATTCATCA
64 ACTTTCACATTCATCACATCGACCATTAGGCCTTATCAC--ATATATACACTTGCACATTCATCA
36172 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
127 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
36234 ATTATCACATATATACACTTTCACATTCATCACATCG
1 CTTATCACATATATACACTTTCACATTCATCACATCG
36271 AATCCTAAAT
Statistics
Matches: 215, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
188 49 0.23
190 46 0.21
192 120 0.56
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATACACTTGCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:36266 original size:25 final size:25
Alignment explanation
Indices: 36190--36268 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
36180 ATTAGGCCTT
36190 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
**** ***
36215 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
36237 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
36262 ATCACAT
1 ATCACAT
36269 CGAATCCTAA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41054 original size:39 final size:40
Alignment explanation
Indices: 40946--41130 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
40936 TCGAATGATG
* * *
40946 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
40985 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41026 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41065 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41104 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41131 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41152 original size:79 final size:79
Alignment explanation
Indices: 41002--41153 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
40992 CTAAGATCCA
* **
41002 AAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
41067 CGGGTTAAGTCCCG
66 CGGGTTAAGTCCCG
* * *
41081 AAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTAT
1 AAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAA
41144 ATCC-GGTTAA
63 ATCCGGGTTAA
41154 ATTCTGAAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.59
80 24 0.38
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATC
CGGGTTAAGTCCCG
Found at i:46087 original size:48 final size:48
Alignment explanation
Indices: 46016--46394 Score: 352
Period size: 48 Copynumber: 7.9 Consensus size: 48
46006 GTAAACTGCT
* * *
46016 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCC
* * * * * * *
46064 GATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCGTCTTAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCC
* * **
46112 GATGCCATGTCCTAGACATGGTCTTACACAAGCTCACATAAT-GTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAAGGCC
* **
46160 AATGCCATGTCCCAGACATGGTCTTACACTAGCAT-ACATATCAACACC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGC-TCACATATCAAGGCC
* * * * *
46208 GATGCCATATCCCAAACATGGTCTTACGCTGGCTCACATATCAAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCC
* * * * * **
46256 GATGCCACGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCC
* * * * ** *
46304 GATGCCATGTCCTAGATATGGTCTTACACTGGCTCTCATAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATCAAGGCC
** *
46352 GATGCCATGTCCCAGACAT-GTCTTACTTTAGCACACATATCAA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAA
46395 CCAAATGTCA
Statistics
Matches: 264, Mismatches: 61, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
46 2 0.01
47 17 0.06
48 242 0.92
49 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAGGCC
Found at i:46180 original size:96 final size:96
Alignment explanation
Indices: 46016--46377 Score: 426
Period size: 96 Copynumber: 3.8 Consensus size: 96
46006 GTAAACTGCT
*
46016 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
* * *
46081 ATGGTCTTATACTAGCTCTCGTCTTAATGTC
66 ATGGTCTTACACTAGCTCTCATCTCAATGTC
* ** * *
46112 GATGCCATGTCCTAGACATGGTCTTACACAAGCTCACATAAT-GTGGCCAATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCGAGGCCGATGCCATGTCCCAGA
* * ***
46176 CATGGTCTTACACTAGCAT-ACATATCAACACC
65 CATGGTCTTACACTAGC-TCTCATCTCAATGTC
* * * * * * *
46208 GATGCCATATCCCAAACATGGTCTTACGCTGGCTCACATATCAAGGCTGATGCCACGTCCTAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
*
46273 ATGGTCTTACACTAGCTCTCATCTCAATGTT
66 ATGGTCTTACACTAGCTCTCATCTCAATGTC
* * * * *
46304 GATGCCATGTCCTAGATATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCGAGGCCGATGCCATGTCCCAGA
46368 CAT-GTCTTAC
65 CATGGTCTTAC
46378 TTTAGCACAC
Statistics
Matches: 219, Mismatches: 42, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
95 10 0.05
96 205 0.94
97 4 0.02
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (96 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAGCTCTCATCTCAATGTC
Found at i:46356 original size:144 final size:141
Alignment explanation
Indices: 46015--46394 Score: 408
Period size: 144 Copynumber: 2.7 Consensus size: 141
46005 GGTAAACTGC
*
46015 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAGA
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGA
* * * * * * *
46080 CATGGTCTTATACTAGCTCTCGTCTTAATGTCGATGCCATGTCCTAGACATGGTCTTACACAAGC
66 CATGGTCTTACACTAGCTCACATATCAAGGTCGATGCCACGTCCTAGACATGGTCTTACACAAGC
46145 TCACATAATGT
131 TCACATAATGT
* * * ** *
46156 GGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCAT-ACATATCAACACCGATGCCATATCC
1 TG---ATGCCATGTCCCAGACATGGTCTTACACTGGC-TCACATATCGAGGCCGATGCCATGTCC
* * *
46220 CAAACATGGTCTTACGCTGGCTCACATATCAAGG-CTGATGCCACGTCCTAGACATGGTCTTACA
62 CAGACATGGTCTTACACTAGCTCACATATCAAGGTC-GATGCCACGTCCTAGACATGGTCTTACA
* *
46284 CTAGCTCTCATCTCAATGT
126 CAAGCTCACA--T-AATGT
* * * * *
46303 TGATGCCATGTCCTAGATATGGTCTTACACTGGCTCTCATAAT-GTGGCTGATGCCATGTCCCAG
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCGAGGCCGATGCCATGTCCCAG
** *
46367 ACAT-GTCTTACTTTAGCACACATATCAA
65 ACATGGTCTTACACTAGCTCACATATCAA
46395 CCAAATGTCA
Statistics
Matches: 194, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
141 1 0.01
143 22 0.11
144 161 0.83
145 3 0.02
146 1 0.01
147 6 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (141 bp):
TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGAGGCCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCTCACATATCAAGGTCGATGCCACGTCCTAGACATGGTCTTACACAAGC
TCACATAATGT
Found at i:50575 original size:23 final size:20
Alignment explanation
Indices: 50545--50607 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 20
50535 TGAAAGTATA
50545 ATTTTATTTTTATTAATTTAAAT
1 ATTTTATTTTTATTAATTT---T
50568 ATTTTATTTTTATTAATTTT
1 ATTTTATTTTTATTAATTTT
*
50588 ATTTTA-TTTTATAAATTTT
1 ATTTTATTTTTATTAATTTT
50607 A
1 A
50608 AAGCCCCTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 13 0.33
20 7 0.18
23 19 0.49
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTATTTTTATTAATTTT
Found at i:58078 original size:40 final size:39
Alignment explanation
Indices: 58047--58215 Score: 241
Period size: 39 Copynumber: 4.3 Consensus size: 39
58037 GGACTAAGAT
*
58047 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGC
1 CCGAAGGCATTGGTGCGAGTTACTAATTCCGGGCTAAGC
*
58086 CCGAAGGCATTGGTGCGAGTTACTAATTTCGGGCTAAGC
1 CCGAAGGCATTGGTGCGAGTTACTAATTCCGGGCTAAGC
* *
58125 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTGGTGCGAGTTACTAATTCCGGGCTAAG-C
* * *
58165 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTGGTGCGAGTTACTAAT-TCCGGGCTAAG-C
58205 CCGAAGGCATT
1 CCGAAGGCATT
58216 TGAACGAGTA
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 73 0.62
40 45 0.38
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTGGTGCGAGTTACTAATTCCGGGCTAAGC
Found at i:58095 original size:39 final size:40
Alignment explanation
Indices: 57994--58217 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
57984 TCGAATGATG
* * *
57994 TCCGGGAC-AAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGG-CTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
58033 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
58074 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
58113 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
58152 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
58191 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
58218 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
39 74 0.46
40 78 0.48
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:58248 original size:79 final size:79
Alignment explanation
Indices: 58047--58250 Score: 200
Period size: 79 Copynumber: 2.6 Consensus size: 79
58037 GGACTAAGAT
* ** * * *
58047 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCT-AAGCCCGAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
**
58111 ATTTCGGGCTAAGC
66 ATACCGGGCTAAGC
** * *
58125 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
*
58189 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * * *
58205 CCGAAGGCATTTGAACGAG-TAGCTATAT-CTGGTTAAATTCCGAAGG
1 CCGAAGGCATTGGAACGAGTTA-CTAAATCCGGGTTAAATCCCGAAGG
58251 TACGTGATTC
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
78 34 0.32
79 50 0.47
80 22 0.21
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTGGAACGAGTTACTAAATCCGGGTTAAATCCCGAAGGCATTGGTGCGAGTTACTA
ATACCGGGCTAAGC
Found at i:62336 original size:54 final size:53
Alignment explanation
Indices: 62203--62401 Score: 217
Period size: 54 Copynumber: 3.7 Consensus size: 53
62193 TTAAGGATAT
* * *
62203 CATGTAAGACCATGCAAAGGCATGGCAATTGGTAAGGTT-TCTAAGGC-AAGGAAAT-
1 CATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTCTATAAGGCAAAGG---TC
* *
62258 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-CTATAAGGCAAAGGTC
* * *
62312 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAAGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAAGGT-C
* *
62365 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
62402 TCAAAAGGAT
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
52 12 0.10
53 39 0.31
54 40 0.32
55 30 0.24
56 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (53 bp):
CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAAGGTC
Found at i:62391 original size:107 final size:109
Alignment explanation
Indices: 62203--62401 Score: 305
Period size: 107 Copynumber: 1.8 Consensus size: 109
62193 TTAAGGATAT
* *
62203 CATGTAAGACCATGCAAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
1 CATGTAAGACCATGCAAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAAGAAACCATGTAAGAC
*
62268 CATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
62312 CATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAAGATACCATGTAAGA
1 CATGTAAGACCATGCAAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAAGAAACCATGTAAGA
*
62374 CCATGTCAAGACATGGCAATGGTAAGTT
65 CCATGTCAAGACATGGCAATGATAAGTT
62402 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 3 0.04
107 47 0.57
108 7 0.09
109 25 0.30
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (109 bp):
CATGTAAGACCATGCAAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAAGAAACCATGTAAGAC
CATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:62661 original size:16 final size:16
Alignment explanation
Indices: 62640--62670 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62630 ATAAATTTGA
62640 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
62656 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
62671 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:68869 original size:16 final size:16
Alignment explanation
Indices: 68848--68885 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
68838 TTTCAAATTA
68848 ATTCATGCAAGTCACT
1 ATTCATGCAAGTCACT
68864 ATTCATGCAAGTCACT
1 ATTCATGCAAGTCACT
*
68880 ACTCAT
1 ATTCAT
68886 TTAGAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (16 bp):
ATTCATGCAAGTCACT
Found at i:72966 original size:42 final size:42
Alignment explanation
Indices: 72906--73059 Score: 202
Period size: 42 Copynumber: 3.6 Consensus size: 42
72896 CGAGACTATG
* * *
72906 TGTAAGACCATATTTGGGATATGGCATC-ATTATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGA-TACGAGATTTCA
*
72948 TGTAAGACTATATCTGGGATATGGCATCGATACGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATACGAGATTTCA
* * * **
72990 TGTAATACCATAGCTGGGCTATTGGCATCGATACGAGATCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATACGAGATTTCA
73033 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
73060 TGGTGTGGTA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 59 0.61
43 38 0.39
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATACGAGATTTCA
Done.