Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold800
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: 101545
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1563 original size:155 final size:155
Alignment explanation
Indices: 1389--1731 Score: 386
Period size: 155 Copynumber: 2.2 Consensus size: 155
1379 ACCGACGTCA
* * **
1389 AAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACCAACTCCTAGGTTGTCACCTGGTCT
1 AAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACAAACTCCTAAGTCATCACCTGGTCT
* * * *** *
1454 GCTTTTACGCCAA-AGGTGGGCATTTAGGATAGTTTCATTTCC-TCTTCTCATCTTTTTAAGTTC
66 GCTTTTACGCCAAGA-GTAGACATTTAGGATAATTTCA--TCCATCTTAAAATCTTTTTAAGGTC
*
1517 -ATTAGGGGTATCAGGTACTTTTATGTC
128 TATTAGGGGTATCAAGTACTTTTATGTC
* * ** * *
1544 AAAGGAATCCCTTAGGGGTATTTTTGTAATTCTTTAGAACAAACTCCTAAGTCATCACTTGGTCT
1 AAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACAAACTCCTAAGTCATCACCTGGTCT
* * * * ** *
1609 GCTTTTATGCCGAGAGTAGATATTTAGGATAATTTCATCCATTTTAAAATCTTTTTTTGGTCTTT
66 GCTTTTACGCCAAGAGTAGACATTTAGGATAATTTCATCCATCTTAAAATCTTTTTAAGGTCTAT
1674 TAGGGGTATCAAGTACTTTTATGTC
131 TAGGGGTATCAAGTACTTTTATGTC
* * *
1699 AAAAGTATCCCCTAGGGGGATTTTCATAGTTTT
1 AAAGGTATCCCCTAGGGGTATTTTCATAATTTT
1732 CCTTGAACTT
Statistics
Matches: 152, Mismatches: 33, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
153 3 0.02
154 14 0.09
155 134 0.88
156 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (155 bp):
AAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTAGAACAAACTCCTAAGTCATCACCTGGTCT
GCTTTTACGCCAAGAGTAGACATTTAGGATAATTTCATCCATCTTAAAATCTTTTTAAGGTCTAT
TAGGGGTATCAAGTACTTTTATGTC
Found at i:5413 original size:20 final size:21
Alignment explanation
Indices: 5387--5439 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5377 TTGCCAACAA
5387 AATGTATCGATACA-ATACAT
1 AATGTATCGATACATATACAT
* * * *
5407 GATGTATTGATACATTTACTT
1 AATGTATCGATACATATACAT
5428 AATGTATCGATA
1 AATGTATCGATA
5440 AATTTCCACT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATATACAT
Found at i:7429 original size:13 final size:13
Alignment explanation
Indices: 7411--7436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7401 TACACAAAGT
7411 ATGTATCGATACA
1 ATGTATCGATACA
7424 ATGTATCGATACA
1 ATGTATCGATACA
7437 CAAAAAAATG
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:7434 original size:32 final size:33
Alignment explanation
Indices: 7393--7456 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
7383 TAGCCAAACT
**
7393 TGTATCGATACAC-AAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAATGTATCGATACAA
7425 TGTATCGATACACAAAAAAATGTATCGATACA
1 TGTATCGATACACAAAAAAATGTATCGATACA
7457 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACAAAAAAATGTATCGATACAA
Found at i:13630 original size:13 final size:13
Alignment explanation
Indices: 13612--13637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13602 ACATCATTCT
13612 TTGTATCGATACA
1 TTGTATCGATACA
13625 TTGTATCGATACA
1 TTGTATCGATACA
13638 GGGGGATTAT
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:13783 original size:21 final size:20
Alignment explanation
Indices: 13759--13805 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
13749 AAATCTTTTG
*
13759 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACATCGTTTTTCA--T
*
13780 CAAATTACATCGTTTTTCAT
1 CAAAATACATCGTTTTTCAT
13800 CAAAAT
1 CAAAAT
13806 CACCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:15548 original size:22 final size:22
Alignment explanation
Indices: 15502--15542 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
15492 AAATTTGTTA
15502 AAATTATCTTATTAAGGGGGAG
1 AAATTATCTTATTAAGGGGGAG
15524 AAATTAT-TT-TTAAGGGGGA
1 AAATTATCTTATTAAGGGGGA
15543 AAGAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (22 bp):
AAATTATCTTATTAAGGGGGAG
Found at i:16189 original size:19 final size:20
Alignment explanation
Indices: 16165--16215 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
16155 TAGCCAAACT
**
16165 TGTATCGATACA-CAAAGTA
1 TGTATCGATACACCAAAAAA
16184 TGTATCGATACACCAAAAAA
1 TGTATCGATACACCAAAAAA
16204 TGTATCGATACA
1 TGTATCGATACA
16216 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (20 bp):
TGTATCGATACACCAAAAAA
Found at i:20205 original size:22 final size:23
Alignment explanation
Indices: 20149--20206 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
20139 GAATTGGGAG
*
20149 AAAAAAGAGGAAATTGCAAAAAA
1 AAAAAAGAAGAAATTGCAAAAAA
20172 AAAAAAGAAAGAAA-T-CAAAACAA
1 AAAAAAG-AAGAAATTGCAAAA-AA
20195 AAAAAAGAAGAA
1 AAAAAAGAAGAA
20207 GAAAAAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 10 0.31
23 17 0.53
24 5 0.16
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAAAGAAGAAATTGCAAAAAA
Found at i:20214 original size:23 final size:25
Alignment explanation
Indices: 20167--20216 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
20157 GGAAATTGCA
20167 AAAAAAAAAAAGAAAGAAATCAAAAC
1 AAAAAAAAAAAGAAAGAAA-CAAAAC
*
20193 AAAAAAAAGAAG-AAGAAA-AAAAC
1 AAAAAAAAAAAGAAAGAAACAAAAC
20216 A
1 A
20217 GCATTCGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
25 6 0.26
26 11 0.48
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAGAAAGAAACAAAAC
Found at i:20573 original size:22 final size:22
Alignment explanation
Indices: 20528--20604 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
20518 CGCAACACTC
* * *
20528 TAGCAAGCAAAGTAAAACCAAAA
1 TAGCAAGC-AAGGAAAAACGAAA
* *
20551 TAGCAGGCAAGGAAAAATGAAA
1 TAGCAAGCAAGGAAAAACGAAA
*
20573 TAGCAAGTAAGGAAAAACGAAA
1 TAGCAAGCAAGGAAAAACGAAA
*
20595 CAGCAAGCAA
1 TAGCAAGCAA
20605 AAGCAAAGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 37 0.84
23 7 0.16
ACGTcount: A:0.57, C:0.14, G:0.21, T:0.08
Consensus pattern (22 bp):
TAGCAAGCAAGGAAAAACGAAA
Found at i:25960 original size:13 final size:13
Alignment explanation
Indices: 25942--25966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25932 CATTATGCTT
25942 TGTATCGATACAA
1 TGTATCGATACAA
25955 TGTATCGATACA
1 TGTATCGATACA
25967 TGTTCATTGT
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):
TGTATCGATACAA
Found at i:25963 original size:33 final size:32
Alignment explanation
Indices: 25921--25985 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
25911 ACACTTTTAG
*
25921 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
25954 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
25986 CAAACAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:26080 original size:33 final size:33
Alignment explanation
Indices: 26037--26101 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
26027 TACCACTATT
*
26037 TGTATCGATACATGGCACAA-TGTATCGATACAA
1 TGTATCGATACAT-GAACAATTGTATCGATACAA
*
26070 TGTATTGATACATGAACAATTGTATCGATACA
1 TGTATCGATACATGAACAATTGTATCGATACA
26102 TTGCCTCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGAACAATTGTATCGATACAA
Found at i:29289 original size:167 final size:163
Alignment explanation
Indices: 28853--29417 Score: 652
Period size: 167 Copynumber: 3.4 Consensus size: 163
28843 TAACTTTCTT
* * * *
28853 TTGAAATTCTTTCTATTTTCAAACTACAGGATTTTCTTCTCCATAAAATTTTTTGGGAGGATTTT
1 TTGAAATT-TTTCTATTTTCAAAATAGAAG-TTTTCTACTCCAT-AAATTTTTTGGG-GGATTTT
* **
28918 CATAGGTTTAAAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTTAATTTGTTTTTA
62 CTTA-GTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTTAATTTGTTTTTA
*
28983 GAAATTTATTCATTTTTGTGAGTTTTTAAATTTTTTTC
126 GAAATTTATTCATTTTTGTGAGTATTTAAATTTTTTTC
* * *
29021 TTGAAATTTTCCTATTTTCGAAATAGAAGTTTTCTACTCCGTAAATTTTTTTGGGGAGATTTTTC
1 TTGAAATTTTTCTATTTTCAAAATAGAAGTTTTCTACTCCATAAA-TTTTTTGGGG-GA-TTTTC
*
29086 TTAGTTTTTAATTTTTAAAATTTATCAAATATTATTATTAAATTCATATTTAATTTGTGTTTTA-
63 TTAGTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTTAATTTGT-TTTTAG
29150 AAATTTATTCATTTTTGTGAGTATTTAAAGTTTTTTTC
127 AAATTTATTCATTTTTGTGAGTATTTAAA-TTTTTTTC
*
29188 TTGAAATTTTTTTATTTTCAAAATATGAAGTTTTCTACTCCATAAATTTTTTCGGGGCGATTTTC
1 TTGAAATTTTTCTATTTTCAAAATA-GAAGTTTTCTACTCCATAAATTTTTT-GGGG-GATTTTC
* ** ** * *
29253 TTAGTTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTCATATAAAATCAGTTTTCAAA
63 TTAGTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTTAATTTGTTTTTAGA
* * ** *
29318 AATTCATTCATCTTCATGAGT-TTT-TATTTTTTTCC
128 AATTTATTCATTTTTGTGAGTATTTAAATTTTTTT-C
* * * * * * *
29353 TTGAAATTCTCCT-TTTCTCAAAAAATCAATTTTTCTATTCCATAAATATTTATGGGGGGATTTT
1 TTGAAATTTTTCTATTT-TCAAAATA-GAAGTTTTCTACTCCATAAAT-TTT-TTGGGGGATTTT
29417 C
62 C
29418 CTTGGTCTAG
Statistics
Matches: 348, Mismatches: 37, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
164 10 0.03
165 49 0.14
166 116 0.33
167 140 0.40
168 33 0.09
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (163 bp):
TTGAAATTTTTCTATTTTCAAAATAGAAGTTTTCTACTCCATAAATTTTTTGGGGGATTTTCTTA
GTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTTAATTTGTTTTTAGAAAT
TTATTCATTTTTGTGAGTATTTAAATTTTTTTC
Found at i:31497 original size:155 final size:155
Alignment explanation
Indices: 31139--31513 Score: 407
Period size: 155 Copynumber: 2.4 Consensus size: 155
31129 TCATTTTAGT
* * * * ** *
31139 GTCCACTAGGGGTATCAGGTACTTTTATGTCGAAGGTATCCTCT-AGGGGCATTTTTATGATTTT
1 GTCCTCTAGGGGTATCAGGTACTTCTACGTCGAAGGTAT-CTCTGAAGGGCATTTTCGTAATTTT
* * * *
31203 TCATAACCGAGTCCTAGGTTGTCACCAAGTTCTCTTTTATGCCAAAAATGGATATTTAGGATAGG
65 TCAGAACCAAGTCCTAGGTTGTCACCAAGTCCACTTTTATGCCAAAAATGGATATTTAGGATAGG
31268 TTAATCCCTTTCAAAATCCTTTTTAA
130 TTAATCCCTTTCAAAATCCTTTTTAA
* * * * * *
31294 GTCCTTTAGGGGT-GCAGGGCACTTCTACGTCAAAGGTATC-CCGTAAGGGCATTTTGGTAATTT
1 GTCCTCTAGGGGTATCA-GGTACTTCTACGTCGAAGGTATCTCTG-AAGGGCATTTTCGTAATTT
* * ** * * ** *
31357 TTTAGAACCAAGTCTTAGGTTGTCACCGGGTCCACTTTTATGTCGAAGGTGGGTATTTAGGATAG
64 TTCAGAACCAAGTCCTAGGTTGTCACCAAGTCCACTTTTATGCCAAAAATGGATATTTAGGATAG
* *
31422 GTTCATCCCATTT-ATAATCCTTTTTAA
129 GTTAATCCC-TTTCAAAATCCTTTTTAA
* * *
31449 GTCCTCTAGGGGTATCAAGTACTTCTACGTCGAAGGTATCTTTGAAGGGTATTTTCGTAATTTTT
1 GTCCTCTAGGGGTATCAGGTACTTCTACGTCGAAGGTATCTCTGAAGGGCATTTTCGTAATTTTT
31514 ATTAAACTTA
Statistics
Matches: 178, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
153 1 0.01
154 3 0.02
155 168 0.94
156 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (155 bp):
GTCCTCTAGGGGTATCAGGTACTTCTACGTCGAAGGTATCTCTGAAGGGCATTTTCGTAATTTTT
CAGAACCAAGTCCTAGGTTGTCACCAAGTCCACTTTTATGCCAAAAATGGATATTTAGGATAGGT
TAATCCCTTTCAAAATCCTTTTTAA
Found at i:34251 original size:13 final size:13
Alignment explanation
Indices: 34233--34258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34223 CATTTTTTGG
34233 TGTATCGATACAT
1 TGTATCGATACAT
34246 TGTATCGATACAT
1 TGTATCGATACAT
34259 ACTTTGTGTA
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):
TGTATCGATACAT
Found at i:34273 original size:32 final size:33
Alignment explanation
Indices: 34213--34276 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
34203 TACAAGCTAA
**
34213 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
34246 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
34277 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:34846 original size:299 final size:299
Alignment explanation
Indices: 34308--34894 Score: 1156
Period size: 299 Copynumber: 2.0 Consensus size: 299
34298 TCCCAATGAC
34308 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
*
34373 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
66 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
34438 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
131 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
34503 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
196 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
34568 TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
261 TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
*
34607 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
34672 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
66 ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
34737 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
131 CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
34802 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
196 ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
34867 TGAATAAAACACATTTTTGGTATTTTCA
261 TGAATAAAACACATTTTTGGTATTTTCA
34895 GAATAATTCC
Statistics
Matches: 286, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 286 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (299 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
ATCGATACTTTTAAGGGTTTTGACCATTTTAGCCTAAGTCAAACTTAATGTATCGATACAAATAC
CTATGTATCGATACTTTGATCTATTTTATCTTAAACATCAATCATTTTAAGCCTTGAAAACATTT
ATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTATAAAGTACTTAAT
TGAATAAAACACATTTTTGGTATTTTCAAAATTATAAAG
Found at i:35227 original size:20 final size:22
Alignment explanation
Indices: 35198--35238 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
35188 TTCTTTTCTT
*
35198 TCCCCTTTAA-AA-ATAATTTC
1 TCCCCCTTAATAAGATAATTTC
35218 TCCCCCTTAATAAGATAATTT
1 TCCCCCTTAATAAGATAATTT
35239 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (22 bp):
TCCCCCTTAATAAGATAATTTC
Found at i:37121 original size:13 final size:13
Alignment explanation
Indices: 37103--37128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37093 ATAAACCCCC
37103 TGTATCGATACAA
1 TGTATCGATACAA
37116 TGTATCGATACAA
1 TGTATCGATACAA
37129 AGAAAGATGT
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:43280 original size:13 final size:13
Alignment explanation
Indices: 43262--43287 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43252 CATTTTTTGG
43262 TGTATCGATACAT
1 TGTATCGATACAT
43275 TGTATCGATACAT
1 TGTATCGATACAT
43288 ACTTTGTGTA
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):
TGTATCGATACAT
Found at i:43302 original size:32 final size:33
Alignment explanation
Indices: 43242--43305 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
43232 TACAAGCTAA
**
43242 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
43275 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
43306 AGTTTGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:53512 original size:90 final size:90
Alignment explanation
Indices: 53428--53604 Score: 214
Period size: 90 Copynumber: 2.0 Consensus size: 90
53418 CAAATTTTAC
* *
53428 CCCT-CTTGACTGTATT-TGGTCAAAACTATCCTCATTTAACTGTACTCGATCAAATATTACCTT
1 CCCTACTTGACTGTATTCT-GCCAAAACTATCCTCATTTAACTGTACTCGATCAAATATTACCCT
*
53491 TCTTGACTGTACTTGGTCAAATCTGA
65 ACTTGACTGTACTTGGTCAAATCTGA
* ** * * * * *
53517 CCCTATTTGACTGTATTCTGCCAAGTCTTTCTTTATTTAACTGTACTTGATCAAATCTTACCCTA
1 CCCTACTTGACTGTATTCTGCCAAAACTATCCTCATTTAACTGTACTCGATCAAATATTACCCTA
* *
53582 CTTGATTGTATTTGGTCAAATCT
66 CTTGACTGTACTTGGTCAAATCT
53605 TAATTCATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 4 0.05
90 68 0.93
91 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (90 bp):
CCCTACTTGACTGTATTCTGCCAAAACTATCCTCATTTAACTGTACTCGATCAAATATTACCCTA
CTTGACTGTACTTGGTCAAATCTGA
Found at i:53527 original size:30 final size:30
Alignment explanation
Indices: 53340--53638 Score: 146
Period size: 30 Copynumber: 9.9 Consensus size: 30
53330 AGTTTGAAAC
53340 ATTTGACTGTA-TTCGGTCAAAT-TTCACCCT
1 ATTTGACTGTACTT-GGTCAAATCTT-ACCCT
* * * * *
53370 CGTTTGATTGTACTTAGTCAAGTCTT-TCCT
1 -ATTTGACTGTACTTGGTCAAATCTTACCCT
* **** *
53400 CATTTGACTATACGCACTCAAATTTTACCCCT
1 -ATTTGACTGTACTTGGTCAAATCTTA-CCCT
* * * *
53432 -CTTGACTGTATTTGGTCAAAAC-TATCCT
1 ATTTGACTGTACTTGGTCAAATCTTACCCT
* * * *
53460 CATTTAACTGTACTCGATCAAATATTA-CCT
1 -ATTTGACTGTACTTGGTCAAATCTTACCCT
* *
53490 TTCTTGACTGTACTTGGTCAAATCTGACCCT
1 AT-TTGACTGTACTTGGTCAAATCTTACCCT
* * * * **
53521 ATTTGACTGTA-TTCTGCCAAGTCTTTCTTT
1 ATTTGACTGTACTT-GGTCAAATCTTACCCT
* *
53551 ATTTAACTGTACTTGATCAAATCTTACCCT
1 ATTTGACTGTACTTGGTCAAATCTTACCCT
* * * **
53581 ACTTGATTGTATTTGGTCAAATCTTA-ATT
1 ATTTGACTGTACTTGGTCAAATCTTACCCT
*
53610 CATTTGACTATACTTGGTCAAATCTTACC
1 -ATTTGACTGTACTTGGTCAAATCTTACC
53639 TCACTTGATT
Statistics
Matches: 190, Mismatches: 65, Indels: 26
0.68 0.23 0.09
Matches are distributed among these distances:
28 3 0.02
29 6 0.03
30 151 0.79
31 23 0.12
32 7 0.04
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (30 bp):
ATTTGACTGTACTTGGTCAAATCTTACCCT
Found at i:53660 original size:30 final size:29
Alignment explanation
Indices: 53567--53653 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
53557 CTGTACTTGA
*
53567 TCAAATCTTACC-CTACTTGATTGTATTTGG
1 TCAAATCTTACCTC-ACTTGATTATA-TTGG
** * *
53597 TCAAATCTTAATTCATTTGACTATACTTGG
1 TCAAATCTTACCTCACTTGATTATA-TTGG
53627 TCAAATCTTACCTCACTTGATTATATT
1 TCAAATCTTACCTCACTTGATTATATT
53654 CAGTCAAGCC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 2 0.04
30 43 0.93
31 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.44
Consensus pattern (29 bp):
TCAAATCTTACCTCACTTGATTATATTGG
Found at i:53660 original size:60 final size:60
Alignment explanation
Indices: 53493--53660 Score: 185
Period size: 60 Copynumber: 2.8 Consensus size: 60
53483 ATTACCTTTC
* * * * * * ** *
53493 TTGACTGTACTTGGTCAAATCTGACCCTATTTGACTGTATTCTGCCAAGTCTTTCTTTAT
1 TTGACTGTACTTGGTCAAATCTTACCCTACTTGATTGTATTCAGTCAAATCTTAATTCAT
* * **
53553 TTAACTGTACTTGATCAAATCTTACCCTACTTGATTGTATTTGGTCAAATCTTAATTCAT
1 TTGACTGTACTTGGTCAAATCTTACCCTACTTGATTGTATTCAGTCAAATCTTAATTCAT
* *
53613 TTGACTATACTTGGTCAAATCTTA-CCTCACTTGATTATATTCAGTCAA
1 TTGACTGTACTTGGTCAAATCTTACCCT-ACTTGATTGTATTCAGTCAA
53661 GCCTTTCCCC
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
59 3 0.03
60 86 0.97
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (60 bp):
TTGACTGTACTTGGTCAAATCTTACCCTACTTGATTGTATTCAGTCAAATCTTAATTCAT
Found at i:55475 original size:165 final size:164
Alignment explanation
Indices: 54763--55520 Score: 642
Period size: 167 Copynumber: 4.6 Consensus size: 164
54753 TTTTCATAGG
* * **
54763 TTTAAAATTTTTAAAATTCATCAAATATTATTATTTAATTCATAATAAATTGGTTTTCAAAAATT
1 TTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATT
* * * * *
54828 CATTCATTTTCATGAGTTTCTTAATTTTTTCCTTGAAATTTCCTTATTTCCAAAAAATGAAATTT
66 CATTCATTTTCATGAGTTT-TAAATTTTTTCCTTGAAAATTCCTTTTTTCTAAAAAATG-AGTTT
* * * *
54893 TCTACTCCGTAAATTATTTTGGGAA-AATTTTCATGA
129 TCTACTCCATAAATT-TTTTCGAAAGAATTTTCTTGA
** *
54929 GTTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAGTTCAGTTTTTAAAAAT
1 -TTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAAT
* * * *
54994 TTATTCATTTTCATGGGGTTTTAAATTTTTTCCTTGAAAATTTCTTGTTTT-TGAAAAATAGAGT
65 TCATTCATTTTCAT-GAGTTTTAAATTTTTTCCTTGAAAATTCCTT-TTTTCTAAAAAAT-GAGT
* * * *
55058 TTTCTACTCTATAAATTTTTTCGAGGAGATTTTTCTTGG
127 TTTCTACTCCATAAATTTTTTCGA-AAGAATTTTCTTGA
** * * *
55097 TTTTTAAGTTTTAAAATTCATAAAATATTATTATTTAATGT-ATATTAAATTATTTTTCAAAAAT
1 TTTAAAATTTTTAAAATTCATAAAATATTATTATTTAAT-TCATATTAAATCAGTTTTCAAAAAT
* * * * * * *
55161 TCATTTATTTTCATGAGTTTTAGAGTTTTTT--TGTG-AAATCCCTTTTTTTCCAATAACTAAGT
65 TCATTCATTTTCATGAGTTTTA-AATTTTTTCCT-TGAAAATTCC-TTTTTTCTAAAAAATGAGT
* * * ** *
55223 TTTCTAATCCATAAA-TTTTTCTAAGGGGCTTTTCTTTGG
127 TTTCTACTCCATAAATTTTTTCGAA-AGAATTTTC-TTGA
*** * * ** * * *
55262 TTTAAAATTTTTAAAATGT-AGCTAATAATATCATGGAACTC-TCATTAAATCAGTTTTGAAAAT
1 TTTAAAATTTTTAAAAT-TCATAAAATATTATTATTTAATTCAT-ATTAAATCAGTTTTCAAAAA
* * ** *
55325 TTTATCCATTTTCATGAGTTTTTTATTTTTT-CTT-AAAATGCCTATTTTTCTAAAAAACTGAGT
64 TTCATTCATTTTCATGAGTTTTAAATTTTTTCCTTGAAAATTCCT-TTTTTCTAAAAAA-TGAGT
55388 TTTCTACTCCATAAATTTTTTCGAAAGAATTTTCTTCGA
127 TTTCTACTCCATAAATTTTTTCGAAAGAATTTTCTT-GA
* * * * * ** *
55427 TTGAAATTTTTTAGAATTCATATAATATTATCATTTAATTCCCATTAAATCAGTATTTGAAAAA-
1 TTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAAATCAGT-TTTCAAAAAT
*
55491 TCAATTTATTTT-ATGAGTTTTAAATTTTTT
65 TC-ATTCATTTTCATGAGTTTTAAATTTTTT
55521 TGTATTTATT
Statistics
Matches: 468, Mismatches: 98, Indels: 52
0.76 0.16 0.08
Matches are distributed among these distances:
163 1 0.00
164 41 0.09
165 175 0.37
166 44 0.09
167 189 0.40
168 18 0.04
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (164 bp):
TTTAAAATTTTTAAAATTCATAAAATATTATTATTTAATTCATATTAAATCAGTTTTCAAAAATT
CATTCATTTTCATGAGTTTTAAATTTTTTCCTTGAAAATTCCTTTTTTCTAAAAAATGAGTTTTC
TACTCCATAAATTTTTTCGAAAGAATTTTCTTGA
Found at i:61379 original size:20 final size:20
Alignment explanation
Indices: 61354--61408 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
61344 ACGTACCCTG
*
61354 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
61374 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
*
61394 ATGTATCAATACATT
1 ATGTATCGATACATT
61409 CTGTCTTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:69899 original size:27 final size:27
Alignment explanation
Indices: 69804--70271 Score: 531
Period size: 27 Copynumber: 17.1 Consensus size: 27
69794 TGGCATTCCT
*
69804 TTTTAAGTCCACAACTTCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
*
69831 TTTTAAAGTCCACAACTCCGTGGCAGCCC
1 TTTT-AAGTCCACAACTCCGTGGCA-ACC
* * *
69860 TTTTTAAGTCCACAACTTCATGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCAACC
*
69888 TTTTAAGCCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
69915 TTTTAAGTCCACAACTCTGTGGCAAAC
1 TTTTAAGTCCACAACTCCGTGGCAACC
**** *
69942 TTTTAAGTCCACAACTCTACAGCACCC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* * **
69969 TTGTAAGCCCACAACTTTGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
69996 TTTTAAATCCACAACTCCATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
*
70023 TTTTAAGTCCACAACTCCATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
70050 TTTTAAGTCCACAACTCCATGGCAACA
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
70077 TTTTAAAGTCCACAACTCCATGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCAACC
* * * *
70105 TTGTAAGCCCATAACTTCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
70132 TTTTAAGTCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
70159 TTTTAAAGTCCATAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCAACC
*
70187 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCAACC
* *
70214 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCAACC
* * * * *
70242 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTT-TAAGTCCACAACTCCGTGGCAACC
70270 TT
1 TT
70272 CCAAAGCCCA
Statistics
Matches: 383, Mismatches: 51, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
27 241 0.63
28 118 0.31
29 20 0.05
30 4 0.01
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCAACC
Found at i:70264 original size:28 final size:28
Alignment explanation
Indices: 70123--70801 Score: 439
Period size: 28 Copynumber: 23.2 Consensus size: 28
70113 CCATAACTTC
* * * * *
70123 GTGGCAACCTTT-TAAGTCCACAACTCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * * * * *
70150 GTGGCAACCTTTTAAAGTCCATAACTCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * * *
70178 GTGGCACCCTTT-TAAGTCCACAACTCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * * *
70205 GTGGCACCCTTTTAAAGTCCACAACTCT
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
70233 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
70261 GTGGCACCCTTCCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
** *
70289 GTGGCACCCCTTTTTAAGCCCACAAGTTA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCA
*** *
70318 GTGGCATTATTTCAAAGCCCACACAAGTCG
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
* * * *
70348 GTGGCAACTCATTTGAAAACCCACATAAGTCG
1 GTGGC-AC-CCTTTCAAAGCCCAC--AAGTCA
*
70380 GTGGTAACCCATTTCAAAGCCCACATAAGTCA
1 GTGG-CACCC-TTTCAAAGCCCAC--AAGTCA
* *
70412 GTGGCATCCTTCTCAAAGCCCACACAAGTCG
1 GTGGCACCCTT-TCAAAG-CC-CACAAGTCA
* *
70443 GTGGCAACTCTTTTCAAAGCCCACAAGTAA
1 GTGGC-AC-CCTTTCAAAGCCCACAAGTCA
* **
70473 GTGTCA-TTTCTTCAAAAGCCCACAAGTCA
1 GTGGCACCCT-TTC-AAAGCCCACAAGTCA
* * *
70502 ATAGCACCCTTTCAAAGCCCACACAAGTCG
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
* *
70532 GTGGCAACTCTTTTCAAAGCCCACATGTCA
1 GTGGC-AC-CCTTTCAAAGCCCACAAGTCA
* * * *
70562 GTGGCA-TCTCTTCAAAAGACAACAAGTTA
1 GTGGCACCCT-TTC-AAAGCCCACAAGTCA
* *
70591 GTGGCATCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
** * **
70619 GTCACATACCCTTTCAAAGCCCATAAGTTG
1 GTGGC--ACCCTTTCAAAGCCCACAAGTCA
* *
70649 GTGGCACCCTTTCAAAGCCCACACAATTCG
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
*
70679 GTGGCAACTCTTTTCAAAGCCCACAAGTCA
1 GTGGC-AC-CCTTTCAAAGCCCACAAGTCA
* *
70709 GTGGCACCCCTTCACAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
70737 GTGGTACCCCTTCAAAGCTCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
70765 GTGACATCCCCTTTCAAAGCCTACACAAGTCG
1 GTGGCA--CCCTTTCAAAGCC--CACAAGTCA
70797 GTGGC
1 GTGGC
70802 TTCAAAGTCC
Statistics
Matches: 529, Mismatches: 87, Indels: 67
0.77 0.13 0.10
Matches are distributed among these distances:
27 40 0.08
28 185 0.35
29 74 0.14
30 111 0.21
31 33 0.06
32 80 0.15
33 6 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.23
Consensus pattern (28 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCA
Found at i:70334 original size:57 final size:56
Alignment explanation
Indices: 70163--70801 Score: 269
Period size: 60 Copynumber: 10.9 Consensus size: 56
70153 GCAACCTTTT
* * * * * * * * **
70163 AAAGTCCATAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCACCCTTTT
1 AAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCATTCC
* * *
70218 AAAGTCCACAACTCTGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCC
1 AAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCATTCC
* ** * ** *
70274 AAAGCCCACAAGTCAGTGGCACCCCTTTTTAAGCCCACAAGTTAGTGGCATTATTTC
1 AAAGCCCACAACTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACCATTCC
* * * * * * * *
70331 AAAGCCCACACAAGTCGGTGGCAACTCATTTGAAAACCCACATAAGTCGGTGGTAACCCATTTC
1 AAAG-CC-CACAACTCAGTGGC-AC-CCTTTCAAAGCCCAC--AAGTCAGTGG-CA-CCATTCC
* * * * *
70395 AAAGCCCACATAAGTCAGTGGCATCCTTCTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTC
1 AAAGCCCAC--AACTCAGTGGCACCCTT-TCAAAG-CC-CACAAGTCAGTGGC-AC-CATTCC
* * * ** * * * *
70458 AAAGCCCACAAGTAAGTGTCA-TTTCTTCAAAAGCCCACAAGTCAATAGCACCCTTTC
1 AAAGCCCACAACTCAGTGGCACCCT-TTC-AAAGCCCACAAGTCAGTGGCACCATTCC
* * * * *
70515 AAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACATGTCAGTGGCATCTC-TTCA
1 AAAG-CC-CACAACTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCA-C-CATTCC
* * * * * * ** * *
70576 AAAGACAACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTCACATACCCTTTC
1 AAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC--ACCATTCC
* * ** * * * *
70634 AAAGCCCATAAGTTGGTGGCACCCTTTCAAAGCCCACACAATTCGGTGGCAACTCTTTTC
1 AAAGCCCACAACTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-AC-CATTCC
* * * * *
70694 AAAGCCCACAAGTCAGTGGCACCCCTTCACAGCCCACAAGTCAGTGGTACCCCTT-C
1 AAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCATTCC
* * * *
70750 AAAGCTCACAAGTCAGTGACATCCCCTTTCAAAGCCTACACAAGTCGGTGGC
1 AAAGCCCACAACTCAGTGGCA--CCCTTTCAAAGCC--CACAAGTCAGTGGC
70802 TTCAAAGTCC
Statistics
Matches: 456, Mismatches: 91, Indels: 69
0.74 0.15 0.11
Matches are distributed among these distances:
55 25 0.05
56 60 0.13
57 67 0.15
58 60 0.13
59 54 0.12
60 90 0.20
61 25 0.05
62 18 0.04
63 33 0.07
64 21 0.05
65 3 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (56 bp):
AAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCATTCC
Found at i:70378 original size:32 final size:32
Alignment explanation
Indices: 70326--70703 Score: 221
Period size: 32 Copynumber: 12.5 Consensus size: 32
70316 TAGTGGCATT
70326 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
* * * * *
70358 ATTTGAAAACCCACATAAGTCGGTGGTAACCC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
* *
70390 ATTTCAAAGCCCACATAAGTCAGTGGC-A-TC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
*
70420 CTTCTCAAAGCCCACACAAGTCGGTGGCAACTC
1 ATT-TCAAAGCCCACACAAGTCGGTGGCAACTC
* ** * **
70453 TTTTCAAAG-CC-CACAAGTAAGTGTCATTTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
** *
70483 --TTCAAAAG-CC-CACAAGTCAATAGC-AC-C
1 ATTTC-AAAGCCCACACAAGTCGGTGGCAACTC
*
70510 CTTTCAAAGCCCACACAAGTCGGTGGCAACTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
* * * *
70542 TTTTCAAAG-CC-CACATGTCAGTGGCATCTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
* **
70572 --TTCAAAAG-ACA-ACAAGTTAGTGGC-A-TC
1 ATTTC-AAAGCCCACACAAGTCGGTGGCAACTC
* ** **
70599 CTTTCAAAG-CC-CACAAGTTAGTCACATAC-C
1 ATTTCAAAGCCCACACAAGTCGGTGGCA-ACTC
* * *
70629 CTTTCAAAG-CC-CATAAGTTGGTGGC-AC-C
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
* *
70657 CTTTCAAAGCCCACACAATTCGGTGGCAACTC
1 ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
*
70689 TTTTCAAAGCCCACA
1 ATTTCAAAGCCCACA
70704 AGTCAGTGGC
Statistics
Matches: 277, Mismatches: 47, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
27 3 0.01
28 38 0.14
29 42 0.15
30 78 0.28
31 31 0.11
32 81 0.29
33 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (32 bp):
ATTTCAAAGCCCACACAAGTCGGTGGCAACTC
Found at i:70575 original size:89 final size:89
Alignment explanation
Indices: 70195--70801 Score: 463
Period size: 89 Copynumber: 6.8 Consensus size: 89
70185 CCTTTTAAGT
* * ** * * * *
70195 CCACAACTCCGTGGCA-CCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTCAAAG-CC-CACAA
1 CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
* * *
70257 GTCAGTGGC-AC-CCTTCCAAAGC
66 GTCGGTGGCAACTCTTTTCAAAGC
* *** * **
70279 CCACAAGTCAGTGGCACCCCTTTTTAAGCCCACAAGTTAGTGGCATTATTTCAAAGCCCACACAA
1 CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
* * *
70344 GTCGGTGGCAACTCATTTGAAAAC
66 GTCGGTGGCAACTCTTTTCAAAGC
* * *
70368 CCACATAAGTCGGTGGTAACCCATTTC-AAAGCCCACATAAGTCAGTGGCATCCTTCTCAAAGCC
1 CCAC--AAGTCAGTGGCATCCC--TTCAAAAGCCCAC--AAGTCAGTGGCATCCTT-TCAAAGCC
70432 CACACAAGTCGGTGGCAACTCTTTTCAAAGC
59 CACACAAGTCGGTGGCAACTCTTTTCAAAGC
* * ** * * *
70463 CCACAAGTAAGTGTCATTTCTTCAAAAGCCCACAAGTCAATAGCACCCTTTCAAAGCCCACACAA
1 CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
70528 GTCGGTGGCAACTCTTTTCAAAGC
66 GTCGGTGGCAACTCTTTTCAAAGC
* * * * *
70552 CCACATGTCAGTGGCATCTCTTCAAAAGACAACAAGTTAGTGGCATCCTTTCAAAG-CC-CACAA
1 CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
** ** *
70615 GTTAGTCACATAC-CCTTTCAAAGC
66 GTCGGTGGCA-ACTCTTTTCAAAGC
* ** * * *
70639 CCATAAGTTGGTGGCA-CCCTTTC-AAAGCCCACACAATTCGGTGGCAACTCTTTTCAAAG-CC-
1 CCACAAGTCAGTGGCATCCC-TTCAAAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAGCCCA
* ** *
70700 CACAAGTCAGTGGC-AC-CCCTTCACAGC
61 CACAAGTCGGTGGCAACTCTTTTCAAAGC
* * * * *
70727 CCACAAGTCAGTGGTACCCCTTC-AAAGCTCACAAGTCAGTGACATCCCCTTTCAAAGCCTACAC
1 CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAGCCCACAC
70791 AAGTCGGTGGC
64 AAGTCGGTGGC
70802 TTCAAAGTCC
Statistics
Matches: 421, Mismatches: 78, Indels: 44
0.78 0.14 0.08
Matches are distributed among these distances:
84 15 0.04
85 32 0.08
86 28 0.07
87 52 0.12
88 59 0.14
89 100 0.24
90 37 0.09
91 16 0.04
92 17 0.04
93 11 0.03
94 14 0.03
95 40 0.10
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (89 bp):
CCACAAGTCAGTGGCATCCCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAA
GTCGGTGGCAACTCTTTTCAAAGC
Found at i:70674 original size:147 final size:148
Alignment explanation
Indices: 70195--70801 Score: 585
Period size: 147 Copynumber: 4.1 Consensus size: 148
70185 CCTTTTAAGT
* * * * * * *
70195 CCACAACTCCGTGGCACCCTTTTAAAG-TC-CACAACTCTGTGGC-AC-CCTTTCAAAGCCCACA
1 CCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
* **
70256 AGTCAGTGGCA-CCCTTCCAAAGCCCACAAGTCAGTGGCACCCCTTTTTAAGCCCACAAGTTAGT
66 AGTCAGTGGCATCCCTTCCAAAGCCAACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTTAGT
*
70320 GGCATTA---TTTCAAAGCC
131 GACA-TACCCTTTCAAAG-C
* * * * * * *
70337 CACACAAGTCGGTGGCAACTCATTTGAAAACCCACATAAGTCGGTGGTAACCCATTTCAAAGCCC
1 C-CACAAGTCGGTGGC-AC-CCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCC
* * *
70402 ACATAAGTCAGTGGCAT-CCTTCTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCA
63 AC--AAGTCAGTGGCATCCCTTC-CAAAG-CCA-ACAAGTCAGTGGC-ACCCCTTTCAAAGCCCA
* * **
70466 CAAGTAAGTGTCAT-TTC-TTCAAAAGC
122 CAAGTTAGTGACATACCCTTTC-AAAGC
** *
70492 CCACAAGTCAATAGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
1 CCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
* * * * * *
70557 TGTCAGTGGCATCTCTTCAAAAGACAACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGT
66 AGTCAGTGGCATCCCTTCCAAAGCCAACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTTAGT
*
70621 CACATACCCTTTCAAAGC
131 GACATACCCTTTCAAAGC
* * *
70639 CCATAAGTTGGTGGCACCCTTTCAAAGCCCACACAATTCGGTGGCAACTCTTTTCAAAGCCCACA
1 CCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
* * * * * *
70704 AGTCAGTGGCACCCCTT-CACAGCCCACAAGTCAGTGGTACCCC-TTCAAAGCTCACAAGTCAGT
66 AGTCAGTGGCATCCCTTCCAAAGCCAACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTTAGT
*
70767 GACATCCCCTTTCAAAGC
131 GACATACCCTTTCAAAGC
70785 CTACACAAGTCGGTGGC
1 C--CACAAGTCGGTGGC
70802 TTCAAAGTCC
Statistics
Matches: 378, Mismatches: 63, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
142 1 0.00
143 12 0.03
144 2 0.01
145 7 0.02
146 77 0.20
147 92 0.24
148 28 0.07
149 16 0.04
150 16 0.04
151 21 0.06
152 45 0.12
153 4 0.01
154 24 0.06
155 29 0.08
156 4 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (148 bp):
CCACAAGTCGGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
AGTCAGTGGCATCCCTTCCAAAGCCAACAAGTCAGTGGCACCCCTTTCAAAGCCCACAAGTTAGT
GACATACCCTTTCAAAGC
Found at i:71004 original size:48 final size:48
Alignment explanation
Indices: 70937--71115 Score: 243
Period size: 48 Copynumber: 3.8 Consensus size: 48
70927 GGCACCTTTA
* *
70937 TTAGCACAATGTCACTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* * * *
70985 TTAGCTCAATGTCGTTGGCCTTAAATCAGCATATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* *
71033 TTAGCTCAATGCCGCTGGCCTTGAATAAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
* * * *
71081 TTGGCTCGATGT-GTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTG
71116 ACATTCCTCT
Statistics
Matches: 114, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 20 0.18
48 94 0.82
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCC
Found at i:71812 original size:19 final size:18
Alignment explanation
Indices: 71788--71850 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
71778 CAATGATTTA
71788 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
71807 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
71820 TATCGATACATAAGTATTG
1 TATCGATACATAAGT-TTG
71839 TATCGATACATA
1 TATCGATACATA
71851 TGAAGCTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:71823 original size:13 final size:13
Alignment explanation
Indices: 71805--71829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71795 ACATAAGTGT
71805 TGTATCGATACAA
1 TGTATCGATACAA
71818 TGTATCGATACA
1 TGTATCGATACA
71830 TAAGTATTGT
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):
TGTATCGATACAA
Found at i:71829 original size:32 final size:32
Alignment explanation
Indices: 71788--71848 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
71778 CAATGATTTA
*
71788 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTATTGTATCGATACAATG
71820 TATCGATACATAAGTATTGTATCGATACA
1 TATCGATACATAAGTATTGTATCGATACA
71849 TATGAAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATCGATACAATG
Found at i:71969 original size:52 final size:52
Alignment explanation
Indices: 71905--72046 Score: 198
Period size: 52 Copynumber: 2.7 Consensus size: 52
71895 ATTGATACAT
*** *
71905 TGTATCGATACACTAATCTTTGTATCGATACATGCTA-GCAAATTTGCCCAGA
1 TGTATCGATACACTAATAAATGTATCGATACATAC-AGGCAAATTTGCCCAGA
*
71957 TGTATCGATACACTATTAAATGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATAAATGTATCGATACATACAGGCAAATTTGCCCAGA
*
72009 TGTATCGATACACT-ATGAAATGTATCGATACATGCAGG
1 TGTATCGATACACTAAT-AAATGTATCGATACATACAGG
72047 TAAAATTTCA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTAATAAATGTATCGATACATACAGGCAAATTTGCCCAGA
Found at i:75504 original size:20 final size:20
Alignment explanation
Indices: 75479--75555 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
75469 AAGTACCCAG
75479 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
75499 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
75519 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
75539 ATGTATCGATGCATTTT
1 ATGTATCGATACATTTT
75556 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:82482 original size:53 final size:53
Alignment explanation
Indices: 82424--82537 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
82414 TGAAACATGT
82424 AAGTTTTTATTATTTCTTTTTTATACCCCTCTGGAATGCTAGAAGAATATAAA
1 AAGTTTTTATTATTTCTTTTTTATACCCCTCTGGAATGCTAGAAGAATATAAA
82477 AAGTTTTTATTATTTCTTTTTTATACCCCTCTGGAATGCTAGAAGAATATAAA
1 AAGTTTTTATTATTTCTTTTTTATACCCCTCTGGAATGCTAGAAGAATATAAA
82530 AA-TTTTTA
1 AAGTTTTTA
82538 AAAACCAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 6 0.10
53 55 0.90
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (53 bp):
AAGTTTTTATTATTTCTTTTTTATACCCCTCTGGAATGCTAGAAGAATATAAA
Found at i:84267 original size:69 final size:69
Alignment explanation
Indices: 84191--84324 Score: 189
Period size: 69 Copynumber: 1.9 Consensus size: 69
84181 CTTTGAGCTC
* * *
84191 CTGATGGCTACTATGAGAGCTGTTGGAAGTTGCT-AGAGGTTGTTGTAGGAGCCGCTGAAGCTGT
1 CTGATGGCTACTATGAGAGCTATTGGAAGTTGCTGA-AGGTTATTGTAGGAGCCACTGAAGCTGT
84255 CATTG
65 CATTG
* * * *
84260 CTGATGGCTACTGTGGGAGCTATTGGAAGTTGCTGAAGGTTATTGTGGGAGCTACTGAAGCTGTC
1 CTGATGGCTACTATGAGAGCTATTGGAAGTTGCTGAAGGTTATTGTAGGAGCCACTGAAGCTGTC
84325 GTTGGCTACT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 56 0.98
70 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.35, T:0.31
Consensus pattern (69 bp):
CTGATGGCTACTATGAGAGCTATTGGAAGTTGCTGAAGGTTATTGTAGGAGCCACTGAAGCTGTC
ATTG
Found at i:84850 original size:38 final size:38
Alignment explanation
Indices: 84799--84894 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
84789 TGCTTTGTTG
* *
84799 TTCCACTTTGCTTTGTCTTCATCACTGCTGTTTTGCTT
1 TTCCACGTTGCTTTGTCTTCATCACTGCTATTTTGCTT
* *
84837 TTCCATGTTGCTTTGTCTTCATCATTGCTATTTTGCTT
1 TTCCACGTTGCTTTGTCTTCATCACTGCTATTTTGCTT
84875 TTCCACGTTGCTTTGTCTTC
1 TTCCACGTTGCTTTGTCTTC
84895 CACTTTCTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.08, C:0.25, G:0.14, T:0.53
Consensus pattern (38 bp):
TTCCACGTTGCTTTGTCTTCATCACTGCTATTTTGCTT
Found at i:85260 original size:16 final size:17
Alignment explanation
Indices: 85227--85268 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
85217 GCTTTCACAC
85227 ATTTTTTTTGAATTTTTT
1 ATTTTTTTTGAA-TTTTT
*
85245 ATTTTTTTTGGA-TTTT
1 ATTTTTTTTGAATTTTT
85261 ATTTTTTT
1 ATTTTTTT
85269 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
18 11 0.48
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (17 bp):
ATTTTTTTTGAATTTTT
Found at i:86506 original size:45 final size:45
Alignment explanation
Indices: 86357--86508 Score: 132
Period size: 45 Copynumber: 3.4 Consensus size: 45
86347 CAGATGTACC
* * * * **
86357 GAGTTTGACCAAGGA-TAAACCTTTACGTCAAACAAATAT-AAAAA
1 GAGTTTGA-CTAGGACTAAACCATCACGTCAAACGAGGATGAAAAA
* *
86401 AAGTTTGACTAGGGCTAAACCATCACGTCAAACGAGGATGAAAAA
1 GAGTTTGACTAGGACTAAACCATCACGTCAAACGAGGATGAAAAA
* * * *
86446 GAGTTTGACTGGGACTAAACCATCATGTCAAATGA-GATCTG-AAAG
1 GAGTTTGACTAGGACTAAACCATCACGTCAAACGAGGA--TGAAAAA
*
86491 GAGTTTAACTAGGACTAA
1 GAGTTTGACTAGGACTAA
86509 TGCCAATACA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
43 4 0.05
44 28 0.32
45 54 0.61
46 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (45 bp):
GAGTTTGACTAGGACTAAACCATCACGTCAAACGAGGATGAAAAA
Found at i:86573 original size:47 final size:47
Alignment explanation
Indices: 86480--86574 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
86470 ATGTCAAATG
* ** * * *
86480 AGATCTGAAAGGAGTTTAACTAGGACTAATGCCAATACAGTTAAACA
1 AGATATGAAAGGAGTTTAACTAGGAAAAACGCAAATACAGTCAAACA
* *
86527 AGATATGAAAGGAGTTTGACTAGGAAAAACGCAAATAGAGTCAAACA
1 AGATATGAAAGGAGTTTAACTAGGAAAAACGCAAATACAGTCAAACA
86574 A
1 A
86575 CGGTGAAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (47 bp):
AGATATGAAAGGAGTTTAACTAGGAAAAACGCAAATACAGTCAAACA
Found at i:86902 original size:46 final size:46
Alignment explanation
Indices: 86486--86941 Score: 251
Period size: 46 Copynumber: 9.8 Consensus size: 46
86476 AATGAGATCT
* * * * * *
86486 GAAAGGAGTTTAACTAGGACTAATGCCAATACAGTTAAACAA-GATAT
1 GAAA-GAGTTTGACCAGGACTAATGCCAATATAGTCAAACAAGGGT-G
* ** * * * *
86533 GAAAGGAGTTTGACTAGGAAAAACGCAAATAGAGTCAAACAACGGTG
1 GAAA-GAGTTTGACCAGGACTAATGCCAATATAGTCAAACAAGGGTG
* ** * * * *
86580 AAAAGAGTTCAACCAGGACTAACGCCAATATAGTCAGATAAGGGTA
1 GAAAGAGTTTGACCAGGACTAATGCCAATATAGTCAAACAAGGGTG
* * * * * * * * ** *
86626 AAAAGAGTTTGATCAAGTCTTAACG-CACATACAGTTAAAAAAAAGTA
1 GAAAGAGTTTGACCAGGAC-TAATGCCA-ATATAGTCAAACAAGGGTG
* * * * * *
86673 AAAAGAGTTTAACTAGGTCTTAATGCTAATTTAGTCAAACAAGGGTG
1 GAAAGAGTTTGACCAGGAC-TAATGCCAATATAGTCAAACAAGGGTG
* * * * *
86720 GAAAGAGTTTGACCAGGACTAATGTCAATACAATTAAATGAA----G
1 GAAAGAGTTTGACCAGGACTAATGCCAATATAGTCAAA-CAAGGGTG
* * * *
86763 G-AACAGTTTGACCAGGTCCTAATACCAATATAGTCAAACGAGGGTG
1 GAAAGAGTTTGACCAGG-ACTAATGCCAATATAGTCAAACAAGGGTG
* * ** **
86809 GAAAGAAATTTTGACCAGGTCCTAACACCAATATAGTCAAATGAGGGTG
1 GAAAG--AGTTTGACCAGG-ACTAATGCCAATATAGTCAAACAAGGGTG
* * * *
86858 GAAAGAGTTTAACCAGGACTAACGCCAATTTAATCAAACAAGGGTG
1 GAAAGAGTTTGACCAGGACTAATGCCAATATAGTCAAACAAGGGTG
*
86904 GAAAGAGTTTGACCAGGACTAATGCTAATATAGTCAAA
1 GAAAGAGTTTGACCAGGACTAATGCCAATATAGTCAAA
86942 TTTGAGATGA
Statistics
Matches: 314, Mismatches: 82, Indels: 27
0.74 0.19 0.06
Matches are distributed among these distances:
42 15 0.05
43 17 0.05
46 118 0.38
47 117 0.37
48 3 0.01
49 44 0.14
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (46 bp):
GAAAGAGTTTGACCAGGACTAATGCCAATATAGTCAAACAAGGGTG
Found at i:86909 original size:184 final size:180
Alignment explanation
Indices: 86674--87060 Score: 456
Period size: 184 Copynumber: 2.1 Consensus size: 180
86664 AAAAAAGTAA
* * * * *
86674 AAAGAGTTTAACTAGGTCTTAATGCTAATTTAGTCAAACAAGGGTGGAAAGAGTTTGACCAGGAC
1 AAAGAGTTTAACCAGGAC-TAACGCCAATTTAATCAAACAAGGGTGGAAAGAGTTTGACCAGGAC
* *
86739 TAATG-TCAATACAATTAAA-TGAAGGAACAGTTTGACCAGGTCCTAATACCAATATAGTCAAAC
65 TAATGCT-AATACAATCAAATTG-A-GAACAGTTTGACCAGGTCCTAATACCAATACAGTCAAAC
* * * * * *
86802 G-AGGGTGGAAAGAAATTTTGACCAGGTCCTAACACCAATATAGTCAAATGAGGGTGG
127 GCA-AGT-AAAAG-AA-TTTGACCAGGTCCTAACACCAATACAATCAAATAAGGATGG
86859 AAAGAGTTTAACCAGGACTAACGCCAATTTAATCAAACAAGGGTGGAAAGAGTTTGACCAGGACT
1 AAAGAGTTTAACCAGGACTAACGCCAATTTAATCAAACAAGGGTGGAAAGAGTTTGACCAGGACT
* * ** * *
86924 AATGCTAATATAGTCAAATTTGAGATGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAAGGCA
66 AATGCTAATACAATCAAA-TTGAGAACAGTTTGACCAGGTCCTAATACCAATACAGTCAAACGCA
* * *
86989 AGTAAAAGAATTTGACTAGGTTCTACCACCAATACAATCAAATAAGGATGG
130 AGTAAAAGAATTTGACCAGGTCCTAACACCAATACAATCAAATAAGGATGG
* *
87040 AAAGAGTTTGACCAAGACTAA
1 AAAGAGTTTAACCAGGACTAA
87061 TGGTAATACA
Statistics
Matches: 174, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
181 53 0.30
182 2 0.01
183 4 0.02
184 94 0.54
185 19 0.11
186 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (180 bp):
AAAGAGTTTAACCAGGACTAACGCCAATTTAATCAAACAAGGGTGGAAAGAGTTTGACCAGGACT
AATGCTAATACAATCAAATTGAGAACAGTTTGACCAGGTCCTAATACCAATACAGTCAAACGCAA
GTAAAAGAATTTGACCAGGTCCTAACACCAATACAATCAAATAAGGATGG
Found at i:87431 original size:19 final size:18
Alignment explanation
Indices: 87407--87464 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
87397 CACATGAATT
*
87407 TTCATGATTTGATTTATTC-
1 TTCATG-TTTCATTT-TTCA
87426 TTCATGTTTCATTTTTCA
1 TTCATGTTTCATTTTTCA
* *
87444 TTCATTTTTTAGTTTTTCA
1 TTCATGTTTCA-TTTTTCA
87463 TT
1 TT
87465 TTTCTTTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.09
18 16 0.47
19 15 0.44
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (18 bp):
TTCATGTTTCATTTTTCA
Found at i:87858 original size:92 final size:92
Alignment explanation
Indices: 87702--87938 Score: 300
Period size: 92 Copynumber: 2.6 Consensus size: 92
87692 TTTGTCATCA
* * * * * *
87702 TGTGATACATCGATACCATCCAAT-GACTAA-AAAAAAGGATATGATTGGGAATGTGTGGTTAAG
1 TGTGATGCATCAATACCATCTAATAG-CTAAGAGAAAAGGATATGATTGGGAATGGGTAGTTAAG
* *
87765 ATACCTTTGCCTCATGGAAATTAGGCTT
65 ATACCTTTGCCTCAAGGAAATCAGGCTT
* * * *
87793 TGTGATGCATCAATATCATCTAATAGTTGAA-TGAAAGGGATATGATTGGGAATGGGTAGTTAAG
1 TGTGATGCATCAATACCATCTAATAGCT-AAGAGAAAAGGATATGATTGGGAATGGGTAGTTAAG
*
87857 ATACCTTTGCCTCAAGGAAATCAGGTTT
65 ATACCTTTGCCTCAAGGAAATCAGGCTT
* *
87885 TGTGATGCATCAATACCATCTAGTGGCTAAGAGAAAAGGATATGATTGGGAATG
1 TGTGATGCATCAATACCATCTAATAGCTAAGAGAAAAGGATATGATTGGGAATG
87939 TATGGCCAGG
Statistics
Matches: 124, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
91 23 0.19
92 101 0.81
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (92 bp):
TGTGATGCATCAATACCATCTAATAGCTAAGAGAAAAGGATATGATTGGGAATGGGTAGTTAAGA
TACCTTTGCCTCAAGGAAATCAGGCTT
Found at i:87965 original size:92 final size:89
Alignment explanation
Indices: 87869--88121 Score: 251
Period size: 90 Copynumber: 2.8 Consensus size: 89
87859 ACCTTTGCCT
* *
87869 CAAGGAAATCAGGTTTTGTGATGCATCAATACCATCTAGTGGCTAAGAGAAAAGGATATGATTGG
1 CAAGGAAATCAGGCTTTGTGATGCATCAATACCATCTAGTGG-TAAGAGAAAAGGATATGATTAG
*
87934 GAATGTATGGCCAGGATGTCCTTACTC-
65 GAATGTATGGCCAGCA--TCCTTAC-CA
* * * * ** * *
87961 CAAGGAAATTAGGCTTTGTGATGCATTAATACTATCTAATGGTTGGACG-AAGGAGATATGACTA
1 CAAGGAAATCAGGCTTTGTGATGCATCAATACCATCTAGTGGTAAGA-GAAAAG-GATATGATTA
* * *
88025 GGAATGTGTGGTCTGCATCCTTACCA
64 GGAATGTATGGCCAGCATCCTTACCA
* * * *
88051 TAAGGAAATCAGGCTTTGTGATGTATCAATACCATCTAGTGGTTGAA-AGAAATGGATATAATTA
1 CAAGGAAATCAGGCTTTGTGATGCATCAATACCATCTAGTGG-T-AAGAGAAAAGGATATGATTA
88115 GGAATGT
64 GGAATGT
88122 GTGGTCTGCC
Statistics
Matches: 130, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
89 1 0.01
90 59 0.45
91 11 0.08
92 59 0.45
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (89 bp):
CAAGGAAATCAGGCTTTGTGATGCATCAATACCATCTAGTGGTAAGAGAAAAGGATATGATTAGG
AATGTATGGCCAGCATCCTTACCA
Found at i:88082 original size:90 final size:90
Alignment explanation
Indices: 87780--88156 Score: 289
Period size: 92 Copynumber: 4.1 Consensus size: 90
87770 TTTGCCTCAT
* * * * * * *
87780 GGAAATTAGGCTTTGTGATGCATCAATATCATCTAATAGTTGAATGAAAGGGATATGATTGGGAA
1 GGAAATCAGGCTTTGTGATGCATCAATACCATCTAATGGTTGAAAGAAAGGGATATAACTAGGAA
* * *
87845 TGGGTAGT-TAAG-ATACCTTTGCC-TCAA
66 TGTGTGGTCT--GCAT-CC-TTACCAT-AA
* * * * * * *
87872 GGAAATCAGGTTTTGTGATGCATCAATACCATCTAGTGGCT-AAGAGAAAAGGATATGATTGGGA
1 GGAAATCAGGCTTTGTGATGCATCAATACCATCTAATGGTTGAA-AGAAAGGGATATAACTAGGA
* * * * *
87936 ATGTATGGCCAGGATGTCCTTACTC-CAA
65 ATGTGTGGTCTGCA--TCCTTAC-CATAA
* * * * * *
87964 GGAAATTAGGCTTTGTGATGCATTAATACTATCTAATGGTTGGACG-AAGGAGATATGACTAGGA
1 GGAAATCAGGCTTTGTGATGCATCAATACCATCTAATGGTTGAAAGAAAGG-GATATAACTAGGA
88028 ATGTGTGGTCTGCATCCTTACCATAA
65 ATGTGTGGTCTGCATCCTTACCATAA
* * * *
88054 GGAAATCAGGCTTTGTGATGTATCAATACCATCTAGTGGTTGAAAGAAATGGATATAATTAGGAA
1 GGAAATCAGGCTTTGTGATGCATCAATACCATCTAATGGTTGAAAGAAAGGGATATAACTAGGAA
* * *
88119 TGTGTGGTCTGCCTCCTTGCCTTAA
66 TGTGTGGTCTGCATCCTTACCATAA
* *
88144 AGAAATCAAGCTT
1 GGAAATCAGGCTT
88157 CCAATATTGA
Statistics
Matches: 229, Mismatches: 46, Indels: 22
0.77 0.15 0.07
Matches are distributed among these distances:
89 1 0.00
90 93 0.41
91 9 0.04
92 121 0.53
93 4 0.02
94 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (90 bp):
GGAAATCAGGCTTTGTGATGCATCAATACCATCTAATGGTTGAAAGAAAGGGATATAACTAGGAA
TGTGTGGTCTGCATCCTTACCATAA
Found at i:89060 original size:13 final size:13
Alignment explanation
Indices: 89042--89067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89032 CAATTTTTTG
89042 TGTATCGATACAT
1 TGTATCGATACAT
89055 TGTATCGATACAT
1 TGTATCGATACAT
89068 ACTTTGTGCA
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):
TGTATCGATACAT
Found at i:89081 original size:32 final size:33
Alignment explanation
Indices: 89022--89085 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
89012 TACAAGCCAA
** *
89022 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGCATCGATACAT
89055 TGTATCGATAC-ATACTTTGTGCATCGATACA
1 TGTATCGATACAATACTTTGTGCATCGATACA
89086 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGCATCGATACAT
Found at i:89832 original size:19 final size:19
Alignment explanation
Indices: 89808--89853 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
89798 TTTATAAGGT
89808 AATTTA-CACACATATCAAA
1 AATTTATCACACATA-CAAA
*
89827 AATTTATTCGCACATACAAA
1 AATTTA-TCACACATACAAA
89847 AATTTAT
1 AATTTAT
89854 TTGCACATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 10 0.42
21 7 0.29
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (19 bp):
AATTTATCACACATACAAA
Found at i:89848 original size:20 final size:20
Alignment explanation
Indices: 89816--89864 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
89806 GTAATTTACA
89816 CACATATCAAAAATTTATTCG
1 CACATA-CAAAAATTTATTCG
*
89837 CACATACAAAAATTTATTTG
1 CACATACAAAAATTTATTCG
89857 CACATACA
1 CACATACA
89865 TCTATTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (20 bp):
CACATACAAAAATTTATTCG
Found at i:91190 original size:21 final size:20
Alignment explanation
Indices: 91161--91203 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
91151 GACTAGTGTG
* *
91161 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
91182 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
91202 GG
1 GG
91204 TGGTGTTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:91652 original size:13 final size:13
Alignment explanation
Indices: 91634--91671 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
91624 ATAATCCCCC
91634 TGTATCGATACAG
1 TGTATCGATACAG
*
91647 TGTATCGATACAT
1 TGTATCGATACAG
91660 TGTATCGATACA
1 TGTATCGATACA
91672 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:93745 original size:15 final size:15
Alignment explanation
Indices: 93725--93755 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
93715 ATTTCGTTTG
*
93725 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
93740 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
93755 G
1 G
93756 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:96181 original size:21 final size:21
Alignment explanation
Indices: 96155--96230 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
96145 CTGCCAAGAG
*
96155 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
96176 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
96196 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
96217 ATGTATCGATACAT
1 ATGTATCGATACAT
96231 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:96201 original size:20 final size:20
Alignment explanation
Indices: 96176--96248 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
96166 CATCTTTTTT
96176 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
96196 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
96217 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
96237 ATGTATCGATAC
1 ATGTATCGATAC
96249 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:96212 original size:41 final size:41
Alignment explanation
Indices: 96155--96248 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
96145 CTGCCAAGAG
*
96155 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
96196 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
96237 ATGTATCGATAC
1 ATGTATCGATAC
96249 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:98698 original size:13 final size:13
Alignment explanation
Indices: 98680--98718 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
98670 ATAATCACCC
*
98680 TGTATCGATACAG
1 TGTATCGATACAA
98693 TGTATCGATACAA
1 TGTATCGATACAA
98706 TGTATCGATACAA
1 TGTATCGATACAA
98719 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:98729 original size:20 final size:20
Alignment explanation
Indices: 98704--98782 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
98694 GTATCGATAC
98704 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
98724 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
98749 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
98769 CATGTATCGATACA
1 AATGTATCGATACA
98783 TTTTTGGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:100805 original size:15 final size:15
Alignment explanation
Indices: 100785--100821 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
100775 ATAAAAATGT
*
100785 CCCAAAATGAGGAAG
1 CCCAAAATGAAGAAG
100800 CCCAAAATGAAGAAG
1 CCCAAAATGAAGAAG
100815 CTCCAAA
1 C-CCAAA
100822 CGAAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.49, C:0.24, G:0.19, T:0.08
Consensus pattern (15 bp):
CCCAAAATGAAGAAG
Done.