Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015068.1 Kokia drynarioides strain JFW-HI SEQ_130112, whole genome shotgun sequence
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: 452914
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 400 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:243443 original size:17 final size:17
Alignment explanation
Indices: 243421--243459 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
243411 AGGTGGAGAA
* *
243421 CTTGTTCATTGAGAGTT
1 CTTGTTCATAGAGAATT
*
243438 CTTGTTCGTAGAGAATT
1 CTTGTTCATAGAGAATT
243455 CTTGT
1 CTTGT
243460 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:250773 original size:29 final size:29
Alignment explanation
Indices: 250736--250795 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
250726 ATTTGCATCA
250736 ACTTCCCAATAACGTTCCAAACCACAACT
1 ACTTCCCAATAACGTTCCAAACCACAACT
*
250765 ACTTCCCAATAATGTTCCAAACCACAACT
1 ACTTCCCAATAACGTTCCAAACCACAACT
250794 AC
1 AC
250796 AGATGGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.37, G:0.03, T:0.22
Consensus pattern (29 bp):
ACTTCCCAATAACGTTCCAAACCACAACT
Found at i:253626 original size:2 final size:2
Alignment explanation
Indices: 253619--253645 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
253609 CCTAAAAGGA
253619 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
253646 TGCAGGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:260954 original size:25 final size:24
Alignment explanation
Indices: 260926--260991 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
260916 AATGATTGGC
*
260926 TAATCGAAAGAGTTTCTCAGATGGG
1 TAATCGAAAGAATTTCTCAGAT-GG
* *
260951 TAATCG-ATGAATTTTTCAGATGG
1 TAATCGAAAGAATTTCTCAGATGG
* *
260974 -AATTGAAAGACTTTCTCA
1 TAATCGAAAGAATTTCTCA
260992 CACAAATGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 12 0.36
25 6 0.18
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (24 bp):
TAATCGAAAGAATTTCTCAGATGG
Found at i:262699 original size:31 final size:32
Alignment explanation
Indices: 262650--262713 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
262640 ATATGAATAT
262650 TATTTATAAAGAAAAAAATATAATTAAT-TAA
1 TATTTATAAAGAAAAAAATATAATTAATATAA
* *
262681 TATTTTTAAA-AAATAAAATATATTTAATATAA
1 TATTTATAAAGAAA-AAAATATAATTAATATAA
262713 T
1 T
262714 GATAAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 22 0.76
32 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (32 bp):
TATTTATAAAGAAAAAAATATAATTAATATAA
Found at i:262794 original size:16 final size:16
Alignment explanation
Indices: 262773--262804 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
262763 TAATTTTTTG
262773 ATTTATTAAATAAAAA
1 ATTTATTAAATAAAAA
*
262789 ATTTATTAATTAAAAA
1 ATTTATTAAATAAAAA
262805 GATGAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTATTAAATAAAAA
Found at i:274385 original size:31 final size:31
Alignment explanation
Indices: 274350--274414 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
274340 AACAACTCAG
*
274350 TGACTTAAATAAAAATTTAT-AAATAATTTAA
1 TGACTGAAATAAAAATTT-TCAAATAATTTAA
*
274381 TGACTGAAATAAAAATTTTCGAATAATTTAA
1 TGACTGAAATAAAAATTTTCAAATAATTTAA
274412 TGA
1 TGA
274415 TTATTTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (31 bp):
TGACTGAAATAAAAATTTTCAAATAATTTAA
Found at i:274763 original size:18 final size:18
Alignment explanation
Indices: 274740--274774 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
274730 AATGGATGTT
*
274740 GATCAATATCAAGATAAA
1 GATCAAGATCAAGATAAA
274758 GATCAAGATCAAGATAA
1 GATCAAGATCAAGATAA
274775 GGTTTGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.20
Consensus pattern (18 bp):
GATCAAGATCAAGATAAA
Found at i:275544 original size:87 final size:87
Alignment explanation
Indices: 275398--275574 Score: 354
Period size: 87 Copynumber: 2.0 Consensus size: 87
275388 TTATGTTATC
275398 AATGTGATATGAAAGGTTTTTAGCCACATATGTGGTGTATGCTAAAATATTTTGTTTGGGTTAAT
1 AATGTGATATGAAAGGTTTTTAGCCACATATGTGGTGTATGCTAAAATATTTTGTTTGGGTTAAT
275463 ATTCTTTGAGGAAGAATATGAG
66 ATTCTTTGAGGAAGAATATGAG
275485 AATGTGATATGAAAGGTTTTTAGCCACATATGTGGTGTATGCTAAAATATTTTGTTTGGGTTAAT
1 AATGTGATATGAAAGGTTTTTAGCCACATATGTGGTGTATGCTAAAATATTTTGTTTGGGTTAAT
275550 ATTCTTTGAGGAAGAATATGAG
66 ATTCTTTGAGGAAGAATATGAG
275572 AAT
1 AAT
275575 ATAGTAATGA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.39
Consensus pattern (87 bp):
AATGTGATATGAAAGGTTTTTAGCCACATATGTGGTGTATGCTAAAATATTTTGTTTGGGTTAAT
ATTCTTTGAGGAAGAATATGAG
Found at i:278232 original size:18 final size:18
Alignment explanation
Indices: 278209--278243 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
278199 AAAGTTTATA
*
278209 TTAAAATCCTTGAAGGAC
1 TTAAAATCCCTGAAGGAC
278227 TTAAAATCCCTGAAGGA
1 TTAAAATCCCTGAAGGA
278244 TATAGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (18 bp):
TTAAAATCCCTGAAGGAC
Found at i:279925 original size:14 final size:15
Alignment explanation
Indices: 279906--279934 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
279896 ACAATTATGT
279906 ATATTTATA-GTTTA
1 ATATTTATACGTTTA
279920 ATATTTATACGTTTA
1 ATATTTATACGTTTA
279935 TTTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
ATATTTATACGTTTA
Found at i:282998 original size:16 final size:17
Alignment explanation
Indices: 282969--283000 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
282959 ATCATATAAA
282969 AAATAATTTATATATTC
1 AAATAATTTATATATTC
282986 AAATAATTT-TATATT
1 AAATAATTTATATATT
283001 ATTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATAATTTATATATTC
Found at i:283477 original size:30 final size:29
Alignment explanation
Indices: 283441--283509 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
283431 TTAAATTTTT
*
283441 AATGATAAAATTGCACTTTGACCCTCCAAA
1 AATGATAAAATT-CAATTTGACCCTCCAAA
* * **
283471 AATGATACAAATTTAATTTGATCCTTTAAA
1 AATGATA-AAATTCAATTTGACCCTCCAAA
283501 AATGATAAA
1 AATGATAAA
283510 GATATAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 26 0.79
31 5 0.15
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (29 bp):
AATGATAAAATTCAATTTGACCCTCCAAA
Found at i:285532 original size:7 final size:7
Alignment explanation
Indices: 285522--285546 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
285512 TTGAGGAGTG
285522 TAAAAAA
1 TAAAAAA
285529 TAAAAAA
1 TAAAAAA
285536 TAAAAAA
1 TAAAAAA
285543 TAAA
1 TAAA
285547 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:288133 original size:60 final size:60
Alignment explanation
Indices: 288061--288188 Score: 168
Period size: 63 Copynumber: 2.1 Consensus size: 60
288051 NNNNNNNNNN
*
288061 TTTTTTTTACCCAATTTGATACTTAAACTTGACA-CTTTTTCTTAATTTGATACCTAAAC
1 TTTTTTTTACCCAATTTGATACTTAAACTTGACATCTTTTTCCTAATTTGATACCTAAAC
* * * * *
288120 TTTTTTTTAACCCAATTTGGTACTTGAACTTGCCATTTTTTTTTCCTAATTTGATACCTAAGC
1 TTTTTTTT-ACCCAATTTGATACTTAAACTTGACA--TCTTTTTCCTAATTTGATACCTAAAC
288183 TTTTTT
1 TTTTTT
288189 AGATTCAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 8 0.14
60 23 0.39
63 28 0.47
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (60 bp):
TTTTTTTTACCCAATTTGATACTTAAACTTGACATCTTTTTCCTAATTTGATACCTAAAC
Found at i:288464 original size:31 final size:29
Alignment explanation
Indices: 288362--288533 Score: 97
Period size: 31 Copynumber: 5.8 Consensus size: 29
288352 AATCAGGTAT
* *
288362 CAAATTAAGAAAAAAATCAAGTTCAAGTAC
1 CAAATTAAG-AAAAAATCAAATTTAAGTAC
** *
288392 CAAATT-AGACCTCAAA--AAGTTTAAGTAC
1 CAAATTAAGA--AAAAATCAAATTTAAGTAC
* *
288420 CAACTTAAAAAAAAGAGTCAAATTTAAGTAC
1 CAAATTAAGAAAAA-A-TCAAATTTAAGTAC
* * * *
288451 CAAATTATGAAAAAGTATCAAGTTTGATTAC
1 CAAATTAAGAAAAA--ATCAAATTTAAGTAC
*
288482 C-AATT-AGACAAAAA--AAATTTAAATAC
1 CAAATTAAGA-AAAAATCAAATTTAAGTAC
288508 CAAATTAAGAAAAAATGTCAAATTTA
1 CAAATTAAGAAAAAA--TCAAATTTA
288534 GGTAGAGCCA
Statistics
Matches: 108, Mismatches: 19, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
26 10 0.09
27 11 0.10
28 22 0.20
29 6 0.06
30 17 0.16
31 41 0.38
32 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (29 bp):
CAAATTAAGAAAAAATCAAATTTAAGTAC
Found at i:288487 original size:89 final size:88
Alignment explanation
Indices: 288362--288533 Score: 204
Period size: 88 Copynumber: 1.9 Consensus size: 88
288352 AATCAGGTAT
** * * *
288362 CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGACCTCAAAAAGTTTAAGTACCAACTTA
1 CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGA-CAAAAAAAATTTAAATACCAAATTA
288427 A-AAAAAAGAGTCAAATTTAAGTAC
65 AGAAAAAA-AGTCAAATTTAAGTAC
* * ** *
288451 CAAATTATGAAAAAGTATCAAGTTTGATTACC-AATTAGACAAAAAAAATTTAAATACCAAATTA
1 CAAATTAAGAAAAA-AATCAAGTTCAAGTACCAAATTAGACAAAAAAAATTTAAATACCAAATTA
*
288515 AGAAAAAATGTCAAATTTA
65 AGAAAAAAAGTCAAATTTA
288534 GGTAGAGCCA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
88 31 0.44
89 26 0.37
90 13 0.19
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (88 bp):
CAAATTAAGAAAAAAATCAAGTTCAAGTACCAAATTAGACAAAAAAAATTTAAATACCAAATTAA
GAAAAAAAGTCAAATTTAAGTAC
Found at i:289268 original size:26 final size:27
Alignment explanation
Indices: 289207--289268 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
289197 CACAATTTGA
* *
289207 TTCTCAATTTTCTTATTCTCAATATTT
1 TTCTAAATTTTCTAATTCTCAATATTT
* *
289234 TTCTTAATTTT-TAATTCTCGAT-TTT
1 TTCTAAATTTTCTAATTCTCAATATTT
289259 TATCTAAATT
1 T-TCTAAATT
289269 CCAAATTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.13
26 16 0.53
27 10 0.33
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.60
Consensus pattern (27 bp):
TTCTAAATTTTCTAATTCTCAATATTT
Found at i:291551 original size:24 final size:24
Alignment explanation
Indices: 291524--291597 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
291514 TCATTTTTAC
291524 GTTTACGCTCGTCAGCATGGATAT
1 GTTTACGCTCGTCAGCATGGATAT
* * * *
291548 GTTTATGCTTGTCAACATGGGTAT
1 GTTTACGCTCGTCAGCATGGATAT
* *
291572 ATTTACGCTCGTCAGCATGAATAT
1 GTTTACGCTCGTCAGCATGGATAT
291596 GT
1 GT
291598 ATACTTACCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCATGGATAT
Found at i:293755 original size:22 final size:22
Alignment explanation
Indices: 293727--293785 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
293717 GGTGTTGCTT
*
293727 GCAAAAAGAAGAACAAACATAA
1 GCAAAAACAAGAACAAACATAA
293749 GCAAAAACAAGAACAAACATAA
1 GCAAAAACAAGAACAAACATAA
293771 GCAAAAACAAGAACA
1 GCAAAAACAAGAACA
293786 TAGCGCACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.68, C:0.17, G:0.12, T:0.03
Consensus pattern (22 bp):
GCAAAAACAAGAACAAACATAA
Found at i:294786 original size:30 final size:29
Alignment explanation
Indices: 294738--294816 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
294728 TTGACCCTAG
294738 CTTTCTAAAAATTGCATTTCGACCCCCAAA
1 CTTTCTAAAAATTGCATTTCGA-CCCCAAA
* * * *
294768 CTTTCTCAAACTTTCATTTTGACCCCAAA
1 CTTTCTAAAAATTGCATTTCGACCCCAAA
* *
294797 CTTTTCTAAAATTTACATTT
1 C-TTTCTAAAAATTGCATTT
294817 AACCCTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.20
30 33 0.80
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (29 bp):
CTTTCTAAAAATTGCATTTCGACCCCAAA
Found at i:294821 original size:29 final size:29
Alignment explanation
Indices: 294738--294821 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
294728 TTGACCCTAG
* * * *
294738 CTTTCTAAAAATTGCATTTCGACCCCCAAA
1 CTTTCTCAAAATTTCATTT-TAACCCCAAA
* *
294768 CTTTCTCAAACTTTCATTTTGACCCCAAA
1 CTTTCTCAAAATTTCATTTTAACCCCAAA
294797 CTTT-TCTAAAATTTACA-TTTAACCC
1 CTTTCTC-AAAATTT-CATTTTAACCC
294822 TTAAAGTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.55
30 18 0.41
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (29 bp):
CTTTCTCAAAATTTCATTTTAACCCCAAA
Found at i:295051 original size:28 final size:29
Alignment explanation
Indices: 295020--295079 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
295010 TTTTTTTAAA
* *
295020 TTTCGTCCTTATATG-TTTTAAATTATAT
1 TTTCATCCTTATACGTTTTTAAATTATAT
*
295048 TTTCATCCTTATGCGTTTTTAAATTATAT
1 TTTCATCCTTATACGTTTTTAAATTATAT
295077 TTT
1 TTT
295080 TTCTTTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTCATCCTTATACGTTTTTAAATTATAT
Found at i:298999 original size:24 final size:24
Alignment explanation
Indices: 298972--299025 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
298962 TTTCAGAAAT
298972 TTAGCTCATACGAGCCCAG-ATAGG
1 TTAGCTCATACGAGCCCAGAAT-GG
* *
298996 TTAGCTCTTATGAGCCCAGAATGG
1 TTAGCTCATACGAGCCCAGAATGG
299020 TTAGCT
1 TTAGCT
299026 TTTACAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAGAATGG
Found at i:299039 original size:24 final size:24
Alignment explanation
Indices: 298972--299041 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
298962 TTTCAGAAAT
* *
298972 TTAGCTCATACGAGCCCAG-ATAGG
1 TTAGCTCTTACAAGCCCAGAAT-GG
**
298996 TTAGCTCTTATGAGCCCAGAATGG
1 TTAGCTCTTACAAGCCCAGAATGG
* *
299020 TTAGCTTTTACAAGCTCAGAAT
1 TTAGCTCTTACAAGCCCAGAAT
299042 CAGAATAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 37 0.95
25 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTACAAGCCCAGAATGG
Found at i:299167 original size:27 final size:27
Alignment explanation
Indices: 299032--299168 Score: 184
Period size: 27 Copynumber: 5.0 Consensus size: 27
299022 AGCTTTTACA
* *
299032 AGCTCAGAATCAGAATAATGCTCTTTCA
1 AGCT-AGAATCAGAATAACGCTCTTTCG
* *
299060 AGCTAGAATCAGAATAATGCTCTTTCA
1 AGCTAGAATCAGAATAACGCTCTTTCG
*
299087 AGCTAGAATCAGAATAACACTCTTTCG
1 AGCTAGAATCAGAATAACGCTCTTTCG
* *
299114 AGCCAGAATCAGAATAACACTCTTTCG
1 AGCTAGAATCAGAATAACGCTCTTTCG
* *
299141 AGCTAGAATTAGAATAACGTTCTTTCG
1 AGCTAGAATCAGAATAACGCTCTTTCG
299168 A
1 A
299169 ACCAAAATCA
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 97 0.96
28 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (27 bp):
AGCTAGAATCAGAATAACGCTCTTTCG
Found at i:301688 original size:19 final size:20
Alignment explanation
Indices: 301664--301701 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
301654 CCATTTATGT
301664 AATTTG-CTT-TATGTAAAGA
1 AATTTGTCTTCTA-GTAAAGA
301683 AATTTGTCTTCTAGTAAAG
1 AATTTGTCTTCTAGTAAAG
301702 TTATTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
AATTTGTCTTCTAGTAAAGA
Found at i:305018 original size:17 final size:18
Alignment explanation
Indices: 304978--305018 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
304968 TAGGTTTAAG
*
304978 GGAGAAGAAAAGAGAGTT
1 GGAGAAGAAAAGAGAGTA
304996 GGAGAAGAAATAG-GAG-A
1 GGAGAAGAAA-AGAGAGTA
305013 GGAGAA
1 GGAGAA
305019 AAGCACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.41, T:0.07
Consensus pattern (18 bp):
GGAGAAGAAAAGAGAGTA
Found at i:310008 original size:40 final size:38
Alignment explanation
Indices: 309900--310467 Score: 250
Period size: 38 Copynumber: 14.9 Consensus size: 38
309890 CTACACATCA
*
309900 CCAATCTCTTATCCCGATCATAGGGTAGATTGAAGCAT
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
* * *** * *
309938 CTAATCTTTTACCTTAATCAGAGGGTAGATTGAAGACTT
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAG-CAT
* *
309977 GCCAATCTCTTACCCCGATCATAAGGCAGATTGAAGCA-
1 -CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
* * * * *
310015 --AA-C-CCTA-----ACCAGAGGGCAGATTGAAGACACA
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAG-CA-T
* * * * * * *
310046 CCAGTTTCTTTCCCAGATCATGGGGCAGATTGAAACA-
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
** * * * *
310083 CCTAATCTCTTACCCTAATTAGAGGGCAGATTGAAGACTT
1 CC-AATCTCTTACCCCGATCATAGGGTAGATTGAAG-CAT
* * * *
310123 GTCAATCTCTTACCCCGATCATGGGGCAAATTGAAGACA-
1 -CCAATCTCTTACCCCGATCATAGGGTAGATTGAAG-CAT
* * * *
310162 CGTCAATCTCTTACCTCGATCATGGGGCAGATCGAAGCAT
1 C--CAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
* ** * * *
310202 CCAATCTTTTACCCTAATCAGAGGGCAGATTGGAG-ATT
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCA-T
* *
310240 CGCTAATCTCTTACCCCGATCATGGGGCAGATTGAAGCAT
1 C-C-AATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
* ** * * *
310280 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAGGACAAAT
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAG-C--AT
* * * * *
310321 -CAATTTCTTACCCCGATTATAGGGTAAATTGAAACAC
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
* * * * *
310358 CCAATCTTTTACCTCAATCAT-GAGGCAGATTGAAACAT
1 CCAATCTCTTACCCCGATCATAG-GGTAGATTGAAGCAT
* * * *
310396 CTAATCTCTTACCCCGATCAT-GAGGCAGATTGAAACAC
1 CCAATCTCTTACCCCGATCATAG-GGTAGATTGAAGCAT
** * *
310434 CCAATCTCTTACCTTGATCGTGGGGTAGATTGAA
1 CCAATCTCTTACCCCGATCATAGGGTAGATTGAA
310468 AACGTCATTC
Statistics
Matches: 399, Mismatches: 100, Indels: 62
0.71 0.18 0.11
Matches are distributed among these distances:
28 16 0.04
29 2 0.01
33 4 0.01
34 1 0.00
35 4 0.01
37 5 0.01
38 194 0.49
39 13 0.03
40 156 0.39
41 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (38 bp):
CCAATCTCTTACCCCGATCATAGGGTAGATTGAAGCAT
Found at i:310117 original size:38 final size:39
Alignment explanation
Indices: 310026--310468 Score: 286
Period size: 38 Copynumber: 11.4 Consensus size: 39
310016 ACCCTAACCA
* * * * *
310026 GAGGGCAGATTGAAGACACACCAGTTTCTTTCCCAGATCAT
1 GAGGGCAGATTGAA-ACAC-CTAATCTCTTACCCTGATCAT
* *
310067 G-GGGCAGATTGAAACACCTAATCTCTTACCCTAATTA-
1 GAGGGCAGATTGAAACACCTAATCTCTTACCCTGATCAT
*** *
310104 GAGGGCAGATTGAAGACTTGTCAATCTCTTACCCCGATCAT
1 GAGGGCAGATTGAA-ACACCT-AATCTCTTACCCTGATCAT
* *
310145 G-GGGCAAATTGAAGACACGTCAATCTCTTA-CCTCGATCAT
1 GAGGGCAGATTGAA-ACACCT-AATCTCTTACCCT-GATCAT
* * * *
310185 G-GGGCAGATCGAAGCATCC-AATCTTTTACCCTAATCA-
1 GAGGGCAGATTGAAACA-CCTAATCTCTTACCCTGATCAT
* ** *
310222 GAGGGCAGATTGGAGATTCGCTAATCTCTTACCCCGATCAT
1 GAGGGCAGATT-GAAACAC-CTAATCTCTTACCCTGATCAT
* * *
310263 G-GGGCAGATTGAAGCATCC-AATCTTTTACCCTAATCA-
1 GAGGGCAGATTGAAACA-CCTAATCTCTTACCCTGATCAT
* ** * * *
310300 GAGGGCAGATTGAGGACAAATCAATTTCTTACCCCGATTAT
1 GAGGGCAGATTGA-AACACCT-AATCTCTTACCCTGATCAT
* * * * *
310341 -AGGGTAAATTGAAACACCCAATCTTTTA-CCTCAATCAT
1 GAGGGCAGATTGAAACACCTAATCTCTTACCCT-GATCAT
* *
310379 GA-GGCAGATTGAAACATCTAATCTCTTACCCCGATCAT
1 GAGGGCAGATTGAAACACCTAATCTCTTACCCTGATCAT
* * *
310417 GA-GGCAGATTGAAACACCCAATCTCTTACCTTGATCGT
1 GAGGGCAGATTGAAACACCTAATCTCTTACCCTGATCAT
*
310455 G-GGGTAGATTGAAA
1 GAGGGCAGATTGAAA
310469 ACGTCATTCG
Statistics
Matches: 309, Mismatches: 71, Indels: 47
0.72 0.17 0.11
Matches are distributed among these distances:
37 5 0.02
38 154 0.50
39 28 0.09
40 119 0.39
41 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (39 bp):
GAGGGCAGATTGAAACACCTAATCTCTTACCCTGATCAT
Found at i:310145 original size:78 final size:80
Alignment explanation
Indices: 310016--310446 Score: 213
Period size: 78 Copynumber: 5.5 Consensus size: 80
310006 ATTGAAGCAA
* * * *
310016 ACCCTAACCAGAGGGCAGATTGAAGACACACCAGTTTCTTTCCCAGATCATGGGGCAGATTGAA-
1 ACCCTAACCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCAGATCATGGGGCAAATTGAAG
310080 ACACCT-AATCTCTT
66 ACACCTCAATCTCTT
** **** *
310094 ACCCTAATTAGAGGGCAGATTGAAGACTTGTCAATCTCTTACCCCGATCATGGGGCAAATTGAAG
1 ACCCTAACCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCAGATCATGGGGCAAATTGAAG
*
310159 ACACGTCAATCTCTT
66 ACACCTCAATCTCTT
* * * * * *
310174 A-CCTCGATCATG-GGGCAGATCGAAG-CA-TCCAATCTTTTACCCTA-ATCA-GAGGGCAGATT
1 ACCCT-AACCA-GAGGGCAGATTGAAGACACACCAATCTCTTACCC-AGATCATG-GGGCAAATT
* **
310233 GGAGATTCGCT-AATCTCTT
62 GAAGACAC-CTCAATCTCTT
** * * * *
310252 ACCCCGATCATG-GGGCAGATTGAAG-CA-TCCAATCTTTTACCCTA-ATCA-GAGGGCAGATTG
1 ACCCTAACCA-GAGGGCAGATTGAAGACACACCAATCTCTTACCC-AGATCATG-GGGCAAATTG
* ** *
310312 AGGACAAATCAATTTCTT
63 AAGACACCTCAATCTCTT
** ** * * * * * *
310330 ACCCCGATTATAGGGTAAATTGAA-ACAC-CCAATCTTTTACCTCA-ATCATGAGGCAGATTGAA
1 ACCCTAACCAGAGGGCAGATTGAAGACACACCAATCTCTTACC-CAGATCATGGGGCAAATTGAA
*
310392 -ACATCT-AATCTCTT
65 GACACCTCAATCTCTT
** *
310406 ACCCCGATCATGA-GGCAGATTGAA-ACAC-CCAATCTCTTACC
1 ACCCTAACCA-GAGGGCAGATTGAAGACACACCAATCTCTTACC
310447 TTGATCGTGG
Statistics
Matches: 290, Mismatches: 48, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
76 41 0.14
77 7 0.02
78 203 0.70
79 14 0.05
80 24 0.08
81 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (80 bp):
ACCCTAACCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCAGATCATGGGGCAAATTGAAG
ACACCTCAATCTCTT
Found at i:310248 original size:118 final size:118
Alignment explanation
Indices: 310061--310276 Score: 330
Period size: 118 Copynumber: 1.8 Consensus size: 118
310051 TTCTTTCCCA
* *
310061 GATCATGGGGCAGATTGAAACACCTAATCTCTTACCCTAATTAGAGGGCAGATTGAAGACTTGTC
1 GATCATGGGGCAGATCGAAACACCTAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACTTGTC
310126 AATCTCTTACCCCGATCATGGGGCAAATTGAAGACACGTCAATCTCTTACCTC
66 AATCTCTTACCCCGATCATGGGGCAAATTGAAGACACGTCAATCTCTTACCTC
* * *
310179 GATCATGGGGCAGATCGAAGCATCC-AATCTTTTACCCTAATCAGAGGGCAGATTGGAGA-TTCG
1 GATCATGGGGCAGATCGAAACA-CCTAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACTT-G
*
310242 -CTAATCTCTTACCCCGATCATGGGGCAGATTGAAG
64 TC-AATCTCTTACCCCGATCATGGGGCAAATTGAAG
310277 CATCCAATCT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
117 3 0.03
118 84 0.94
119 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (118 bp):
GATCATGGGGCAGATCGAAACACCTAATCTCTTACCCTAATCAGAGGGCAGATTGAAGACTTGTC
AATCTCTTACCCCGATCATGGGGCAAATTGAAGACACGTCAATCTCTTACCTC
Found at i:310333 original size:118 final size:118
Alignment explanation
Indices: 310062--310309 Score: 307
Period size: 118 Copynumber: 2.1 Consensus size: 118
310052 TCTTTCCCAG
* * *
310062 ATCATGGGGCAGATTGAAACA-CCTAATC-TCTTACCCTAATTAGAGGGCAGATTGAAGACTTGT
1 ATCATGGGGCAGATCGAAGCATCC-AATCTTCTTACCCTAATCAGAGGGCAGATTGAAGACTTGT
*
310125 CAATCTCTTACCCCGATCATGGGGCAAATTGAAGACACGTCAATCTCTTACCTCG
65 CAATCTCTTACCCCGATCATGGGGCAAATTGAAGACACG-CAATCTCTTACCTCA
*
310180 ATCATGGGGCAGATCGAAGCATCCAATCTT-TTACCCTAATCAGAGGGCAGATTGGAGA-TTCG-
1 ATCATGGGGCAGATCGAAGCATCCAATCTTCTTACCCTAATCAGAGGGCAGATTGAAGACTT-GT
* *
310242 CTAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATC-CAATCTTTTACC-CTA
65 C-AATCTCTTACCCCGATCATGGGGCAAATTGAAGACA-CGCAATCTCTTACCTC-A
310296 ATCA-GAGGGCAGAT
1 ATCATG-GGGCAGAT
310310 TGAGGACAAA
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
115 2 0.02
116 23 0.20
117 5 0.04
118 83 0.72
119 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (118 bp):
ATCATGGGGCAGATCGAAGCATCCAATCTTCTTACCCTAATCAGAGGGCAGATTGAAGACTTGTC
AATCTCTTACCCCGATCATGGGGCAAATTGAAGACACGCAATCTCTTACCTCA
Found at i:312284 original size:42 final size:42
Alignment explanation
Indices: 312232--312312 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
312222 ACCATTTTAT
312232 TTTCACATATACATTTGTCATCACATATATATCATCATAATA
1 TTTCACATATACATTTGTCATCACATATATATCATCATAATA
312274 TTTCACATATACATTTGTCATCACATATATATCATCATA
1 TTTCACATATACATTTGTCATCACATATATATCATCATA
312313 TACCTCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (42 bp):
TTTCACATATACATTTGTCATCACATATATATCATCATAATA
Found at i:314926 original size:30 final size:31
Alignment explanation
Indices: 314865--314949 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
314855 GACACCAAGC
* ** *
314865 TTTCTAAAAATTGCATTTCGA-CCTCCAAAC-
1 TTTCTAAAACTTGCATTTTAACCCT-CGAACT
*
314895 TTTCTCAAACTTGCATTTTAACCCTCGAACT
1 TTTCTAAAACTTGCATTTTAACCCTCGAACT
* *
314926 TTTCTAAAATTTGCATTTTGACCC
1 TTTCTAAAACTTGCATTTTAACCC
314950 CCAAAATTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (31 bp):
TTTCTAAAACTTGCATTTTAACCCTCGAACT
Found at i:314940 original size:31 final size:31
Alignment explanation
Indices: 314859--314959 Score: 100
Period size: 30 Copynumber: 3.3 Consensus size: 31
314849 TACTTTGACA
* *
314859 CCAAGCTTTCTAAAAATTGCATTTCGA-CCT
1 CCAAACTTTCTAAAAATTGCATTTTGACCCT
* * *
314889 CCAAACTTTCTCAAACTTGCATTTTAACCCT
1 CCAAACTTTCTAAAAATTGCATTTTGACCCT
* *
314920 -CGAACTTTTCTAAAATTTGCATTTTGACCC-
1 CCAAAC-TTTCTAAAAATTGCATTTTGACCCT
*
314950 CCAAAATTTC
1 CCAAACTTTC
314960 CAAATCTTGT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
30 30 0.53
31 27 0.47
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36
Consensus pattern (31 bp):
CCAAACTTTCTAAAAATTGCATTTTGACCCT
Found at i:316111 original size:31 final size:28
Alignment explanation
Indices: 316066--316164 Score: 83
Period size: 31 Copynumber: 3.3 Consensus size: 28
316056 AACAATCACA
316066 ACATAG-ACCAATTTATTTTACACCAGC
1 ACATAGCACCAATTTATTTTACACCAGC
* * *
316093 ACCATAGCACCTGCATTTATTCCTACACCAAC
1 A-CATAGCACC--AATTTATT-TTACACCAGC
* *
316125 ACAGTCATCACCAATTTATTTTACACAAGC
1 ACA-T-AGCACCAATTTATTTTACACCAGC
316155 AACATAGCAC
1 -ACATAGCAC
316165 ACTCAATTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
27 1 0.02
28 5 0.09
29 7 0.13
30 8 0.15
31 19 0.35
32 10 0.18
33 5 0.09
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.26
Consensus pattern (28 bp):
ACATAGCACCAATTTATTTTACACCAGC
Found at i:316774 original size:37 final size:37
Alignment explanation
Indices: 316724--316800 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
316714 CCCATGTCAC
316724 ATAAGTAACCATATACCAATTTAATACTATTCAAAGA
1 ATAAGTAACCATATACCAATTTAATACTATTCAAAGA
316761 ATAAGTAACCATATACCAATTTAATACTATTCAAAGA
1 ATAAGTAACCATATACCAATTTAATACTATTCAAAGA
316798 ATA
1 ATA
316801 CCGTTATACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (37 bp):
ATAAGTAACCATATACCAATTTAATACTATTCAAAGA
Found at i:318644 original size:89 final size:89
Alignment explanation
Indices: 318525--318705 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
318515 GTCTCCTAAG
318525 CTAGTTGTGAGGCAATAATTACATTTGGTTTTCCTCTCCTCTCAAACAGCATAGGAAAATAATAA
1 CTAGTTGTGAGGCAATAATTACATTTGGTTTTCCTCTCCTCTCAAACAGCATAGGAAAATAATAA
318590 GTAACCCAAATAATTCCAACACTT
66 GTAACCCAAATAATTCCAACACTT
* *
318614 CTAGTTGTGAGGTAATAATTACATTTGGTTTTCCTCTCCTCTCAAACAGCATAGGAAACTAATAA
1 CTAGTTGTGAGGCAATAATTACATTTGGTTTTCCTCTCCTCTCAAACAGCATAGGAAAATAATAA
318679 GTAACCCAAATAATTCCAACACTT
66 GTAACCCAAATAATTCCAACACTT
318703 CTA
1 CTA
318706 ATGTAACACC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (89 bp):
CTAGTTGTGAGGCAATAATTACATTTGGTTTTCCTCTCCTCTCAAACAGCATAGGAAAATAATAA
GTAACCCAAATAATTCCAACACTT
Found at i:323274 original size:25 final size:25
Alignment explanation
Indices: 323246--323311 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
323236 TAGTTCATAA
*
323246 GAGCCCAGATAGGGTTAGCTCTTAC
1 GAGCCCAGATAGAGTTAGCTCTTAC
* *
323271 GAGCCCAAACAGAGTTAGCTCTTAC
1 GAGCCCAGATAGAGTTAGCTCTTAC
* *
323296 AAGCCTAGATAGAGTT
1 GAGCCCAGATAGAGTT
323312 TAACCTGTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (25 bp):
GAGCCCAGATAGAGTTAGCTCTTAC
Found at i:328404 original size:13 final size:13
Alignment explanation
Indices: 328386--328410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328376 TTCATATAAT
328386 GTATAACGGAATA
1 GTATAACGGAATA
328399 GTATAACGGAAT
1 GTATAACGGAAT
328411 GAAAGGAAAA
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:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (13 bp):
GTATAACGGAATA
Found at i:328853 original size:158 final size:158
Alignment explanation
Indices: 328565--328898 Score: 460
Period size: 158 Copynumber: 2.1 Consensus size: 158
328555 TGTGGATTCT
* * * * *
328565 CCACAGCTCGTGTAAGCAAGCCCATTTCACAGCTCGTGTGAGCATTACAGGTTATATGGGTGTTG
1 CCACAGCTCGTGTGAGCAAGCCCATTCCACAACTCGTGTGAGCATTACAAGTTATATGGGTGCTG
* * * * * * *
328630 GTCTTGGATGTCCTACTGATGGCTGAGGTACTGTATTGGTTGTGGATTCTCCATAACTCGTGTGA
66 GTCTTAGATGTCCTACCGATGGCTGAGGTACTGCATTGATTGCGGATTCTCCACAACTCATGTGA
328695 G-AAGCATCGCGTAG-CCTAACATCTTGAC
131 GCAA-CATCGCGTAGCCCT-ACATCTTGAC
*
328723 CCACAACTCGTGTGAGC-AGACCCATTCCACAACTCGTGTGAGCATTACAAGTTATATGGGTGCT
1 CCACAGCTCGTGTGAGCAAG-CCCATTCCACAACTCGTGTGAGCATTACAAGTTATATGGGTGCT
* *
328787 GGTCTTAGATGTCCTACCGATGGCTGAGGT-CTAGCATTTATTGCGGATTCTCCACAGCTCATGT
65 GGTCTTAGATGTCCTACCGATGGCTGAGGTACT-GCATTGATTGCGGATTCTCCACAACTCATGT
*
328851 GAGCAACATCGTGTAGCCCTACATCTTGAC
129 GAGCAACATCGCGTAGCCCTACATCTTGAC
328881 CCACAGCTCGTGTGAGCA
1 CCACAGCTCGTGTGAGCA
328899 TATATGGTTA
Statistics
Matches: 154, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
157 4 0.03
158 145 0.94
159 5 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (158 bp):
CCACAGCTCGTGTGAGCAAGCCCATTCCACAACTCGTGTGAGCATTACAAGTTATATGGGTGCTG
GTCTTAGATGTCCTACCGATGGCTGAGGTACTGCATTGATTGCGGATTCTCCACAACTCATGTGA
GCAACATCGCGTAGCCCTACATCTTGAC
Found at i:333517 original size:17 final size:17
Alignment explanation
Indices: 333484--333516 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
333474 AGAGATATTT
*
333484 TTAACAAAAGTATAAAA
1 TTAACAAAAATATAAAA
333501 TTAA-AAAAATATAAAA
1 TTAACAAAAATATAAAA
333517 AAATTACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAACAAAAATATAAAA
Found at i:340308 original size:15 final size:15
Alignment explanation
Indices: 340288--340319 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
340278 CCTTCATCCA
340288 TGCTCGCAACTTCAG
1 TGCTCGCAACTTCAG
340303 TGCTCGCAACTTCAG
1 TGCTCGCAACTTCAG
340318 TG
1 TG
340320 TTCATGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.31, G:0.22, T:0.28
Consensus pattern (15 bp):
TGCTCGCAACTTCAG
Found at i:341317 original size:7 final size:7
Alignment explanation
Indices: 341305--341350 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
341295 CTTTTATTGT
341305 TTTTTAA
1 TTTTTAA
341312 TTTTTAAA
1 TTTTT-AA
341320 TTTTT--
1 TTTTTAA
341325 TTTTTAA
1 TTTTTAA
*
341332 TTTTTTA
1 TTTTTAA
*
341339 TTATTAA
1 TTTTTAA
341346 TTTTT
1 TTTTT
341351 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
5 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:341326 original size:27 final size:27
Alignment explanation
Indices: 341296--341357 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
341286 GTTTACTATC
** * *
341296 TTTTATTGTTTTTTAATTTTTAAATTT
1 TTTTATTAATTTTTTATTATTAAATTT
*
341323 TTTTTTTAATTTTTTATTATT-AATTT
1 TTTTATTAATTTTTTATTATTAAATTT
*
341349 TTTTTTTAA
1 TTTTATTAA
341358 ATTATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTATTAATTTTTTATTATTAAATTT
Found at i:341333 original size:12 final size:12
Alignment explanation
Indices: 341312--341357 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
341302 TGTTTTTTAA
*
341312 TTTTTAAATTTT
1 TTTTTTAATTTT
341324 TTTTTTAATTTT
1 TTTTTTAATTTT
341336 TTATTATTAATTTT
1 TT-TT-TTAATTTT
341350 TTTTTTAA
1 TTTTTTAA
341358 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTAATTTT
Found at i:341335 original size:26 final size:26
Alignment explanation
Indices: 341305--341366 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
341295 CTTTTATTGT
*
341305 TTTTTAATTTTTAAATTTTTTTTTTAA
1 TTTTTAATTATT-AATTTTTTTTTTAA
*
341332 TTTTTTATTATTAATTTTTTTTTTAAA
1 TTTTTAATTATTAATTTTTTTTTT-AA
341359 TTATTTAA
1 TT-TTTAA
341367 ATGATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 12 0.40
27 14 0.47
28 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTAATTATTAATTTTTTTTTTAA
Found at i:356383 original size:15 final size:16
Alignment explanation
Indices: 356351--356390 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
356341 TATCAAGCTT
356351 AAATTTTCTTAAACTC
1 AAATTTTCTTAAACTC
**
356367 AAATTTT-TTAAGTTC
1 AAATTTTCTTAAACTC
356382 AAATTTTCT
1 AAATTTTCT
356391 CGAACTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATTTTCTTAAACTC
Found at i:357542 original size:42 final size:42
Alignment explanation
Indices: 357487--357675 Score: 236
Period size: 42 Copynumber: 4.5 Consensus size: 42
357477 TATGCTCTAA
* * * * * * *
357487 CGAGTCATAAGTCTTCCTTTAATCATATTTTCATTCTCGTCC
1 CGAGACATGAGTCTTCCTTTAATAATAATCTCATTCTCATCT
*
357529 CGAGACATGAGTCTTCCTTTAATTATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATAATAATCTCATTCTCATCT
357571 CGAGACATGAGTCTTCCTTTAATAATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATAATAATCTCATTCTCATCT
* **
357613 CGAGACATGAGTCTTCCTTTAATACA-AATCCTCATGCTCAAGT
1 CGAGACATGAGTCTTCCTTTAATA-ATAAT-CTCATTCTCATCT
**
357656 CGAGACACAAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
357676 TATACGTCAA
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 103 0.78
43 29 0.22
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATAATAATCTCATTCTCATCT
Found at i:360166 original size:16 final size:16
Alignment explanation
Indices: 360128--360168 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
360118 AAATTTATAA
360128 TATTT-TATATTATGT
1 TATTTATATATTATGT
360143 TATTTTTATATATTATGT
1 TA--TTTATATATTATGT
360161 TATTTATA
1 TATTTATA
360169 ACACATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 6 0.26
17 3 0.13
18 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
TATTTATATATTATGT
Found at i:360287 original size:19 final size:18
Alignment explanation
Indices: 360265--360300 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
360255 TTTTCAATAA
*
360265 ATTAAAAATATATAAAATT
1 ATTAAAAA-AAATAAAATT
360284 ATTAAAAAAAATAAAAT
1 ATTAAAAAAAATAAAAT
360301 AAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAAAAAAATAAAATT
Found at i:360298 original size:28 final size:26
Alignment explanation
Indices: 360245--360321 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 26
360235 TTAAGATGAC
* * *
360245 TATATAAAAATTTTCAATAAATTAAAAA
1 TATAT-AAAATTTTAAAAAAAAT-AAAA
360273 TATATAAAATTATTAAAAAAAATAAAA
1 TATATAAAATT-TTAAAAAAAATAAAA
*
360300 TAAAATAAATATTTTAAAAAAA
1 T-ATATAAA-ATTTTAAAAAAA
360322 TATATAATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 11 0.26
28 28 0.67
29 3 0.07
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
TATATAAAATTTTAAAAAAAATAAAA
Found at i:360530 original size:26 final size:26
Alignment explanation
Indices: 360494--360546 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
360484 TCTCTAATAG
360494 AGTCTAAAAAACTCTTATGGTGATGT
1 AGTCTAAAAAACTCTTATGGTGATGT
360520 AGTCTAAAAAACTCTTATGGTGATGT
1 AGTCTAAAAAACTCTTATGGTGATGT
360546 A
1 A
360547 TTAAATAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (26 bp):
AGTCTAAAAAACTCTTATGGTGATGT
Found at i:360814 original size:27 final size:27
Alignment explanation
Indices: 360778--360836 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
360768 TAATAATATG
*
360778 GAATTTTAAAAAAAAAAC-TTAGGACT
1 GAATTTTAAAAAAAAAACATTAGAACT
*
360804 GAATTTCTAAAAACAAAACATTAGAACT
1 GAATTT-TAAAAAAAAAACATTAGAACT
*
360832 CAATT
1 GAATT
360837 CCAAATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 11 0.39
28 11 0.39
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (27 bp):
GAATTTTAAAAAAAAAACATTAGAACT
Found at i:361114 original size:20 final size:20
Alignment explanation
Indices: 361089--361132 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
361079 ACACACGCTT
361089 TCTCCCT-CCTCCTCTCTCTC
1 TCTCCCTACC-CCTCTCTCTC
*
361109 TCTCCCTACCCCTCTCTCTT
1 TCTCCCTACCCCTCTCTCTC
361129 TCTC
1 TCTC
361133 TCTCTTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.41
Consensus pattern (20 bp):
TCTCCCTACCCCTCTCTCTC
Found at i:374692 original size:19 final size:19
Alignment explanation
Indices: 374668--374719 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
374658 ATTTTTATAT
*
374668 ATAATTTTTTATATTTTAA
1 ATAATTTTCTATATTTTAA
** *
374687 ATAATTTTGAATTTTTTAA
1 ATAATTTTCTATATTTTAA
374706 ATAAATTTTCTATA
1 AT-AATTTTCTATA
374720 GAATTAGGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATAATTTTCTATATTTTAA
Found at i:377308 original size:17 final size:17
Alignment explanation
Indices: 377279--377321 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
377269 ATTGTTCAAG
377279 TTAATTT-TT-AAATCAA
1 TTAATTTATTAAAAT-AA
377295 TT-ATTTATTAAAATAA
1 TTAATTTATTAAAATAA
377311 TTAATTTATTA
1 TTAATTTATTA
377322 CAAACTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 8 0.33
17 12 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATTTATTAAAATAA
Found at i:383941 original size:3 final size:3
Alignment explanation
Indices: 383933--383961 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
383923 ATTCAATCTT
383933 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
383962 TTAAAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:397828 original size:29 final size:29
Alignment explanation
Indices: 397779--398038 Score: 296
Period size: 29 Copynumber: 8.9 Consensus size: 29
397769 TAGATCTTCA
* *
397779 AACTTTCAAAAATCAAAATTTTACCCTCG
1 AACTTTCAAAAATCACATTTTTACCCTCG
* * *
397808 AACTTCTCAAAAATTATATTTTTACCCTTG
1 AACTT-TCAAAAATCACATTTTTACCCTCG
* * *
397838 AACTTCTCAAAAATTACA-TTTTCCCCTCA
1 AACTT-TCAAAAATCACATTTTTACCCTCG
*
397867 AACTTCTCAAAAATCACATTTTTATCCTCG
1 AACTT-TCAAAAATCACATTTTTACCCTCG
*
397897 AACTTTCAAAGATCACATTTTTACTCC-CG
1 AACTTTCAAAAATCACATTTTTAC-CCTCG
* *
397926 AACTTTAAAAAATCACATTTTTACCCCCG
1 AACTTTCAAAAATCACATTTTTACCCTCG
* *
397955 AACTTTAAAAAATCACATTTTTACCCCCG
1 AACTTTCAAAAATCACATTTTTACCCTCG
397984 AACTTTCAAAAATCACA-TTTTACTCC-CG
1 AACTTTCAAAAATCACATTTTTAC-CCTCG
*
398012 AACTTTAAAAAATCAC-TTTTTAACCCT
1 AACTTTCAAAAATCACATTTTT-ACCCT
398039 AAACTCTTCG
Statistics
Matches: 205, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
28 31 0.15
29 122 0.60
30 52 0.25
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTTCAAAAATCACATTTTTACCCTCG
Found at i:402027 original size:15 final size:16
Alignment explanation
Indices: 402002--402032 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
401992 CTTGAAACCT
402002 AAGGTAAAAAAAGAAA
1 AAGGTAAAAAAAGAAA
402018 AAGG-AAAAAAAGAAA
1 AAGGTAAAAAAAGAAA
402033 GGAAAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAGGTAAAAAAAGAAA
Found at i:402895 original size:11 final size:11
Alignment explanation
Indices: 402876--402973 Score: 78
Period size: 11 Copynumber: 8.9 Consensus size: 11
402866 GATTCGATGT
*
402876 AGAAAAAAAAA
1 AGAAGAAAAAA
402887 AGAAGAAAAAA
1 AGAAGAAAAAA
* *
402898 GGAAAAAAGAAA
1 AGAAGAAA-AAA
*
402910 AAAGAGAGAAAAA
1 AGA-AGA-AAAAA
*
402923 AGAAG-AAAGA
1 AGAAGAAAAAA
402933 AGAA-AAATAAA
1 AGAAGAAA-AAA
402944 AG-AGAAAAAA
1 AGAAGAAAAAA
402954 A-AAGAAAAAA
1 AGAAGAAAAAA
*
402964 AGAGGAAAAA
1 AGAAGAAAAA
402974 GAAAAGGAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
10 24 0.35
11 30 0.43
12 6 0.09
13 7 0.10
14 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:402897 original size:10 final size:10
Alignment explanation
Indices: 402882--402973 Score: 86
Period size: 10 Copynumber: 9.5 Consensus size: 10
402872 ATGTAGAAAA
402882 AAAAAAGAAG
1 AAAAAAGAAG
402892 AAAAAAG--G
1 AAAAAAGAAG
402900 AAAAAAGAA-
1 AAAAAAGAAG
*
402909 AAAAGAG-AG
1 AAAAAAGAAG
402918 AAAAAAGAAG
1 AAAAAAGAAG
* *
402928 AAAGAAGAAA
1 AAAAAAGAAG
402938 AATAAAAG-AG
1 AA-AAAAGAAG
*
402948 AAAAAAAAAG
1 AAAAAAGAAG
*
402958 AAAAAAAGAGG
1 -AAAAAAGAAG
402969 AAAAA
1 AAAAA
402974 GAAAAGGAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
8 9 0.14
9 16 0.24
10 29 0.44
11 12 0.18
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:402905 original size:18 final size:18
Alignment explanation
Indices: 402882--402973 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
402872 ATGTAGAAAA
402882 AAAAAAGAAGAAAAAAGG
1 AAAAAAGAAGAAAAAAGG
*
402900 AAAAAAGAA-AAAAGAGAG
1 AAAAAAGAAGAAAAAAG-G
*
402918 AAAAAAGAAGAAAGAA-G
1 AAAAAAGAAGAAAAAAGG
* *
402935 AAAAATAAAAG-AGAAA--
1 AAAAA-AGAAGAAAAAAGG
402951 AAAAAAGAA-AAAAAGAGG
1 AAAAAAGAAGAAAAA-AGG
402969 AAAAA
1 AAAAA
402974 GAAAAGGAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
15 6 0.10
16 6 0.10
17 15 0.25
18 28 0.47
19 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (18 bp):
AAAAAAGAAGAAAAAAGG
Found at i:402909 original size:7 final size:7
Alignment explanation
Indices: 402876--402978 Score: 72
Period size: 7 Copynumber: 14.9 Consensus size: 7
402866 GATTCGATGT
402876 AGAAAAA
1 AGAAAAA
402883 A-AAAAGA
1 AGAAAA-A
402890 AGAAAAA
1 AGAAAAA
402897 AGGAAAAA
1 A-GAAAAA
402905 AGAAAAA
1 AGAAAAA
*
402912 AGAGAGAA
1 AGA-AAAA
*
402920 A-AAAGA
1 AGAAAAA
*
402926 AGAAAGA
1 AGAAAAA
402933 AG-AAAA
1 AGAAAAA
* *
402939 ATAAAAG
1 AGAAAAA
402946 AGAAAAA
1 AGAAAAA
402953 A-AAAGAA
1 AGAAA-AA
*
402960 A-AAAAG
1 AGAAAAA
*
402966 AGGAAAA
1 AGAAAAA
402973 AGAAAA
1 AGAAAA
402979 GGAGAGGTCG
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
6 16 0.21
7 45 0.59
8 15 0.20
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (7 bp):
AGAAAAA
Found at i:402920 original size:40 final size:38
Alignment explanation
Indices: 402876--402966 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 38
402866 GATTCGATGT
*
402876 AGAAAAAAA-AAAGAAGAAAAAAGGAAAAAAGAAAAAAGAG
1 AGAAAAAAAGAAAGAAG-AAAAA-GAAAAAAGAAAAAA-AA
* *
402916 AGAAAAAAGAAGAAAGAAGAAAAATAAAAGAGAAAAAAAA
1 AG-AAAAA-AAGAAAGAAGAAAAAGAAAAAAGAAAAAAAA
402956 AGAAAAAAAGA
1 AGAAAAAAAGA
402967 GGAAAAAGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
38 4 0.09
39 5 0.11
40 5 0.11
41 17 0.38
42 7 0.16
43 7 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (38 bp):
AGAAAAAAAGAAAGAAGAAAAAGAAAAAAGAAAAAAAA
Found at i:402985 original size:17 final size:17
Alignment explanation
Indices: 402883--402978 Score: 74
Period size: 17 Copynumber: 5.6 Consensus size: 17
402873 TGTAGAAAAA
402883 AAAAAGAAGAAAAA-AGG
1 AAAAAGAA-AAAAAGAGG
*
402900 AAAAAAGAAAAAAGAGAGA
1 -AAAAAGAAAAAA-AGAGG
* *
402919 AAAAAG-AAGAAAGAAG
1 AAAAAGAAAAAAAGAGG
* *
402935 AAAAATAAAAGAGAA-A-A
1 AAAAAGAAAA-A-AAGAGG
402952 AAAAAGAAAAAAAGAGG
1 AAAAAGAAAAAAAGAGG
402969 AAAAAGAAAA
1 AAAAAGAAAA
402979 GGAGAGGTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
15 2 0.03
16 10 0.16
17 29 0.47
18 17 0.27
19 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAGG
Found at i:404201 original size:146 final size:148
Alignment explanation
Indices: 403987--404293 Score: 377
Period size: 146 Copynumber: 2.1 Consensus size: 148
403977 GGTGTGACGA
* * * * *
403987 GAAAGGTTGAGGTCGTAATGGCGAACCCGGTACCGTGAAGATTTGAAGGGAAAGGTTGATGCCGC
1 GAAAGGTTGAGGTCGTAATGGAGAACCCGGTACCATGAAGATTTGAAGGGAAAAGTTGAGGCCAC
* * * * * *
404052 AACGACAAACCTGGTACCTCA-AAAATGTGATGGGAAAGATTGAGGCTGCAATAG-CGAATCCTG
66 AACGACAAACCCGATACCTCAGAAAATGTGACGGGAAAGATTGAGACCGCAA-AGACGAATCCGG
*
404115 TACCATGAA-ATGTGATGG
130 TACCATGAAGATGTGAAGG
* *
404133 GAAAGGTTGAGGTCGTAATGGATAACCCTGTACCATGAAGATTTGAAGGGAAAAGTTGAGGCCAC
1 GAAAGGTTGAGGTCGTAATGGAGAACCCGGTACCATGAAGATTTGAAGGGAAAAGTTGAGGCCAC
* * * * * * *
404198 AACGGCGAACCCGATACCTTAGAAGATGTGACGGGAAAGGTTGAGACCGTAACGACGAATCCGGT
66 AACGACAAACCCGATACCTCAGAAAATGTGACGGGAAAGATTGAGACCGCAAAGACGAATCCGGT
*
404263 ACCATGAAGATTTGAAGG
131 ACCATGAAGATGTGAAGG
*
404281 GAAAGATTGAGGT
1 GAAAGGTTGAGGT
404294 TATGGCGGTG
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
146 75 0.56
147 41 0.30
148 19 0.14
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (148 bp):
GAAAGGTTGAGGTCGTAATGGAGAACCCGGTACCATGAAGATTTGAAGGGAAAAGTTGAGGCCAC
AACGACAAACCCGATACCTCAGAAAATGTGACGGGAAAGATTGAGACCGCAAAGACGAATCCGGT
ACCATGAAGATGTGAAGG
Found at i:404235 original size:50 final size:50
Alignment explanation
Indices: 403924--404698 Score: 290
Period size: 49 Copynumber: 16.0 Consensus size: 50
403914 AGAAAAACAT
* ** *
403924 GAAGATTTGAAGGGAAAGGTTGAGGTTGCAACGGTGAA-CCTTG-TACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC--GATACCTTA
* * * * * * * * * *
403974 AAAGGTGTGACGAGAAAGGTTGAGGTCGTAATGGCGAACCCGGTACCGT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * * * *
404023 GAAGATTTGAAGGGAAAGGTTGATGCCGCAACGAC-AAACCTGGTACCTCA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * * * ** *
404073 -AAAATGTGATGGGAAAGATTGAGGCTGCAATAGCGAATCCTG-TACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * * * ** * *
404121 GAA-ATGTGATGGGAAAGGTTGAGGTCGTAATGGATAACCCTG-TACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * * *
404169 GAAGATTTGAAGGGAAAAGTTGAGGCCACAACGGCGAACCCGATACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * * * *
404219 GAAGATGTGACGGGAAAGGTTGAGACCGTAACGACGAATCCGGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * ****** * * *
404268 GAAGATTTGAAGGGAAAGATTGAGGTTATGGCGGTGAATCTGATACCTCA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * * * ** * * *
404318 AAAGATGTGATGGGAAAGATTAAAGCCGCAACAACGAATCCGGTATCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * * *
404367 GAA-ATGTGATGGGAAAGGTCGAGGTCGCAACGGCGAA-CCTAATACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * * *
404415 GAAGATTTGAAGGGAAAGGTTGAAGCCGCAATGGCGAATCCGATGCCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * * * ** *
404465 AAATATGTGACGGGAAAGGTTGAGGTCACAACGATGAA-CCTGATACCTCA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * * * *
404515 AAAGATGT-----G--A---TG-GGCTGCAACGACAAATCCGGTA-CTAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCT-TA
* * * * * *
404553 GAAATG-TGTG-G--GAAAGGTTGAGACCGCAATGGTGAACCCGATACCAT-
1 G-AA-GATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
* * * *
404600 GAAGATTTTAAGAGAAAGGTTGAGGCCGCAACGGCGAA-CCTGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCTTA
* * *
404650 GAAGATATGAAGGGAAAGGTTGAGGTCGCAACGGTGAATCCG-TACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
404699 AAAAATAATA
Statistics
Matches: 530, Mismatches: 160, Indels: 71
0.70 0.21 0.09
Matches are distributed among these distances:
38 2 0.00
39 18 0.03
40 5 0.01
41 1 0.00
43 2 0.00
45 2 0.00
46 6 0.01
47 18 0.03
48 83 0.16
49 202 0.38
50 187 0.35
51 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.20
Consensus pattern (50 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCTTA
Found at i:404313 original size:99 final size:100
Alignment explanation
Indices: 404162--404524 Score: 267
Period size: 99 Copynumber: 3.7 Consensus size: 100
404152 GGATAACCCT
* *
404162 GTACCATGAAGATTTGAAGGGAAA-AGTTGAGGCCACAACGGCGAACCCGATACCTTAGAAGATG
1 GTACCATGAAGATTTGAAGGGAAAGAGTTGAGGCCACAACGGCGAACCCGATACCTCAAAAGATG
* * * *
404226 TGACGGGAAAGGTT-GAGACCGTAACGACGAATCCG
66 TGACGGGAAAGATTAAAG-CCGCAACAACGAATCCG
** *** * * *
404261 GTACCATGAAGATTTGAAGGGAAAGA-TTGAGGTTATGGCGGTGAATCTGATACCTCAAAAGATG
1 GTACCATGAAGATTTGAAGGGAAAGAGTTGAGGCCACAACGGCGAACCCGATACCTCAAAAGATG
*
404325 TGATGGGAAAGATTAAAGCCGCAACAACGAATCCG
66 TGACGGGAAAGATTAAAGCCGCAACAACGAATCCG
* * * * * * ** *
404360 GTATCATGAA-ATGTGATGGGAAAG-GTCGAGGTCGCAACGGCGAACCTAATA-C-CATGAAGAT
1 GTACCATGAAGATTTGAAGGGAAAGAGTTGAGGCCACAACGGCGAACCCGATACCTCA-AAAGAT
* * * * ***
404421 TTGAAGGGAAAGGTTGAAGCCGCAATGGCGAATCCG
65 GTGACGGGAAAGATTAAAGCCGCAACAACGAATCCG
* * * * * * ** *
404457 ATGCC-TTAAAATATGTGACGGGAAAG-GTTGAGGTCACAACGATGAACCTGATACCTCAAAAGA
1 GTACCATGAAGAT-T-TGAAGGGAAAGAGTTGAGGCCACAACGGCGAACCCGATACCTCAAAAGA
404520 TGTGA
64 TGTGA
404525 TGGGCTGCAA
Statistics
Matches: 207, Mismatches: 48, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
96 5 0.02
97 39 0.19
98 29 0.14
99 120 0.58
100 12 0.06
101 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (100 bp):
GTACCATGAAGATTTGAAGGGAAAGAGTTGAGGCCACAACGGCGAACCCGATACCTCAAAAGATG
TGACGGGAAAGATTAAAGCCGCAACAACGAATCCG
Found at i:404430 original size:246 final size:245
Alignment explanation
Indices: 403921--404488 Score: 681
Period size: 246 Copynumber: 2.3 Consensus size: 245
403911 CTGAGAAAAA
** * * *
403921 CATGAAGATTTGAAGGGAAAGGTTGAGGTTGCAACGGTGAACCTTG-TACCTTAAAAGGTGTGAC
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC-CGATACCTTAAAAGATGTGAC
* ** * * * * *
403985 GAGAAAGGTTGAGGTCGTAATGGCGAACCCGGTACCGTGAAGATTTGAAGGGAAAGGTTGATGCC
65 GGGAAAGGTTGAGACCGTAACGACGAACCCGGTACCATGAAGATTTGAAGGGAAAGATTGAGGCC
* * * * * * * *
404050 GCAACGACAAACCTGGTACCTCAAAAATGTGATGGGAAAGATTGAGGCTGCAATAGCGAATCCTG
130 ACAACGACAAACCTGATACCTCAAAAATGTGATGGGAAAGATTAAAGCCGCAACAACGAATCCGG
* * * * *
404115 TACCATGAAATGTGATGGGAAAGGTTGAGGTCGTAATGGATAACCCTGTAC
195 TACCATGAAATGTGATGGGAAAGGTCGAGGTCGCAACGGAGAACCCTATAC
* * *
404166 CATGAAGATTTGAAGGGAAAAGTTGAGGCCACAACGGCGAACCCGATACCTTAGAAGATGTGACG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATGTGACG
* **
404231 GGAAAGGTTGAGACCGTAACGACGAATCCGGTACCATGAAGATTTGAAGGGAAAGATTGAGGTTA
66 GGAAAGGTTGAGACCGTAACGACGAACCCGGTACCATGAAGATTTGAAGGGAAAGATTGAGGCCA
*** *** *
404296 TGGCGGTGAATCTGATACCTCAAAAGATGTGATGGGAAAGATTAAAGCCGCAACAACGAATCCGG
131 CAACGACAAACCTGATACCTCAAAA-ATGTGATGGGAAAGATTAAAGCCGCAACAACGAATCCGG
* *
404361 TATCATGAAATGTGATGGGAAAGGTCGAGGTCGCAACGGCGAA-CCTAATAC
195 TACCATGAAATGTGATGGGAAAGGTCGAGGTCGCAACGGAGAACCCT-ATAC
* * * * *
404412 CATGAAGATTTGAAGGGAAAGGTTGAAGCCGCAATGGCGAATCCGATGCCTTAAAATATGTGACG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATGTGACG
404477 GGAAAGGTTGAG
66 GGAAAGGTTGAG
404489 GTCACAACGA
Statistics
Matches: 271, Mismatches: 49, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
244 1 0.00
245 128 0.47
246 142 0.52
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.20
Consensus pattern (245 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAAAAGATGTGACG
GGAAAGGTTGAGACCGTAACGACGAACCCGGTACCATGAAGATTTGAAGGGAAAGATTGAGGCCA
CAACGACAAACCTGATACCTCAAAAATGTGATGGGAAAGATTAAAGCCGCAACAACGAATCCGGT
ACCATGAAATGTGATGGGAAAGGTCGAGGTCGCAACGGAGAACCCTATAC
Found at i:404667 original size:185 final size:186
Alignment explanation
Indices: 404345--404687 Score: 458
Period size: 185 Copynumber: 1.8 Consensus size: 186
404335 GATTAAAGCC
* ** *
404345 GCAACAACGAATCCGGTATCATGAAATGTGATGGGAAAGGTCGAGGTCGCAACGGCGAACCTAAT
1 GCAACAACAAATCCGGTATCATGAAATGTGATGGGAAAGGTCGAGACCGCAACGGCGAACCCAAT
* * * * *
404410 ACCATGAAGATTTGAAGGGAAAGGTTGAAGCCGCAATGGCGAATCCGATGCCTTAAAATATGTGA
66 ACCATGAAGATTTGAAGAGAAAGGTTGAAGCCGCAACGGCGAATCCGATACCTTAAAAGATATGA
*
404475 CGGGAAAGGTTGAGGTCACAACGATGAACCTGATACCTCAAAAGATGTGATGGGCT
131 AGGGAAAGGTTGAGGTCACAACGATGAACCTGATACCTCAAAAGATGTGATGGGCT
* * * * *
404531 GCAACGACAAATCCGGTA-CTATGAAATGTG-TGGGAAAGGTTGAGACCGCAATGGTGAACCCGA
1 GCAACAACAAATCCGGTATC-ATGAAATGTGATGGGAAAGGTCGAGACCGCAACGGCGAACCCAA
* * * *
404594 TACCATGAAGATTTTAAGAGAAAGGTTGAGGCCGCAACGGCGAA-CCTGGTACCTTAGAAGATAT
65 TACCATGAAGATTTGAAGAGAAAGGTTGAAGCCGCAACGGCGAATCC-GATACCTTAAAAGATAT
* *
404658 GAAGGGAAAGGTTGAGGTCGCAACGGTGAA
129 GAAGGGAAAGGTTGAGGTCACAACGATGAA
404688 TCCGTACCTT
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
184 2 0.01
185 106 0.79
186 26 0.19
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (186 bp):
GCAACAACAAATCCGGTATCATGAAATGTGATGGGAAAGGTCGAGACCGCAACGGCGAACCCAAT
ACCATGAAGATTTGAAGAGAAAGGTTGAAGCCGCAACGGCGAATCCGATACCTTAAAAGATATGA
AGGGAAAGGTTGAGGTCACAACGATGAACCTGATACCTCAAAAGATGTGATGGGCT
Found at i:405084 original size:39 final size:39
Alignment explanation
Indices: 405041--405208 Score: 115
Period size: 39 Copynumber: 4.3 Consensus size: 39
405031 CAACCATCCG
* * *
405041 ATCTCTTACCTTGAG-CTTAGGGTAAATCACCATCAGCCA
1 ATCTCTTACCTCGAGCCTGA-GGTAAATCACCATCAACCA
* * *
405080 ATCTCTTACCCCGAGCCTGAGGTAGATCACCATCAATCA
1 ATCTCTTACCTCGAGCCTGAGGTAAATCACCATCAACCA
* * * **** * * *
405119 ATCTTTTACCTCGAGCCTGGGGAAAATTGTAACCATCCG
1 ATCTCTTACCTCGAGCCTGAGGTAAATCACCATCAACCA
* * * * *
405158 ATCTCTTACCCCGAGTCT-AGGATAGATCACTATCAGCCA
1 ATCTCTTACCTCGAGCCTGAGG-TAAATCACCATCAACCA
405197 ATCTCTTACCTC
1 ATCTCTTACCTC
405209 AAGCTTAGGA
Statistics
Matches: 94, Mismatches: 33, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
38 2 0.02
39 89 0.95
40 3 0.03
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCTCGAGCCTGAGGTAAATCACCATCAACCA
Found at i:405187 original size:117 final size:116
Alignment explanation
Indices: 404964--405206 Score: 292
Period size: 117 Copynumber: 2.1 Consensus size: 116
404954 GAAGATTCTG
* * * *
404964 ATCTCTTACCCTGAGCCTGGACAGATCACTATCAACCAATCTCTTACCCTAAGCTTAAGGCAAAT
1 ATCTCTTACCCCGAGCCTGGACAGATCACCATCAACCAATCTCTTACCCTAAGCCTAAGGAAAAT
** *
405029 TGCAACCATCCGATCTCTTACCTTGAGCTTAGGGTAAATCACCATCAGCCA
66 TGCAACCATCCGATCTCTTACCCCGAGCTTAGGATAAATCACCATCAGCCA
** * * * **
405080 ATCTCTTACCCCGAGCCTGAGGTAGATCACCATCAATCAATCTTTTA-CCTCGAGCCTGGGGAAA
1 ATCTCTTACCCCGAGCCTG-GACAGATCACCATCAACCAATCTCTTACCCT-AAGCCTAAGGAAA
* * *
405144 ATTGTAACCATCCGATCTCTTACCCCGAG-TCTAGGATAGATCACTATCAGCCA
64 ATTGCAACCATCCGATCTCTTACCCCGAGCT-TAGGATAAATCACCATCAGCCA
405197 ATCTCTTACC
1 ATCTCTTACC
405207 TCAAGCTTAG
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
116 22 0.21
117 85 0.79
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (116 bp):
ATCTCTTACCCCGAGCCTGGACAGATCACCATCAACCAATCTCTTACCCTAAGCCTAAGGAAAAT
TGCAACCATCCGATCTCTTACCCCGAGCTTAGGATAAATCACCATCAGCCA
Found at i:405233 original size:78 final size:78
Alignment explanation
Indices: 405080--405237 Score: 185
Period size: 78 Copynumber: 2.0 Consensus size: 78
405070 CCATCAGCCA
* * * *
405080 ATCTCTTACCCCGAGCCTGAGGTAGATCACCATCAATCAATCTTTTACCTCGAGCCTGGGGAAAA
1 ATCTCTTACCCCGAGCCTGAGGTAGATCACCATCAACCAATCTCTTACCTCAAGCCTGAGGAAAA
*
405145 TTGTAACCATCCG
66 TTGCAACCATCCG
* * * *
405158 ATCTCTTACCCCGAGTCT-AGGATAGATCACTATCAGCCAATCTCTTACCTCAAG-CTTAGGACA
1 ATCTCTTACCCCGAGCCTGAGG-TAGATCACCATCAACCAATCTCTTACCTCAAGCCTGAGGA-A
* *
405221 GATTGCAGCCATCCG
64 AATTGCAACCATCCG
405236 AT
1 AT
405238 TGCGACCATC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
77 8 0.12
78 59 0.88
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGAGGTAGATCACCATCAACCAATCTCTTACCTCAAGCCTGAGGAAAA
TTGCAACCATCCG
Found at i:405313 original size:92 final size:92
Alignment explanation
Indices: 405150--405324 Score: 239
Period size: 92 Copynumber: 1.9 Consensus size: 92
405140 GAAAATTGTA
* * * * *
405150 ACCATCCGATCTCTTACCCCGAGTCTAGGATAGATCACTATCAGCCAATCTCTTACCTCAAGCTT
1 ACCATCCGATCTCTTACCCCGAGTCTAGGACAGATCACCATCAACCAATCTCTTACCCCAAGCTG
405215 AGGACAGATTGCAGCCATCCGATTGCG
66 AGGACAGATTGCAGCCATCCGATTGCG
* *
405242 ACCATCCGATCTCTTACCTCGAG-CTTGAGG-CAGATCACCATCAACCAATCTCTTACCCCGAGC
1 ACCATCCGATCTCTTACCCCGAGTC-T-AGGACAGATCACCATCAACCAATCTCTTACCCCAAG-
405305 CTGA-GACAGATTGCAGCCAT
63 CTGAGGACAGATTGCAGCCAT
405325 TCGAACTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
91 1 0.01
92 66 0.90
93 6 0.08
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.23
Consensus pattern (92 bp):
ACCATCCGATCTCTTACCCCGAGTCTAGGACAGATCACCATCAACCAATCTCTTACCCCAAGCTG
AGGACAGATTGCAGCCATCCGATTGCG
Found at i:405415 original size:39 final size:39
Alignment explanation
Indices: 405294--405445 Score: 153
Period size: 39 Copynumber: 3.9 Consensus size: 39
405284 AACCAATCTC
* * **
405294 TTACCCCGAGCCTGAGACAGATTGCAGCCATTCGAACTT
1 TTACCTCGAGCTTGAGGTAGATTGCAGCCATTCGAACTT
* * * ** * * *
405333 TTACATCAAGCTTAAGACAGATTGCAACCATTCGATCTC
1 TTACCTCGAGCTTGAGGTAGATTGCAGCCATTCGAACTT
*
405372 TTACCTCGAGCTTGGGGTAGATTGCAGCCATTCGAACTT
1 TTACCTCGAGCTTGAGGTAGATTGCAGCCATTCGAACTT
* *
405411 TTACCCCGAG-TCTGAGGTAGATTGCAGTCATTCGA
1 TTACCTCGAGCT-TGAGGTAGATTGCAGCCATTCGA
405446 TCTCTTATCC
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
38 1 0.01
39 91 0.99
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (39 bp):
TTACCTCGAGCTTGAGGTAGATTGCAGCCATTCGAACTT
Found at i:405433 original size:78 final size:78
Alignment explanation
Indices: 405289--405459 Score: 200
Period size: 78 Copynumber: 2.2 Consensus size: 78
405279 CCATCAACCA
*
405289 ATCTCTTACCCCGAGCCTGAGACAGATTGCAGCCATTCGAACTTTTACATCAAGCTTAAGACAGA
1 ATCTCTTACCCCGAGCCTGAGACAGATTGCAGCCATTCGAACTTTTACACCAAGCTTAAGACAGA
405354 TTGCAACCATTCG
66 TTGCAACCATTCG
* * * ** * * * **
405367 ATCTCTTACCTCGAGCTTGGGGTAGATTGCAGCCATTCGAACTTTTACCCCGAG-TCTGAGGTAG
1 ATCTCTTACCCCGAGCCTGAGACAGATTGCAGCCATTCGAACTTTTACACCAAGCT-TAAGACAG
**
405431 ATTGCAGTCATTCG
65 ATTGCAACCATTCG
*
405445 ATCTCTTATCCCGAG
1 ATCTCTTACCCCGAG
405460 TTTAGGGCAG
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 76 0.99
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGAGACAGATTGCAGCCATTCGAACTTTTACACCAAGCTTAAGACAGA
TTGCAACCATTCG
Found at i:405458 original size:39 final size:39
Alignment explanation
Indices: 405289--405460 Score: 136
Period size: 39 Copynumber: 4.4 Consensus size: 39
405279 CCATCAACCA
* **
405289 ATCTCTTACCCCGAG-CCTGAGACAGATTGCAGCCATTCG
1 ATCTCTTA-CCCGAGTCTTGAGGTAGATTGCAGCCATTCG
* * * * * ** *
405328 AACTTTTACATCAAG-CTTAAGACAGATTGCAACCATTCG
1 ATCTCTTAC-CCGAGTCTTGAGGTAGATTGCAGCCATTCG
*
405367 ATCTCTTACCTCGAG-CTTGGGGTAGATTGCAGCCATTCG
1 ATCTCTTACC-CGAGTCTTGAGGTAGATTGCAGCCATTCG
* * *
405406 AACTTTTACCCCGAGTC-TGAGGTAGATTGCAGTCATTCG
1 ATCTCTTA-CCCGAGTCTTGAGGTAGATTGCAGCCATTCG
405445 ATCTCTTATCCCGAGT
1 ATCTCTTA-CCCGAGT
405461 TTAGGGCAGA
Statistics
Matches: 106, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 102 0.96
40 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (39 bp):
ATCTCTTACCCGAGTCTTGAGGTAGATTGCAGCCATTCG
Found at i:405471 original size:117 final size:116
Alignment explanation
Indices: 405235--405452 Score: 260
Period size: 117 Copynumber: 1.9 Consensus size: 116
405225 GCAGCCATCC
*
405235 GATTGCGACCATCCGATCTCTTACCTCGAGCTTGAGGCAGATCACCATCAACCAATCTCTTACCC
1 GATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAGATCACCAT-AACCAATCTCTTACCC
* *
405300 CGAGCCTGAGACAGATTGCAGCCATTCGAACTTTTACATCAAGCTTAAGACA
65 CGAGCCTGAGACAGATTGCAGCCATTCGAACTCTTACACCAAGCTTAAGACA
* * * * * *
405352 GATTGCAACCATTCGATCTCTTACCTCGAGCTTGGGGTAGATTGCAGCCAT-TCGAA-CTTTTAC
1 GATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAGA-T-CA-CCATAACCAATCTCTTAC
* ** * *
405415 CCCGAGTCTGAGGTAGATTGCAGTCATTCGATCTCTTA
63 CCCGAGCCTGAGACAGATTGCAGCCATTCGAACTCTTA
405453 TCCCGAGTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
117 75 0.88
118 4 0.05
119 2 0.02
120 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (116 bp):
GATTGCAACCATCCGATCTCTTACCTCGAGCTTGAGGCAGATCACCATAACCAATCTCTTACCCC
GAGCCTGAGACAGATTGCAGCCATTCGAACTCTTACACCAAGCTTAAGACA
Found at i:405526 original size:39 final size:39
Alignment explanation
Indices: 405350--405530 Score: 123
Period size: 39 Copynumber: 4.6 Consensus size: 39
405340 AAGCTTAAGA
* * * * *
405350 CAGATTGCAACCATTCGATCTCTTACCTCGAGCTTGGGG
1 CAGATTGCAATCATCCAATCTCTTACCCCGAGGTTGGGG
* ** * * *
405389 TAGATTGCAGCCATTCGAA-CTTTTACCCCGA-GTCTGAGG
1 CAGATTGCAATCA-TCCAATCTCTTACCCCGAGGT-TGGGG
* * * * * * *
405428 TAGATTGCAGTCATTCGATCTCTTATCCCGAGTTTAGGG
1 CAGATTGCAATCATCCAATCTCTTACCCCGAGGTTGGGG
** * * *
405467 CAGATCACCATCAGCTAATCTCTTACCCCGAGGTTGGGG
1 CAGATTGCAATCATCCAATCTCTTACCCCGAGGTTGGGG
405506 CAGATTGCAATCATCCAATCTCTTA
1 CAGATTGCAATCATCCAATCTCTTA
405531 AAAAAAAATC
Statistics
Matches: 103, Mismatches: 35, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
38 3 0.03
39 97 0.94
40 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (39 bp):
CAGATTGCAATCATCCAATCTCTTACCCCGAGGTTGGGG
Found at i:406160 original size:29 final size:30
Alignment explanation
Indices: 406097--406161 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
406087 TTTTTTTTTT
406097 TTTACAAAATACCCATTAACCCAATACACCA
1 TTTACAAAATACCCA-TAACCCAATACACCA
*
406128 --TACAAACTACCCA-AACCCAATGAC-CCA
1 TTTACAAAATACCCATAACCCAAT-ACACCA
406155 TTTACAA
1 TTTACAA
406162 CCTAAGCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
29 17 0.57
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.20
Consensus pattern (30 bp):
TTTACAAAATACCCATAACCCAATACACCA
Found at i:406615 original size:20 final size:18
Alignment explanation
Indices: 406578--406613 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
406568 TATACTTGTT
406578 CATTACACGATATATATA
1 CATTACACGATATATATA
406596 CATTACACGATATATATA
1 CATTACACGATATATATA
406614 TATTGTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (18 bp):
CATTACACGATATATATA
Found at i:407420 original size:29 final size:30
Alignment explanation
Indices: 407380--407539 Score: 168
Period size: 29 Copynumber: 5.8 Consensus size: 30
407370 TAGGTCTCTA
*
407380 AACTT-TCAAAAATCACATTTTTACTCTCG
1 AACTTCTCAAAAATCACATTTTTACCCTCG
* *
407409 AACTTCTCAAAAATTATATTTTTA----C-
1 AACTTCTCAAAAATCACATTTTTACCCTCG
*
407434 --C--CTCAAAAATAACATTTTTACCCTCG
1 AACTTCTCAAAAATCACATTTTTACCCTCG
407460 AACTTC-CAAAAATCACATTTTTACCCTCG
1 AACTTCTCAAAAATCACATTTTTACCCTCG
*
407489 AACTT-TC-AAAATCACATTTTTACCCTCA
1 AACTTCTCAAAAATCACATTTTTACCCTCG
*
407517 AACTTC-AAAAAATCACATTTTTA
1 AACTTCTCAAAAATCACATTTTTA
407540 TCTCAAACTC
Statistics
Matches: 111, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
21 17 0.15
23 1 0.01
25 1 0.01
26 1 0.01
28 26 0.23
29 48 0.43
30 17 0.15
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AACTTCTCAAAAATCACATTTTTACCCTCG
Found at i:407441 original size:51 final size:50
Alignment explanation
Indices: 407385--407539 Score: 175
Period size: 57 Copynumber: 2.9 Consensus size: 50
407375 CTCTAAACTT
* * * *
407385 TCAAAAATCACATTTTTACTCTCGAACTTCTCAAAAATTATATTTTTACCC
1 TCAAAAATAACATTTTTACCCTCGAACTTC-CAAAAATCACATTTTTACCC
407436 TCAAAAATAACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCC
1 TCAAAAATAACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCC
* * *
407486 TCGAACTTTCAAAATCACATTTTTACCCTCAAACTTCAAAAAATCACATTTTTA
1 TC--A-----AAAATAACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTA
407540 TCTCAAACTC
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
50 20 0.22
51 28 0.31
52 1 0.01
57 41 0.46
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.35
Consensus pattern (50 bp):
TCAAAAATAACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCC
Found at i:407451 original size:20 final size:21
Alignment explanation
Indices: 407414--407458 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
407404 TCTCGAACTT
* *
407414 CTCAAAAATTATATTTTTACC
1 CTCAAAAATAACATTTTTACC
407435 CTCAAAAATAACATTTTTACC
1 CTCAAAAATAACATTTTTACC
407456 CTC
1 CTC
407459 GAACTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (21 bp):
CTCAAAAATAACATTTTTACC
Found at i:417571 original size:21 final size:23
Alignment explanation
Indices: 417532--417574 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
417522 CAGTAAATGA
*
417532 TTTTAAAATTATCATAATTATTT
1 TTTTAAAATTATCAAAATTATTT
417555 TTTTAAAA-TAT-AAAATTATT
1 TTTTAAAATTATCAAAATTATT
417575 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAATTATCAAAATTATTT
Found at i:418419 original size:28 final size:29
Alignment explanation
Indices: 418381--418446 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
418371 AAGGAAAATA
* *
418381 AGAAGAAGGGGAATGGGAAGGAGAAG-AGG
1 AGAAG-AGGGGAAGGGGAAGAAGAAGAAGG
* *
418410 GGAAGAGGGGAAGGGGATGAAGAAGAAGG
1 AGAAGAGGGGAAGGGGAAGAAGAAGAAGG
418439 AGAAGAGG
1 AGAAGAGG
418447 AAGGAGAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.03
Consensus pattern (29 bp):
AGAAGAGGGGAAGGGGAAGAAGAAGAAGG
Found at i:418519 original size:11 final size:11
Alignment explanation
Indices: 418495--418566 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 11
418485 TATATTTTAA
*
418495 AAAATAATTCT
1 AAAATAATTTT
*
418506 AAATTAATTTT
1 AAAATAATTTT
418517 AAAATAATTTT
1 AAAATAATTTT
418528 AATAACTTTATATTTT
1 AA-AA---TA-ATTTT
418544 AAAAAATAATTTT
1 --AAAATAATTTT
*
418557 AAAATCATTT
1 AAAATAATTT
418567 GCATGGCATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
11 30 0.60
12 2 0.04
13 5 0.10
14 2 0.04
15 2 0.04
16 5 0.10
17 2 0.04
18 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:418554 original size:29 final size:28
Alignment explanation
Indices: 418472--418558 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
418462 GGATGATGAT
418472 ATTTTAATAATTTTATATTTTAAAAAATA
1 ATTTTAATAA-TTTATATTTTAAAAAATA
*
418501 ATTCT-A-AA-TTA-ATTTT--AAAATA
1 ATTTTAATAATTTATATTTTAAAAAATA
418523 ATTTTAATAACTTTATATTTTAAAAAATA
1 ATTTTAATAA-TTTATATTTTAAAAAATA
418552 ATTTTAA
1 ATTTTAA
418559 AATCATTTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
22 10 0.20
23 1 0.02
24 7 0.14
25 3 0.06
26 3 0.06
27 7 0.14
28 1 0.02
29 17 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTTAATAATTTATATTTTAAAAAATA
Found at i:419049 original size:3 final size:3
Alignment explanation
Indices: 419041--419083 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
419031 AATACAAATA
419041 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
419084 TCATAACTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:427936 original size:19 final size:20
Alignment explanation
Indices: 427900--427937 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
427890 CAAATTTTTT
*
427900 AAAATTCAAATTAAATATTA
1 AAAATTCAAAATAAATATTA
*
427920 AAAATT-AAAATATATATT
1 AAAATTCAAAATAAATATT
427938 TTTAGTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTCAAAATAAATATTA
Found at i:430330 original size:20 final size:20
Alignment explanation
Indices: 430305--430352 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
430295 ACATGTGTTT
430305 CAATTTGAACTAAATTGTAA
1 CAATTTGAACTAAATTGTAA
430325 CAATTTGAACTAAATTGTAA
1 CAATTTGAACTAAATTGTAA
*
430345 CAAATTGA
1 CAATTTGA
430353 TAATTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
CAATTTGAACTAAATTGTAA
Found at i:436145 original size:22 final size:22
Alignment explanation
Indices: 436120--436161 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
436110 ATTACTCAAC
*
436120 TCATATCTCAATCAT-ATCATTT
1 TCATACCTCAA-CATAATCATTT
436142 TCATACCTCAACATAATCAT
1 TCATACCTCAACATAATCAT
436162 CACATCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATACCTCAACATAATCATTT
Found at i:437482 original size:27 final size:28
Alignment explanation
Indices: 437438--437503 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
437428 ACGGTCAAAA
* **
437438 TCAACGGTCAACGATCAATTATCAATGG
1 TCAACGGTCAAAGATCAACGATCAATGG
*
437466 TTAACGGTCAAAG-TCAACGATCAATGG
1 TCAACGGTCAAAGATCAACGATCAATGG
*
437493 TCAATGGTCAA
1 TCAACGGTCAA
437504 TCAACGGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (28 bp):
TCAACGGTCAAAGATCAACGATCAATGG
Found at i:437489 original size:13 final size:13
Alignment explanation
Indices: 437421--437511 Score: 51
Period size: 13 Copynumber: 6.9 Consensus size: 13
437411 TTTCAAAAAA
437421 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
437434 AAAATCAACGGTC
1 AAAGTCAACGGTC
* ***
437447 AACGATCAATTATC
1 AAAG-TCAACGGTC
* *
437461 AATGGTTAACGGTC
1 AA-AGTCAACGGTC
*
437475 AAAGTCAACGATC
1 AAAGTCAACGGTC
* *
437488 AATGGTCAATGGTC
1 AA-AGTCAACGGTC
437502 -AA-TCAACGGT
1 AAAGTCAACGGT
437512 TGGTCAACGA
Statistics
Matches: 56, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
11 7 0.12
13 25 0.45
14 23 0.41
15 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:437504 original size:41 final size:41
Alignment explanation
Indices: 437427--437504 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
437417 AAAAAAAGTC
* *
437427 AACGGTCAAAATCAACGGTCAACGATCAATTATCAATGGTT
1 AACGGTCAAAATCAACGATCAACGATCAATGATCAATGGTT
* * * *
437468 AACGGTCAAAGTCAACGATCAATGGTCAATGGTCAAT
1 AACGGTCAAAATCAACGATCAACGATCAATGATCAAT
437505 CAACGGTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (41 bp):
AACGGTCAAAATCAACGATCAACGATCAATGATCAATGGTT
Found at i:437563 original size:15 final size:16
Alignment explanation
Indices: 437545--437579 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
437535 AGGTTTGGAC
437545 TTGGTTCA-ATTGGGT
1 TTGGTTCATATTGGGT
*
437560 TTGGTTCATTTTGGGT
1 TTGGTTCATATTGGGT
437576 TTGG
1 TTGG
437580 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.51
Consensus pattern (16 bp):
TTGGTTCATATTGGGT
Found at i:437988 original size:17 final size:17
Alignment explanation
Indices: 437966--438003 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
437956 TAGTTTGCTC
*
437966 GCAAGGGATTGACGGTT
1 GCAAGGGATCGACGGTT
437983 GCAAGGGATCGACGGTT
1 GCAAGGGATCGACGGTT
438000 GCAA
1 GCAA
438004 AGATAAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.39, T:0.18
Consensus pattern (17 bp):
GCAAGGGATCGACGGTT
Found at i:441952 original size:3 final size:3
Alignment explanation
Indices: 441946--441971 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
441936 TTAAATCATC
441946 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
441972 ATACTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.