Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 199 of 205
Found at i:58982472 original size:14 final size:15
Alignment explanation
Indices: 58982453--58982492 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
58982443 CTCCTTTTCC
58982453 TCTTCTTCTTTCTTT
1 TCTTCTTCTTTCTTT
58982468 T-TTCTTCTTTCTTT
1 TCTTCTTCTTTCTTT
*
58982482 TCTTTTTCTTT
1 TCTTCTTCTTT
58982493 TCCTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (15 bp):
TCTTCTTCTTTCTTT
Found at i:58982501 original size:18 final size:19
Alignment explanation
Indices: 58982453--58982499 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
58982443 CTCCTTTTCC
58982453 TCTTCTT-C-TTTCTTTTT
1 TCTTCTTCCTTTTCTTTTT
*
58982470 TCTTCTTTCTTTTC-TTTT
1 TCTTCTTCCTTTTCTTTTT
58982488 TCTT-TTCCTTTT
1 TCTTCTTCCTTTT
58982500 TCCCATCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 14 0.52
18 9 0.33
19 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TCTTCTTCCTTTTCTTTTT
Found at i:58982502 original size:7 final size:6
Alignment explanation
Indices: 58982455--58982501 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
58982445 CCTTTTCCTC
*
58982455 TTCTTCT TTCTTTT TTCTTCT TTC-TT TTCTTT TTCTTT TCCTTT TTC
1 TTCTT-T TTC-TTT TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTC
58982502 CCATCATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
5 4 0.11
6 18 0.51
7 11 0.31
8 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:58990798 original size:46 final size:46
Alignment explanation
Indices: 58990731--58990999 Score: 266
Period size: 46 Copynumber: 5.8 Consensus size: 46
58990721 TGTAACCCGC
* *
58990731 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
* *
58990777 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCG--GAC--GTTCACAT
* * * *
58990827 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
* *
58990870 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCG--GAC--GTTCACAT
* * * *
58990920 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
58990963 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
58991000 TGCTCAACCA
Statistics
Matches: 182, Mismatches: 23, Indels: 36
0.76 0.10 0.15
Matches are distributed among these distances:
42 4 0.02
43 6 0.03
44 6 0.03
45 4 0.02
46 89 0.49
47 51 0.28
48 4 0.02
49 6 0.03
50 7 0.04
51 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
Found at i:58990853 original size:47 final size:47
Alignment explanation
Indices: 58990785--58990949 Score: 214
Period size: 47 Copynumber: 3.5 Consensus size: 47
58990775 ATCCATAAGT
58990785 GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTTACATCTCAC
* * * * *
58990832 GAACTCGGACTCAACTCAACGAG-TTCG--GAC-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTT-ACAT-C-TCA-C
58990878 GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTTACATCTCAC
58990925 GAACTCGGACTCAACTCAACGAGTT
1 GAACTCGGACTCAACTCAACGAGTT
58990950 CGGACATTCG
Statistics
Matches: 99, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 2 0.02
46 26 0.26
47 51 0.52
48 2 0.02
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTTAGATGCCTAGTTACATCTCAC
Found at i:58991002 original size:93 final size:93
Alignment explanation
Indices: 58990739--58990995 Score: 478
Period size: 93 Copynumber: 2.8 Consensus size: 93
58990729 GCCCATAAGT
* * * *
58990739 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
58990804 CGAGTTTAGATGCCTAGTTACATCTCAC
66 CGAGTTTAGATGCCTAGTTACATCTCAC
58990832 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
58990897 CGAGTTTAGATGCCTAGTTACATCTCAC
66 CGAGTTTAGATGCCTAGTTACATCTCAC
58990925 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
58990990 CGAGTT
66 CGAGTT
58990996 CGGATGCTCA
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTTAGATGCCTAGTTACATCTCAC
Found at i:58996675 original size:27 final size:27
Alignment explanation
Indices: 58996616--58996883 Score: 322
Period size: 27 Copynumber: 10.0 Consensus size: 27
58996606 ATATATACAA
* * ** *
58996616 CACATAGGGGCAATATAGTCAGCTTAA
1 CACATAAGGGCAAAATAGTCATTTTAC
58996643 CACATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * * *
58996670 CTCATAAAGGCAAAACAGTTATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
58996697 CACATCAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
58996724 CTCATAAGGGCAAAATAATCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
** * *
58996751 CTTATAAGGGCAAAACAATCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
58996778 CACATAAGGGTAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
58996805 CTCATAGGGGCAAAATAGTCA-TTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
58996831 CACATAATGGAAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
58996858 CACATAAGCGCAAAATAGTCATTTTA
1 CACATAAGGGCAAAATAGTCATTTTA
58996884 TCAATTAGGG
Statistics
Matches: 206, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 22 0.11
27 184 0.89
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:59000263 original size:93 final size:93
Alignment explanation
Indices: 59000148--59000319 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
59000138 GCCCATAAGT
* *
59000148 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAATTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
59000212 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* **
59000241 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAATGAACTCGGACTCTTCTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
59000306 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
59000320 CAAACATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:59000315 original size:46 final size:45
Alignment explanation
Indices: 59000140--59000314 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
59000130 TGTAACCCGC
* *
59000140 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
59000186 CCATAATTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
59000232 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAAT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
** *
59000279 CCATAAATGAACTCGGACTCTTCTCAACGAGTTCGG
1 CCATAAATGAACTCGGACTCAACTCAACGAGCTCGG
59000315 ATGCCCAAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 64 0.60
47 32 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (45 bp):
CCATAAATGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:59032571 original size:40 final size:40
Alignment explanation
Indices: 59032484--59032577 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
59032474 ATCTCGGTAT
* *
59032484 CGTACACTTAGTGCCTCATATAGCCGAAGCTATTTCAATT
1 CGTACACTTAGTGCCTCATATAGCCGAAACTATTTCAATA
* *
59032524 CGCACACTTAGTG-CT-ATTTATAGCTGAAACTATTTTCAA-A
1 CGTACACTTAGTGCCTCA--TATAGCCGAAACTA-TTTCAATA
59032564 CGTACACTTA-TGCC
1 CGTACACTTAGTGCC
59032578 AAACATAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
38 1 0.02
39 4 0.09
40 34 0.76
41 6 0.13
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (40 bp):
CGTACACTTAGTGCCTCATATAGCCGAAACTATTTCAATA
Found at i:59035383 original size:27 final size:27
Alignment explanation
Indices: 59035325--59035384 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
59035315 ATACATCTTA
*
59035325 TAGGGGCATATTAGTCATTTTACCATG
1 TAGGGGCATATTAGTCATTTTACAATG
* *
59035352 CAGGGGCATTTTAGTCATTTTATCAAT-
1 TAGGGGCATATTAGTCATTTTA-CAATG
59035379 TAGGGG
1 TAGGGG
59035385 GTCTAGGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (27 bp):
TAGGGGCATATTAGTCATTTTACAATG
Found at i:59048240 original size:34 final size:34
Alignment explanation
Indices: 59048174--59048240 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
59048164 ATATCGATCT
*
59048174 CAATATCAGTGTGCGCCTTAGCTCAATGCAGTAA
1 CAATATCAGTGTGCGCCTTAGCCCAATGCAGTAA
*
59048208 CAATATCAGTGTGGGCCTTAGCCCACAT-CAGTA
1 CAATATCAGTGTGCGCCTTAGCCCA-ATGCAGTA
59048241 TAGTATCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (34 bp):
CAATATCAGTGTGCGCCTTAGCCCAATGCAGTAA
Found at i:59051143 original size:50 final size:51
Alignment explanation
Indices: 59051075--59051203 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
59051065 GACCATGGCA
* *
59051075 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACCAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
*
59051126 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
* * *
59051176 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
59051204 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 47 0.66
51 24 0.34
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAAGACAAATG
Found at i:59051217 original size:31 final size:31
Alignment explanation
Indices: 59051179--59051288 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
59051169 ACAAATGACA
*
59051179 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
* *
59051210 AGTGAAAAGTGGTAGCTCCTGTTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
* *
59051241 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
*
59051272 AGTGAATAGTGGTAGCT
1 AGTGAAAAGTGGTAGCT
59051289 TCGACTACAA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
Found at i:59051506 original size:42 final size:38
Alignment explanation
Indices: 59051458--59051550 Score: 141
Period size: 42 Copynumber: 2.3 Consensus size: 38
59051448 TGTGATTACA
*
59051458 TGTAAGACCATAGCTGGGCTATGGCATCGGTATATGAATATG
1 TGTAAGACCATAGCTGGGCTATGGCATC---A-ATGAAGATG
59051500 TGTAAGACCATAGCTGGGCTATGGCATCAATGAAGATG
1 TGTAAGACCATAGCTGGGCTATGGCATCAATGAAGATG
59051538 TGTAAGACCATAG
1 TGTAAGACCATAG
59051551 TCGAACTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
38 21 0.42
39 1 0.02
42 28 0.56
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (38 bp):
TGTAAGACCATAGCTGGGCTATGGCATCAATGAAGATG
Found at i:59051542 original size:38 final size:40
Alignment explanation
Indices: 59051458--59051567 Score: 145
Period size: 38 Copynumber: 2.8 Consensus size: 40
59051448 TGTGATTACA
*
59051458 TGTAAGACCATAGCTGGGCTATGGCATCGGTATATGAATATG
1 TGTAAGACCATAGCTGGGCTATGGCATC-G-ATATGAAGATG
59051500 TGTAAGACCATAGCTGGGCTATGGCATC-A-ATGAAGATG
1 TGTAAGACCATAGCTGGGCTATGGCATCGATATGAAGATG
**
59051538 TGTAAGACCATAG-TCGAACTATGGCATCGA
1 TGTAAGACCATAGCT-GGGCTATGGCATCGA
59051568 GAAAACGAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
37 1 0.02
38 32 0.51
39 2 0.03
42 28 0.44
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (40 bp):
TGTAAGACCATAGCTGGGCTATGGCATCGATATGAAGATG
Found at i:59055409 original size:27 final size:26
Alignment explanation
Indices: 59055351--59055411 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
59055341 CATACATCTC
* *
59055351 TTAGGGGCATATCAGTCATTTTACCA
1 TTAGGGGCATATCAATCATTTTACAA
* *
59055377 TGTAGGGGCATTTCAATTATTTTATCAA
1 T-TAGGGGCATATCAATCATTTTA-CAA
59055405 TTAGGGG
1 TTAGGGG
59055412 GTCTAAGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 25 0.86
28 3 0.10
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
TTAGGGGCATATCAATCATTTTACAA
Found at i:59057726 original size:27 final size:27
Alignment explanation
Indices: 59057455--59057713 Score: 464
Period size: 27 Copynumber: 9.6 Consensus size: 27
59057445 TAAATTGTGC
*
59057455 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057482 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057509 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057536 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057563 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057590 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
59057617 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
59057644 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
59057672 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
59057699 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59057714 GACTTAATAT
Statistics
Matches: 227, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
27 201 0.89
28 26 0.11
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:59058676 original size:56 final size:56
Alignment explanation
Indices: 59058601--59058714 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
59058591 GAAATAGGCA
* *
59058601 TAGTTGCTTTCGTAACAGATGCTGGCAGCATCAGTGATGTGAGATCGAAAAATCAC
1 TAGTTGCTTTCGTAACAGATGCTGGCAGCAGCAGTGACGTGAGATCGAAAAATCAC
59058657 TAGTTGCTTTCGTAACAGATGCTGGCAGCAGCAGTGACGTGAGATCGAAAAATCAC
1 TAGTTGCTTTCGTAACAGATGCTGGCAGCAGCAGTGACGTGAGATCGAAAAATCAC
59058713 TA
1 TA
59058715 AAAATAGTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (56 bp):
TAGTTGCTTTCGTAACAGATGCTGGCAGCAGCAGTGACGTGAGATCGAAAAATCAC
Found at i:59080272 original size:25 final size:24
Alignment explanation
Indices: 59080219--59080356 Score: 93
Period size: 25 Copynumber: 5.6 Consensus size: 24
59080209 GTACATTTAT
* * *
59080219 GCTCTCACGAGCTGTGAATCAGTAT
1 GCTCTCACGAGCTG-AAATCGGTAA
59080244 GCTCTCACGAGCTAGAAATCGGTAA
1 GCTCTCACGAGCT-GAAATCGGTAA
*
59080269 GCTCAT-ATGAGCTGAGAATCGGTAA
1 GCTC-TCACGAGCTGA-AATCGGTAA
* * * * *
59080294 GCTTTCACAAGGTGCAATCGGTAG
1 GCTCTCACGAGCTGAAATCGGTAA
* *
59080318 GCT-TATATGAGCT-AAGACTCGGTAA
1 GCTCT-CACGAGCTGAA-A-TCGGTAA
59080343 GCTCTCACGAGCTG
1 GCTCTCACGAGCTG
59080357 CAATTGATAA
Statistics
Matches: 86, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
23 2 0.02
24 19 0.22
25 62 0.72
26 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (24 bp):
GCTCTCACGAGCTGAAATCGGTAA
Found at i:59080326 original size:49 final size:49
Alignment explanation
Indices: 59080234--59080360 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
59080224 CACGAGCTGT
* * * * *
59080234 GAATCAGTATGCTCTCACGAGCTAGAAATCGGTAAGCTCATATGAGCTGA
1 GAATCGGTAAGCTCTCACAAGCT-GCAATCGGTAAGCTCATATGAGCTAA
* * * *
59080284 GAATCGGTAAGCTTTCACAAGGTGCAATCGGTAGGCTTATATGAGCTAA
1 GAATCGGTAAGCTCTCACAAGCTGCAATCGGTAAGCTCATATGAGCTAA
* *
59080333 GACTCGGTAAGCTCTCACGAGCTGCAAT
1 GAATCGGTAAGCTCTCACAAGCTGCAAT
59080361 TGATAATCCC
Statistics
Matches: 64, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 46 0.72
50 18 0.28
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (49 bp):
GAATCGGTAAGCTCTCACAAGCTGCAATCGGTAAGCTCATATGAGCTAA
Found at i:59088933 original size:25 final size:25
Alignment explanation
Indices: 59088899--59088972 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
59088889 TCATGTACAT
* * *
59088899 GTATGCTCATACGAGCTGTGAATCG
1 GTATGATCATACGAGCTATAAATCG
**
59088924 GTATGATCATTTGAGCTATAAATCG
1 GTATGATCATACGAGCTATAAATCG
*
59088949 GTATGCTC-TCACGAGCTATAAATC
1 GTATGATCAT-ACGAGCTATAAATC
59088973 AGTAACCCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (25 bp):
GTATGATCATACGAGCTATAAATCG
Found at i:59090493 original size:16 final size:16
Alignment explanation
Indices: 59090448--59090493 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
59090438 ATATAGACCT
59090448 TGAAACTATAGGAATG
1 TGAAACTATAGGAATG
*
59090464 TGAAAAT-TATGGAATG
1 TGAAACTATA-GGAATG
59090480 TGAAACTATAGGAA
1 TGAAACTATAGGAA
59090494 ACTTTTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.24, T:0.26
Consensus pattern (16 bp):
TGAAACTATAGGAATG
Found at i:59103043 original size:25 final size:25
Alignment explanation
Indices: 59103015--59103064 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
59103005 TCGAGAAATC
59103015 TGATTTGTGGAGATAATCAAACTTT
1 TGATTTGTGGAGATAATCAAACTTT
59103040 TGATTTGTGGAGATAATCAAACTTT
1 TGATTTGTGGAGATAATCAAACTTT
59103065 ATGGATTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (25 bp):
TGATTTGTGGAGATAATCAAACTTT
Found at i:59121150 original size:28 final size:27
Alignment explanation
Indices: 59121114--59121233 Score: 141
Period size: 28 Copynumber: 4.3 Consensus size: 27
59121104 CAGTAATAGT
59121114 ACAGTGTGGGCCTTAGCCCGATACAGTA
1 ACAGTGTGGGCCTTAGCCC-ATACAGTA
* * *
59121142 ACAATGTGGGCGTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCCC-ATACAGTA
*
59121170 ACAGTGTGGGCCTTAGCCCATTAAAGTA
1 ACAGTGTGGGCCTTAGCCCA-TACAGTA
* * *
59121198 ACAGTGTGGGCCTTAACCCAAAACAGAA
1 ACAGTGTGGGCCTTAGCCC-ATACAGTA
59121226 ACAGTGTG
1 ACAGTGTG
59121234 ATAATGAAAC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.01
28 76 0.97
29 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (27 bp):
ACAGTGTGGGCCTTAGCCCATACAGTA
Found at i:59121187 original size:56 final size:56
Alignment explanation
Indices: 59121114--59121233 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 56
59121104 CAGTAATAGT
* * * *
59121114 ACAGTGTGGGCCTTAGCCCGA-TACAGTAACAATGTGGGCGTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTTAGCCC-ATTAAAGTAACAATGTGGGCCTTAACCCAAAACAGAA
*
59121170 ACAGTGTGGGCCTTAGCCCATTAAAGTAACAGTGTGGGCCTTAACCCAAAACAGAA
1 ACAGTGTGGGCCTTAGCCCATTAAAGTAACAATGTGGGCCTTAACCCAAAACAGAA
59121226 ACAGTGTG
1 ACAGTGTG
59121234 ATAATGAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 1 0.02
56 57 0.98
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (56 bp):
ACAGTGTGGGCCTTAGCCCATTAAAGTAACAATGTGGGCCTTAACCCAAAACAGAA
Found at i:59121620 original size:27 final size:27
Alignment explanation
Indices: 59121554--59122260 Score: 732
Period size: 27 Copynumber: 26.3 Consensus size: 27
59121544 GGGGTATAAT
* *
59121554 GGTCATTTTACCATAT-AAGGGTATTTC
1 GGTCATTTTACCCT-TCGAGGGTATTTC
* *
59121581 GATCATTTTACCCTGT-GGGGGTATTTC
1 GGTCATTTTACCCT-TCGAGGGTATTTC
*
59121608 GGTCATTTTACCCTTCGAGGGTATTTA
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121635 AGTCATTTTACCTTTCGGAGGTGT-TTT-
1 GGTCATTTTACCCTTC-GAGG-GTATTTC
** * *
59121662 AATCATTTTACCCTTTGGGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121689 GATCATTTTACCCTTCGGGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* * *
59121716 AGTCATTCTACCCTTCGAGGGTATTTT
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121743 GGTCATTTTACCCTTTGAGGGTATTTT
1 GGTCATTTTACCCTTCGAGGGTATTTC
** * *
59121770 GGTCATTTTACTTTTCAAAGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* * *
59121797 GGTCATTTAATCCTTCAAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121824 AGTCATTTTACCCTTCGGGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121851 TGTCATTTTACCCTTCGAGGGTATTTT
1 GGTCATTTTACCCTTCGAGGGTATTTC
* ***
59121878 GGTTATTTTACCCTTCGATAATATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59121905 GGTCATTTTACCCTGCGGGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* * *
59121932 GGTCATTTTACCTTTC-AGGGTCTTTT
1 GGTCATTTTACCCTTCGAGGGTATTTC
59121958 GGTCATTTTACCCTTCGAGGGTA-TTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* * * *
59121984 AGTCATTTTATCTTTCGGGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
*
59122011 GGTCATTTTACCCTTCGAAGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
** *
59122038 TATCATTTTACCCTTCGAAGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
**
59122065 AATCATTTTACCCTTCGAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* * *
59122092 GATTATTTTACCCTTTG-GAGGTATTTC
1 GGTCATTTTACCCTTCGAG-GGTATTTC
* *
59122119 GGTTATTTTACCGTTC-AGGGGTATTTC
1 GGTCATTTTACCCTTCGA-GGGTATTTC
* * *
59122146 GGCCATTTTATCCTTC-AGATGTATTTC
1 GGTCATTTTACCCTTCGAG-GGTATTTC
* *
59122173 GGTCCTTTT-CCCTTCTAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
* *
59122199 GATCATTTTACCTTTCGAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
*
59122226 AGTCATTTTACCCTTCGAGGGTATTTC
1 GGTCATTTTACCCTTCGAGGGTATTTC
59122253 GGTCATTT
1 GGTCATTT
59122261 GCCTACGAAT
Statistics
Matches: 568, Mismatches: 99, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
25 2 0.00
26 71 0.12
27 485 0.85
28 8 0.01
29 2 0.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (27 bp):
GGTCATTTTACCCTTCGAGGGTATTTC
Found at i:59133021 original size:14 final size:14
Alignment explanation
Indices: 59132998--59133034 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
59132988 ACATTCTATT
*
59132998 AAATATCAATATAA
1 AAATACCAATATAA
59133012 AAATACCAATATAA
1 AAATACCAATATAA
59133026 AAATACCAA
1 AAATACCAA
59133035 CTTAACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATACCAATATAA
Found at i:59134832 original size:16 final size:17
Alignment explanation
Indices: 59134811--59134844 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
59134801 AATAATAGGG
*
59134811 GCAAAAGTGT-AATTTT
1 GCAAAAGTATGAATTTT
59134827 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
59134844 G
1 G
59134845 GACTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:59169227 original size:39 final size:40
Alignment explanation
Indices: 59169182--59169407 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
59169172 GCTCCTCGTT
* * * *
59169182 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
59169222 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
59169261 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
59169301 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
59169341 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
59169382 CAAA-GCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAACCCGGAT
59169408 AGCATTCAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 39 0.24
40 106 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:59169408 original size:40 final size:41
Alignment explanation
Indices: 59169149--59169408 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 41
59169139 AAATCACGTA
* * **
59169149 CCTTCGGGATTTAA-CCGGATATAGCT--CCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATATAG-TAACTTCGCACAAATG
* * * * *
59169188 CCTTCGGGACATAGCCCGGTTTTAGTAAC-TCACAC-AATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTTCGCACAAATG
* * *
59169227 CCTTCGGGACTTAACCCGGATTTAATAAC-TCGCACGAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTTCGCACAAATG
* * *
59169267 CCTTCGGGACTTAACCCGGATTTAGTATC-TCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATATAGTAACTTCGCACAAATG
* * *
59169307 CCTTCGGGGCTTAACCCGGA-ATTTGTATC-TCGCACAAATG
1 CCTTCGGGACTTAACCCGGATA-TAGTAACTTCGCACAAATG
** * * *
59169347 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATATAGTAACTTCGCACAAATG
*
59169387 CCTTCGGGACTTAGCCCGGATA
1 CCTTCGGGACTTAACCCGGATA
59169409 GCATTCAATT
Statistics
Matches: 182, Mismatches: 30, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
39 48 0.26
40 121 0.66
41 13 0.07
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (41 bp):
CCTTCGGGACTTAACCCGGATATAGTAACTTCGCACAAATG
Found at i:59180753 original size:30 final size:31
Alignment explanation
Indices: 59180708--59180766 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
59180698 TCCCGAGCCT
59180708 AGGGGAAAAAGTGTAATTATGCAAAAGTTTA
1 AGGGGAAAAAGTGTAATTATGCAAAAGTTTA
* * *
59180739 AGGGTAAAAA-TGTAATTTTGCCAAAGTT
1 AGGGGAAAAAGTGTAATTATGCAAAAGTT
59180767 CATATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (31 bp):
AGGGGAAAAAGTGTAATTATGCAAAAGTTTA
Found at i:59181643 original size:92 final size:92
Alignment explanation
Indices: 59181486--59181668 Score: 348
Period size: 92 Copynumber: 2.0 Consensus size: 92
59181476 AGCTCAATTG
59181486 CTCGAGAAAGGCTATTCTGTTGTGTTCAAGAACAAACAGTGCCACATTGCTGATCCAAGTAGATC
1 CTCGAGAAAGGCTATTCTGTTGTGTTCAAGAACAAACAGTGCCACATTGCTGATCCAAGTAGATC
*
59181551 AAGCCTTATGACAGTCATAATGACTGA
66 AAGCCTTATGACAGTCACAATGACTGA
*
59181578 CTCGAGAAAGGCTATTCTGTTGTGTTCAAGAACAAACAGTGCCACATTGCTGATCCAAGTGGATC
1 CTCGAGAAAGGCTATTCTGTTGTGTTCAAGAACAAACAGTGCCACATTGCTGATCCAAGTAGATC
59181643 AAGCCTTATGACAGTCACAATGACTG
66 AAGCCTTATGACAGTCACAATGACTG
59181669 GCAAATGCTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (92 bp):
CTCGAGAAAGGCTATTCTGTTGTGTTCAAGAACAAACAGTGCCACATTGCTGATCCAAGTAGATC
AAGCCTTATGACAGTCACAATGACTGA
Found at i:59191378 original size:13 final size:13
Alignment explanation
Indices: 59191360--59191386 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59191350 GGCATAAACA
59191360 GAGTAAGGGGATG
1 GAGTAAGGGGATG
59191373 GAGTAAGGGGATG
1 GAGTAAGGGGATG
59191386 G
1 G
59191387 TGCTTGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.56, T:0.15
Consensus pattern (13 bp):
GAGTAAGGGGATG
Found at i:59202074 original size:20 final size:20
Alignment explanation
Indices: 59202049--59202087 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
59202039 GCTACTCATA
59202049 TTTTTA-AAAACTTATCAGAG
1 TTTTTAGAAAACTTA-CAGAG
*
59202069 TTTTTAGAACACTTACAGA
1 TTTTTAGAAAACTTACAGA
59202088 ATCGGTGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTTAGAAAACTTACAGAG
Found at i:59209031 original size:6 final size:6
Alignment explanation
Indices: 59209020--59209070 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
59209010 TTGAGCTCTT
*
59209020 TTTTTC TTTTTC TTTTT- TTTTTCCC TTTATC TTTTT- TTTTTC TTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTT--C TTTTTC TTTTTC TTTTTC TTTTTC
59209067 TTTT
1 TTTT
59209071 CTTCTAGGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 14 0.36
6 21 0.54
8 4 0.10
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:59209047 original size:19 final size:19
Alignment explanation
Indices: 59209025--59209061 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
59209015 CTCTTTTTTT
*
59209025 CTTTTTCTTTTTTTTTTCC
1 CTTTATCTTTTTTTTTTCC
59209044 CTTTATCTTTTTTTTTTC
1 CTTTATCTTTTTTTTTTC
59209062 TTTTTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTATCTTTTTTTTTTCC
Found at i:59209505 original size:10 final size:10
Alignment explanation
Indices: 59209482--59209563 Score: 57
Period size: 9 Copynumber: 8.5 Consensus size: 10
59209472 CCGACTATAT
*
59209482 TTTTTTATT-
1 TTTTTTCTTC
59209491 TTTTTCTCTTC
1 TTTTT-TCTTC
59209502 TTTTTTCTT-
1 TTTTTTCTTC
59209511 TTTTTTCTT-
1 TTTTTTCTTC
* *
59209520 TCTTTCCTT-
1 TTTTTTCTTC
*
59209529 TTTTTTATCTC
1 TTTTTTCT-TC
*
59209540 TTTCTTCTTC
1 TTTTTTCTTC
*
59209550 CTTTTTCTT-
1 TTTTTTCTTC
59209559 TTTTT
1 TTTTT
59209564 CAAACCCTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
9 30 0.52
10 17 0.29
11 11 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:59209507 original size:20 final size:20
Alignment explanation
Indices: 59209482--59209524 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
59209472 CCGACTATAT
59209482 TTTTTTA-TTTTTTTCTCTTC
1 TTTTTTATTTTTTTTCT-TTC
*
59209502 TTTTTTCTTTTTTTTCTTTC
1 TTTTTTATTTTTTTTCTTTC
59209522 TTT
1 TTT
59209525 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTATTTTTTTTCTTTC
Found at i:59209525 original size:29 final size:29
Alignment explanation
Indices: 59209481--59209563 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
59209471 CCCGACTATA
* *
59209481 TTTTTTTATTTTTTTCTCTTCTTTTT-TCT
1 TTTTTTTCTTTCTTTCTCTT-TTTTTATCT
59209510 TTTTTTTCTTTCTTTC-CTTTTTTTTATCT
1 TTTTTTTCTTTCTTTCTC-TTTTTTTATCT
* * * *
59209539 CTTTCTTCTTCCTTTTTCTTTTTTT
1 TTTTTTTCTTTCTTTCTCTTTTTTT
59209564 CAAACCCTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.13
29 38 0.84
30 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTTTTCTTTCTTTCTCTTTTTTTATCT
Found at i:59209555 original size:39 final size:39
Alignment explanation
Indices: 59209489--59209564 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
59209479 TATTTTTTTA
* * *
59209489 TTTTTTTCTCTTCTTTTTTCTTTTTTTTCTTTCTTTCCT
1 TTTTTTTATCTTCTTTCTTCTTCTTTTTCTTTCTTTCCT
*
59209528 TTTTTTTATC-TCTTTCTTCTTCCTTTTTCTTTTTTTC
1 TTTTTTTATCTTCTTTCTTCTT-CTTTTTCTTTCTTTC
59209565 AAACCCTAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 10 0.31
39 22 0.69
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (39 bp):
TTTTTTTATCTTCTTTCTTCTTCTTTTTCTTTCTTTCCT
Found at i:59211102 original size:24 final size:24
Alignment explanation
Indices: 59211052--59211103 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
59211042 AATAGGATTA
*
59211052 AATTAAAAACCCTAAACCCTACTT
1 AATTAAAAACCCTAAACCCTACCT
59211076 AATTAAAAACCCT-AACCCTAACCT
1 AATTAAAAACCCTAAACCCT-ACCT
59211100 AATT
1 AATT
59211104 TAATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (24 bp):
AATTAAAAACCCTAAACCCTACCT
Found at i:59218306 original size:54 final size:54
Alignment explanation
Indices: 59218204--59218311 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
59218194 TGGATTTATA
* * * *
59218204 CACTTAATAATTTTAAATCAAATTTTATTTAAAAAAGGTATTTTAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
* *
59218258 CACTTAATAATCTTAAATCGAATTTGA-TTAGAAACAGGGATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTA-AAAAAGGGATTTCAATCTTAAAT
59218312 TAGTGACGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
Found at i:59220108 original size:17 final size:17
Alignment explanation
Indices: 59220087--59220120 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
59220077 TTATTATTAA
59220087 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
59220104 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
59220121 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:59221466 original size:96 final size:95
Alignment explanation
Indices: 59221297--59221586 Score: 519
Period size: 96 Copynumber: 3.0 Consensus size: 95
59221287 TCCCATCTTG
59221297 ATCACAAACAATTCCTCCTACTGCAGCAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTA
1 ATCA-AAACAATTCCTCCTACTG-AGCAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTA
59221362 AATAGACCTAATTACCTGTCAAGTATGAGGTT
64 AATAGACCTAATTACCTGTCAAGTATGAGGTT
*
59221394 ATCAAAACAATTCCTCCTACT-AGGTTAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTA
1 ATCAAAACAATTCCTCCTACTGA-G-CAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTA
59221458 AATAGACCTAATTACCTGTCAAGTATGAGGTT
64 AATAGACCTAATTACCTGTCAAGTATGAGGTT
59221490 ATCAAAACAATTCCTCCTACTGCAGCAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTAA
1 ATCAAAACAATTCCTCCTACTG-AGCAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTAA
59221555 ATAGACCTAATTACCTGTCAAGTATGAGGTT
65 ATAGACCTAATTACCTGTCAAGTATGAGGTT
59221586 A
1 A
59221587 GAACCGATCT
Statistics
Matches: 187, Mismatches: 2, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
94 1 0.01
95 1 0.01
96 179 0.96
97 5 0.03
98 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (95 bp):
ATCAAAACAATTCCTCCTACTGAGCAAAACTTGTTTCATTTCTGACTGGCCCATCAGTGTTTAAA
TAGACCTAATTACCTGTCAAGTATGAGGTT
Found at i:59225367 original size:61 final size:62
Alignment explanation
Indices: 59225272--59225391 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 62
59225262 TAGGATTAAG
59225272 AGGTTGACAAGTGTTCTATAGGGGTATAGCAAAATATT-AAAAAAACTTAAAAATAGAGTCT
1 AGGTTGACAAGTGTTCTATAGGGGTATAGCAAAATATTAAAAAAAACTTAAAAATAGAGTCT
59225333 AGGTTGACAAGTGTTCTATAGGGGTATAGCAAAATATTAAAAAAAACTTAAAAATAGAG
1 AGGTTGACAAGTGTTCTATAGGGGTATAGCAAAATATTAAAAAAAACTTAAAAATAGAG
59225392 AGATACGTGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 38 0.66
62 20 0.34
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (62 bp):
AGGTTGACAAGTGTTCTATAGGGGTATAGCAAAATATTAAAAAAAACTTAAAAATAGAGTCT
Found at i:59226581 original size:15 final size:15
Alignment explanation
Indices: 59226561--59226614 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
59226551 ACTACTTGAG
59226561 CTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTT
*
59226576 CTTTTTTTTCTTTTCC
1 CTTTTTTTTCTTTT-T
*
59226592 CTTTTTCTT-TTTTT
1 CTTTTTTTTCTTTTT
59226606 CTTTTTTTT
1 CTTTTTTTT
59226615 TCTACTGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.24
15 18 0.53
16 8 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTCTTTTT
Found at i:59226589 original size:22 final size:21
Alignment explanation
Indices: 59226564--59226612 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
59226554 ACTTGAGCTT
59226564 TTTTTTCTTTTTCTTTTTTTTC
1 TTTTTTCTTTTTC-TTTTTTTC
**
59226586 TTTTCCCTTTTTCTTTTTTTC
1 TTTTTTCTTTTTCTTTTTTTC
59226607 TTTTTT
1 TTTTTT
59226613 TTTCTACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTCTTTTTCTTTTTTTC
Found at i:59226760 original size:14 final size:13
Alignment explanation
Indices: 59226733--59226757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59226723 CTGCTGTTGT
59226733 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
59226746 TTTTTTTCTTTT
1 TTTTTTTCTTTT
59226758 TCTGCTGACA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:59226829 original size:19 final size:21
Alignment explanation
Indices: 59226790--59226829 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
59226780 GGATGCCTAC
*
59226790 TGCTGGGCTGTCTGGCCTGCT
1 TGCTGGGCTGTCTGGCATGCT
59226811 TGCTGGG-TG-CTGGCATGCT
1 TGCTGGGCTGTCTGGCATGCT
59226830 ATTAAGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.03, C:0.25, G:0.40, T:0.33
Consensus pattern (21 bp):
TGCTGGGCTGTCTGGCATGCT
Found at i:59226995 original size:12 final size:11
Alignment explanation
Indices: 59226978--59227065 Score: 70
Period size: 12 Copynumber: 7.5 Consensus size: 11
59226968 ATATTTTTAT
59226978 TTTTTTCTCTTC
1 TTTTTTCT-TTC
*
59226990 TTTTTTCTTTT
1 TTTTTTCTTTC
59227001 TCTTTTTCTTTC
1 T-TTTTTCTTTC
59227013 TTTCTTTCTTT-
1 TTT-TTTCTTTC
*
59227024 TGTTTTCTCTCTC
1 T-TTTT-TCTTTC
* *
59227037 TTTCTTCTTCC
1 TTTTTTCTTTC
*
59227048 TTTTTCTTTTTC
1 TTTTT-TCTTTC
59227060 TTTTTT
1 TTTTTT
59227066 TCTCAAACCC
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
11 17 0.28
12 43 0.70
13 1 0.02
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:59227000 original size:6 final size:6
Alignment explanation
Indices: 59226991--59227064 Score: 62
Period size: 6 Copynumber: 11.8 Consensus size: 6
59226981 TTTCTCTTCT
* *
59226991 TTTTTC TTTTTC TTTTTC TTTCTT- TCTTTC TTTTGT- TTTCTCTC TCTTTC
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTT-TC TTT-T-TC TTTTTC
*
59227041 TTCTTCC TTTTTC TTTTTC TTTTT
1 TT-TTTC TTTTTC TTTTTC TTTTT
59227065 TTCTCAAACC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
5 2 0.04
6 40 0.73
7 11 0.20
8 2 0.04
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:59227020 original size:24 final size:24
Alignment explanation
Indices: 59226979--59227068 Score: 94
Period size: 24 Copynumber: 3.6 Consensus size: 24
59226969 TATTTTTATT
59226979 TTTTTCTCTTCTTT-TTTCTTTTTC
1 TTTTTCT-TTCTTTCTTTCTTTTTC
*
59227003 TTTTTCTTTCTTTCTTTCTTTTGTT
1 TTTTTCTTTCTTTCTTTCTTTT-TC
*
59227028 TTCTCTCTCTTTC-TTCTTCCTTTTTC
1 TT-T-T-TCTTTCTTTCTTTCTTTTTC
*
59227054 TTTTTCTTTTTTTCT
1 TTTTTCTTTCTTTCT
59227069 CAAACCCTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
23 11 0.20
24 20 0.36
25 4 0.07
26 4 0.07
27 11 0.20
28 6 0.11
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTCTTTCTTTCTTTCTTTTTC
Found at i:59227052 original size:28 final size:28
Alignment explanation
Indices: 59226981--59227057 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
59226971 TTTTTATTTT
* * *
59226981 TTTC-TCTTCTTTTTTCTTTTTCTTTTTC
1 TTTCTTCTTCCTTTTTC-TTTTCTCTCTC
* *
59227009 TTTCTTTCTTTC-TTTTGTTTTCTCTCTC
1 TTTC-TTCTTCCTTTTTCTTTTCTCTCTC
59227037 TTTCTTCTTCCTTTTTCTTTT
1 TTTCTTCTTCCTTTTTCTTTT
59227058 TCTTTTTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
27 6 0.15
28 25 0.64
29 4 0.10
30 4 0.10
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTCTTCTTCCTTTTTCTTTTCTCTCTC
Found at i:59227171 original size:14 final size:14
Alignment explanation
Indices: 59227154--59227198 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
59227144 CCTCCCCCTT
59227154 CTTTTCTTCTTTCC
1 CTTTTCTTCTTTCC
* *
59227168 CTTTT-TTTTTTCT
1 CTTTTCTTCTTTCC
*
59227181 CTTTTCTTCTCTCC
1 CTTTTCTTCTTTCC
59227195 CTTT
1 CTTT
59227199 CTCTCCTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
CTTTTCTTCTTTCC
Found at i:59227184 original size:13 final size:14
Alignment explanation
Indices: 59227153--59227190 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
59227143 CCCTCCCCCT
59227153 TCTTTTCTTCTTTC
1 TCTTTTCTTCTTTC
* *
59227167 CCTTTT-TTTTTTC
1 TCTTTTCTTCTTTC
59227180 TCTTTTCTTCT
1 TCTTTTCTTCT
59227191 CTCCCTTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTTCTTCTTTC
Found at i:59227754 original size:30 final size:29
Alignment explanation
Indices: 59227686--59227796 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 29
59227676 CAAAACTTTT
* *
59227686 GAGGTCAAAATGTAATTTTAAAAAAATTTA
1 GAGGTCAAAATGTAATTTT-AAAAAGTTGA
*
59227716 GA-GTCAAAATATAATTTTAAGAAAGTTGA
1 GAGGTCAAAATGTAATTTTAA-AAAGTTGA
59227745 GAGGTCAAAATGTAATTTTAAAAAGTT-A
1 GAGGTCAAAATGTAATTTTAAAAAGTTGA
* *
59227773 GGTGGTCGAAATGTAAATTTTAAA
1 -GAGGTCAAAATGT-AATTTTAAA
59227797 TTTTGTATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.04
29 40 0.56
30 28 0.39
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (29 bp):
GAGGTCAAAATGTAATTTTAAAAAGTTGA
Found at i:59235381 original size:50 final size:50
Alignment explanation
Indices: 59235323--59235424 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
59235313 ACGGCGCCGT
59235323 TTTGTAAAATTTTAATACATTTCGCTGCATTTTTTGTCCAAACGCCGCGA
1 TTTGTAAAATTTTAATACATTTCGCTGCATTTTTTGTCCAAACGCCGCGA
59235373 TTTGTAAAATTTTAATACATTTCGCTGCATTTTTTGTCCAAACGCCGCGA
1 TTTGTAAAATTTTAATACATTTCGCTGCATTTTTTGTCCAAACGCCGCGA
59235423 TT
1 TT
59235425 GCTGCCTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTGTAAAATTTTAATACATTTCGCTGCATTTTTTGTCCAAACGCCGCGA
Found at i:59236086 original size:13 final size:13
Alignment explanation
Indices: 59236068--59236118 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
59236058 AAAATAAATA
59236068 TTAATTAATTAAT
1 TTAATTAATTAAT
* *
59236081 TTAATTAATCAAA
1 TTAATTAATTAAT
*
59236094 TTAACTAAATTAAT
1 TTAA-TTAATTAAT
*
59236108 TT-CTTAATTAA
1 TTAATTAATTAA
59236119 ATAGTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
12 7 0.23
13 15 0.50
14 8 0.27
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:59238475 original size:43 final size:43
Alignment explanation
Indices: 59238417--59238498 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
59238407 CGCTTTAGTG
**
59238417 GAAGAGCCGCTAAAGACCCTGATCTTTAGCGACGTTTTTGGGA
1 GAAGAGCCGCTAAAGACCAGGATCTTTAGCGACGTTTTTGGGA
* * * *
59238460 GAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTT
1 GAAGAGCCGCTAAAGACCAGGATCTTTAGCGACGTTTTT
59238499 TTCTCAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (43 bp):
GAAGAGCCGCTAAAGACCAGGATCTTTAGCGACGTTTTTGGGA
Found at i:59238551 original size:43 final size:43
Alignment explanation
Indices: 59238503--59238774 Score: 226
Period size: 43 Copynumber: 6.3 Consensus size: 43
59238493 GTTTTTTTCT
* * *
59238503 CAAACGCCGC-AATAGACCCTGATCTATACCGGCGCTTTGACCA
1 CAAACGCCGCTAA-AGACCCTAATCTTTAGCGGCGCTTTGACCA
* * * ** *
59238546 TAAACGCC-ATGAAAGAACCTAATCTTTAGCGGCGCTTTCCCCT
1 CAAACGCCGCT-AAAGACCCTAATCTTTAGCGGCGCTTTGACCA
* * * *
59238589 CAAACACTGC-AATAGACCCTAATCTATAGCGGCGCTTCGACCA
1 CAAACGCCGCTAA-AGACCCTAATCTTTAGCGGCGCTTTGACCA
* * * * **
59238632 CAAACACCACTAAAGAACCTAATCTTTAGCGGTGCTTTCCCCA
1 CAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTGACCA
* * * * **
59238675 CAAACGCCGCTAAAGACCATGATCTTTAGTGGCGTTTTTTCCA
1 CAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTGACCA
* * *
59238718 CAAACGCCGCTAAAGACCCTTATCTTTAGTGGCGCTTTGACAA
1 CAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTGACCA
* *
59238761 AAAACGCCACTAAA
1 CAAACGCCGCTAAA
59238775 TATGGCAGAT
Statistics
Matches: 179, Mismatches: 45, Indels: 10
0.76 0.19 0.04
Matches are distributed among these distances:
42 2 0.01
43 173 0.97
44 4 0.02
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
CAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTGACCA
Found at i:59238719 original size:86 final size:86
Alignment explanation
Indices: 59238503--59238755 Score: 258
Period size: 86 Copynumber: 2.9 Consensus size: 86
59238493 GTTTTTTTCT
* * * * * * *
59238503 CAAACGCCGCAATAGACCCTGATCTATACCGGCGCTTTGACCATAAACGCCA-TGAAAGAACCTA
1 CAAACACCGCAATAGACCATAATCTATAGCGGCGCTTCGACCACAAACACCACT-AAAGAACCTA
*
59238567 ATCTTTAGCGGCGCTTTCCCCT
65 ATCTTTAGCGGCGCTTTCCCCA
* *
59238589 CAAACACTGCAATAGACCCTAATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
1 CAAACACCGCAATAGACCATAATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
*
59238654 TCTTTAGCGGTGCTTTCCCCA
66 TCTTTAGCGGCGCTTTCCCCA
* * * * * *** * * * *
59238675 CAAACGCCGCTAA-AGACCATGATCTTTAGTGGCGTTTTTTCCACAAACGCCGCTAAAGACCCTT
1 CAAACACCGC-AATAGACCATAATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTA
*
59238739 ATCTTTAGTGGCGCTTT
65 ATCTTTAGCGGCGCTTT
59238756 GACAAAAAAC
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
86 137 0.98
87 3 0.02
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (86 bp):
CAAACACCGCAATAGACCATAATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
TCTTTAGCGGCGCTTTCCCCA
Found at i:59239142 original size:21 final size:21
Alignment explanation
Indices: 59239082--59239152 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
59239072 TTTGACGCTG
* *
59239082 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCCGC
* *
59239103 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCTCTCGCTGCCGC
*
59239124 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCTCTCGCTGCCGC
*
59239145 ATCTGCTT
1 CTCTGCTT
59239153 TAAGCTGCTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCCGC
Found at i:59239200 original size:66 final size:66
Alignment explanation
Indices: 59239123--59239269 Score: 217
Period size: 66 Copynumber: 2.2 Consensus size: 66
59239113 CTCGCTGCCG
* *
59239123 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
59239186 GAA
64 GAA
* * *
59239189 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
59239254 A
66 A
59239255 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
59239270 ATGTTGCCTC
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 69 0.93
67 4 0.05
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:59239285 original size:66 final size:65
Alignment explanation
Indices: 59239123--59239293 Score: 209
Period size: 66 Copynumber: 2.6 Consensus size: 65
59239113 CTCGCTGCCG
* * * * * *
59239123 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGA
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGA
59239188 A
65 A
* * *
59239189 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTG
59239253 AA
64 AA
* *
59239255 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTG
59239294 TAATTTGCTC
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 88 0.94
67 4 0.04
ACGTcount: A:0.13, C:0.27, G:0.19, T:0.40
Consensus pattern (65 bp):
CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAA
Found at i:59244898 original size:18 final size:18
Alignment explanation
Indices: 59244875--59244963 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
59244865 ATATAAAAAG
59244875 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
59244893 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
59244915 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
59244932 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
59244950 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
59244964 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:59244953 original size:35 final size:37
Alignment explanation
Indices: 59244879--59245112 Score: 177
Period size: 39 Copynumber: 6.0 Consensus size: 37
59244869 AAAAAGTTTA
59244879 AGTAATGTAATATATTTAAGTAATGTAAGTTATAAATTTT
1 AGTAA-GTAATATATTTAAGTAATGTAAG-TAT-AATTTT
*
59244919 TGTAAGTAATATATTTAAGTAATGTAA-TAT-ATTTT
1 AGTAAGTAATATATTTAAGTAATGTAAGTATAATTTT
* ** * * *
59244954 AGTAAGTAATGTAAGTAATGTAATATATACTTTAATTTT
1 AGTAAGTAATATATTTAA-GTAATGTA-AGTATAATTTT
* * * ** *
59244993 AGTAAGTCATGTATTTAAGTAATATATTTAATCCAATTCT
1 AGTAAGTAATATATTTAAGTAATGTAAGT-AT--AATTTT
* *
59245033 AGTAAGTAATGTATTTAAGTAATATATTTAAGTA-AATTTT
1 AGTAAGTAATATATTTAAG---TA-ATGTAAGTATAATTTT
*
59245073 AGTAATTAATATATTTAAGTAATGTAAGTTATAAATTTT
1 AGTAAGTAATATATTTAAGTAATGTAAG-TAT-AATTTT
59245112 A
1 A
59245113 AAAATATATA
Statistics
Matches: 158, Mismatches: 22, Indels: 29
0.76 0.11 0.14
Matches are distributed among these distances:
35 19 0.12
36 13 0.08
37 9 0.06
38 11 0.07
39 49 0.31
40 49 0.31
43 3 0.02
44 5 0.03
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (37 bp):
AGTAAGTAATATATTTAAGTAATGTAAGTATAATTTT
Found at i:59244958 original size:31 final size:31
Alignment explanation
Indices: 59244877--59244981 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
59244867 ATAAAAAGTT
59244877 TAAGTAATGTAATATA--TT--TAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
* * *
59244904 TAAGT--TATAA-ATTTTTGTAAGTAA-TATATT
1 TAAGTAATGTAATATATTT-T-AGTAAGTA-ATG
59244934 TAAGTAATGTAATATATTTTAGTAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
59244965 TAAGTAATGTAATATAT
1 TAAGTAATGTAATATAT
59244982 ACTTTAATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.07
26 1 0.02
27 6 0.10
29 2 0.03
30 10 0.16
31 24 0.39
32 7 0.11
33 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (31 bp):
TAAGTAATGTAATATATTTTAGTAAGTAATG
Found at i:59245020 original size:13 final size:13
Alignment explanation
Indices: 59245004--59245095 Score: 73
Period size: 13 Copynumber: 6.9 Consensus size: 13
59244994 GTAAGTCATG
59245004 TATTTAAGTAATA
1 TATTTAAGTAATA
59245017 TATTTAA-TCCAAT-
1 TATTTAAGT--AATA
* * *
59245030 TCTAGTAAGTAATG
1 TAT-TTAAGTAATA
59245044 TATTTAAGTAATA
1 TATTTAAGTAATA
59245057 TATTTAAGTAA-A
1 TATTTAAGTAATA
* *
59245069 TTTTAGTAATTAATA
1 TATT--TAAGTAATA
59245084 TATTTAAGTAAT
1 TATTTAAGTAAT
59245096 GTAAGTTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 5 0.08
13 38 0.61
14 14 0.23
15 5 0.08
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:59245045 original size:40 final size:39
Alignment explanation
Indices: 59244989--59245112 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 39
59244979 TATACTTTAA
* *
59244989 TTTTAGTAAGTCATGTATTTAAGTAATATATTTAATCCAA
1 TTTTAGTAAGTAATGTATTTAAGTAATATATTTAAT-AAA
*
59245029 TTCTAGTAAGTAATGTATTTAAGTAATATATTTAAGTAAA
1 TTTTAGTAAGTAATGTATTTAAGTAATATATTTAA-TAAA
* * * *
59245069 TTTTAGTAATTAATATATTTAAGTAATGTAAGTT-ATAAA
1 TTTTAGTAAGTAATGTATTTAAGTAATAT-ATTTAATAAA
59245108 TTTTA
1 TTTTA
59245113 AAAATATATA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 9 0.12
40 61 0.82
41 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.46
Consensus pattern (39 bp):
TTTTAGTAAGTAATGTATTTAAGTAATATATTTAATAAA
Found at i:59245161 original size:11 final size:11
Alignment explanation
Indices: 59245130--59245162 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
59245120 ATATATTAAT
59245130 AATTCATTGAC
1 AATTCATTGAC
59245141 -ATTCATTGAC
1 AATTCATTGAC
*
59245151 AATTCACTGAC
1 AATTCATTGAC
59245162 A
1 A
59245163 GTCAACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:59248101 original size:8 final size:8
Alignment explanation
Indices: 59248090--59248124 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
59248080 TTTTTATTTC
59248090 ATTTTTAT
1 ATTTTTAT
59248098 ATTTTTAT
1 ATTTTTAT
*
59248106 ATTTTTTT
1 ATTTTTAT
*
59248114 ATTTTTTT
1 ATTTTTAT
59248122 ATT
1 ATT
59248125 CCAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
ATTTTTAT
Found at i:59248740 original size:15 final size:15
Alignment explanation
Indices: 59248720--59248814 Score: 113
Period size: 15 Copynumber: 6.4 Consensus size: 15
59248710 TTAATTGACA
59248720 CCCTAAATTCCTAAC
1 CCCTAAATTCCTAAC
* *
59248735 CCCT-AACTCTTAAC
1 CCCTAAATTCCTAAC
* *
59248749 CCTTAAATCTCCTAGC
1 CCCTAAAT-TCCTAAC
59248765 CCCTAAATTCCTAAC
1 CCCTAAATTCCTAAC
*
59248780 CCCT-AACTCCTAAC
1 CCCTAAATTCCTAAC
*
59248794 CCCTAAATCCCTAAC
1 CCCTAAATTCCTAAC
59248809 CCCTAA
1 CCCTAA
59248815 CCCCTAAACC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
14 24 0.36
15 30 0.45
16 12 0.18
ACGTcount: A:0.31, C:0.43, G:0.01, T:0.25
Consensus pattern (15 bp):
CCCTAAATTCCTAAC
Found at i:59248748 original size:14 final size:14
Alignment explanation
Indices: 59248728--59248821 Score: 98
Period size: 14 Copynumber: 6.4 Consensus size: 14
59248718 CACCCTAAAT
59248728 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
* *
59248742 TCTTAACCCTTAAATC
1 TCCTAACCCCT-AA-C
* *
59248758 TCCTAGCCCCTAAAT
1 TCCTAACCCCT-AAC
59248773 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
59248787 TCCTAACCCCTAAA
1 TCCTAACCCCTAAC
59248801 TCCCTAACCCCTAAC
1 T-CCTAACCCCTAAC
*
59248816 CCCTAA
1 TCCTAA
59248822 ACCATATATC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
14 30 0.45
15 24 0.36
16 12 0.18
ACGTcount: A:0.30, C:0.45, G:0.01, T:0.24
Consensus pattern (14 bp):
TCCTAACCCCTAAC
Found at i:59248769 original size:45 final size:44
Alignment explanation
Indices: 59248720--59248814 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 44
59248710 TTAATTGACA
* * *
59248720 CCCTAAATTCCTAACCCCTAACTCTTAACCCTTAAATCTCCTAGC
1 CCCTAAATTCCTAACCCCTAACTCCTAACCCCTAAATC-CCTAAC
59248765 CCCTAAATTCCTAACCCCTAACTCCTAACCCCTAAATCCCTAAC
1 CCCTAAATTCCTAACCCCTAACTCCTAACCCCTAAATCCCTAAC
59248809 CCCTAA
1 CCCTAA
59248815 CCCCTAAACC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 11 0.23
45 36 0.77
ACGTcount: A:0.31, C:0.43, G:0.01, T:0.25
Consensus pattern (44 bp):
CCCTAAATTCCTAACCCCTAACTCCTAACCCCTAAATCCCTAAC
Found at i:59248784 original size:7 final size:7
Alignment explanation
Indices: 59248774--59248821 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
59248764 CCCCTAAATT
59248774 CCTAACC
1 CCTAACC
*
59248781 CCTAACT
1 CCTAACC
59248788 CCTAACC
1 CCTAACC
*
59248795 CCTAAATC
1 CCT-AACC
59248803 CCTAACC
1 CCTAACC
59248810 CCTAACC
1 CCTAACC
59248817 CCTAA
1 CCTAA
59248822 ACCATATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAACC
Found at i:59248796 original size:29 final size:29
Alignment explanation
Indices: 59248728--59248821 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
59248718 CACCCTAAAT
* * *
59248728 TCCTAACCCCT-AACTCTTAACCCTTAAATC
1 TCCTAACCCCTAAATTCCTAACCCCT-AA-C
*
59248758 TCCTAGCCCCTAAATTCCTAACCCCTAAC
1 TCCTAACCCCTAAATTCCTAACCCCTAAC
*
59248787 TCCTAACCCCTAAATCCCTAACCCCTAAC
1 TCCTAACCCCTAAATTCCTAACCCCTAAC
*
59248816 CCCTAA
1 TCCTAA
59248822 ACCATATATC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
29 33 0.59
30 12 0.21
31 11 0.20
ACGTcount: A:0.30, C:0.45, G:0.01, T:0.24
Consensus pattern (29 bp):
TCCTAACCCCTAAATTCCTAACCCCTAAC
Found at i:59248832 original size:29 final size:29
Alignment explanation
Indices: 59248768--59248839 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
59248758 TCCTAGCCCC
* * * *
59248768 TAAATTCCTAACCCCTAACTCCTAACCCC
1 TAAATCCCTAACCCCTAACCCCTAAACCA
59248797 TAAATCCCTAACCCCTAACCCCTAAACCA
1 TAAATCCCTAACCCCTAACCCCTAAACCA
* *
59248826 TATATCCCAAACCC
1 TAAATCCCTAACCC
59248840 TAATAATCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (29 bp):
TAAATCCCTAACCCCTAACCCCTAAACCA
Found at i:59248838 original size:22 final size:22
Alignment explanation
Indices: 59248791--59248839 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
59248781 CCTAACTCCT
* *
59248791 AACCCCTAAATCCCTAACCCCT
1 AACCCCTAAATCCATAACCCCA
*
59248813 AACCCCTAAA-CCATATATCCCA
1 AACCCCTAAATCCATA-ACCCCA
59248835 AACCC
1 AACCC
59248840 TAATAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.16
Consensus pattern (22 bp):
AACCCCTAAATCCATAACCCCA
Found at i:59249544 original size:19 final size:19
Alignment explanation
Indices: 59249517--59249558 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
59249507 AAAATTATAT
* *
59249517 TTTTTATTTTTTTATTTCA
1 TTTTCATTTTTGTATTTCA
*
59249536 TTTTCATTTTTGTATTTTA
1 TTTTCATTTTTGTATTTCA
59249555 TTTT
1 TTTT
59249559 TTCTTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTCATTTTTGTATTTCA
Found at i:59249971 original size:21 final size:20
Alignment explanation
Indices: 59249941--59249981 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
59249931 CCTAACTCCT
*
59249941 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
59249962 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
59249982 TAAATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:59250701 original size:54 final size:54
Alignment explanation
Indices: 59250636--59250746 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
59250626 AAATAAGCTT
* * *
59250636 TTAAAGGCATTTTTAGTGGCATTTGGATAAAAAATGCCACTAAAGGTCTGAGCA
1 TTAAAGGCATTTTTAGCGGCATTTGGATAAAAAACGCCACTAAAGATCTGAGCA
*
59250690 TTAAAGGCATTTTTAGCGGCATTTGGATAAAAAACGCCGCTAAAGATCTGAGCA
1 TTAAAGGCATTTTTAGCGGCATTTGGATAAAAAACGCCACTAAAGATCTGAGCA
59250744 TTA
1 TTA
59250747 GCGGCGCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (54 bp):
TTAAAGGCATTTTTAGCGGCATTTGGATAAAAAACGCCACTAAAGATCTGAGCA
Found at i:59250772 original size:41 final size:40
Alignment explanation
Indices: 59250719--59250939 Score: 309
Period size: 41 Copynumber: 5.4 Consensus size: 40
59250709 CATTTGGATA
*
59250719 AAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGA-CAGAGCATTAGCGGCGCTTCTTC
*
59250760 AAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCT-AAAGACAGAGCATTAGCGGCGCTTCTTC
*
59250801 AAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTTC
1 AAAAACGCCGCT-AAAGACAGAGCATTAGCGGCGCTTCTTC
* *
59250842 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCACTTAC-TC
1 AAAAACGCCGCTAAA-GACAGAGCATTAGCGGCGCTT-CTTC
* * *
59250883 AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGTTTATTC
1 AAAAACGCCGCTAAA-GACAGAGCATTAGCGGCGCTTCTTC
59250924 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
59250940 GCCCCAAAAA
Statistics
Matches: 168, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
40 4 0.02
41 159 0.95
42 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGACAGAGCATTAGCGGCGCTTCTTC
Found at i:59251082 original size:40 final size:40
Alignment explanation
Indices: 59250997--59251115 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 40
59250987 GCACTTTTCA
* * *
59250997 GAAAA-CGCCGCTAATGCT-TATTTTTAGCGGAATTTTTG
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
* **
59251035 GATAAGCGCCGCTAATGCTCTACCTTTAGTGGCATTTTTT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
* * *
59251075 TAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTTTT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
59251115 G
1 G
59251116 TCCAAACGCC
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
38 4 0.06
39 13 0.20
40 49 0.74
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
Found at i:59252899 original size:75 final size:75
Alignment explanation
Indices: 59252807--59252948 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
59252797 TTTTTCGGTT
* * *
59252807 TATCCGACTAGCGCTGGGCG-CAATCACTGTTAGTTTATCCAACTAGAGCTAGACTCACAATTAT
1 TATCCGACTAGCACTGGGCGAAAAT-ACTGTTAGTCTATCCAACTAGAGCTAGACTCACAATTAT
59252871 TATCATCGGCA
65 TATCATCGGCA
* * * * * *
59252882 TATCCGACTAGCACTGGGTGAAAATATTTTTGGTCTATCCAACTAGAGCTGGGCTCACAATTATT
1 TATCCGACTAGCACTGGGCGAAAATACTGTTAGTCTATCCAACTAGAGCTAGACTCACAATTATT
59252947 AT
66 AT
59252949 TGTCTGTTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 54 0.95
76 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (75 bp):
TATCCGACTAGCACTGGGCGAAAATACTGTTAGTCTATCCAACTAGAGCTAGACTCACAATTATT
ATCATCGGCA
Found at i:59254530 original size:16 final size:16
Alignment explanation
Indices: 59254491--59254533 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
59254481 AAAAAAAAAA
*
59254491 TTGATTGACCAAAATG
1 TTGAGTGACCAAAATG
**
59254507 -AAAGTGACCAAAATG
1 TTGAGTGACCAAAATG
59254522 TTGAGTGACCAA
1 TTGAGTGACCAA
59254534 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (16 bp):
TTGAGTGACCAAAATG
Found at i:59254748 original size:13 final size:13
Alignment explanation
Indices: 59254730--59254755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59254720 TTATTAATTA
59254730 CTTATTTTTTTAT
1 CTTATTTTTTTAT
59254743 CTTATTTTTTTAT
1 CTTATTTTTTTAT
59254756 TCAATAAATT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTATTTTTTTAT
Found at i:59254941 original size:15 final size:16
Alignment explanation
Indices: 59254921--59254950 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59254911 GGGTATAATA
59254921 AAATAT-TAAAAGAAT
1 AAATATATAAAAGAAT
59254936 AAATATATAAAAGAA
1 AAATATATAAAAGAA
59254951 ATGAGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATATATAAAAGAAT
Found at i:59256058 original size:37 final size:36
Alignment explanation
Indices: 59256017--59256086 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
59256007 TTAATCTCAA
*
59256017 ATTTAATATATAATTGAA-TTAAATATAGATTTAAAAT
1 ATTTAATAT-TAATTGAAGTAAAATATA-ATTTAAAAT
* *
59256054 ATTTAATCTTACTTGAAGTAAAATATAATTTAA
1 ATTTAATATTAATTGAAGTAAAATATAATTTAA
59256087 TGAGAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 13 0.45
37 16 0.55
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (36 bp):
ATTTAATATTAATTGAAGTAAAATATAATTTAAAAT
Found at i:59256172 original size:13 final size:13
Alignment explanation
Indices: 59256154--59256179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59256144 AGAGGAAATT
59256154 AAGAAAAAACAAA
1 AAGAAAAAACAAA
59256167 AAGAAAAAACAAA
1 AAGAAAAAACAAA
59256180 TGATACAAAT
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:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAGAAAAAACAAA
Found at i:59258622 original size:91 final size:90
Alignment explanation
Indices: 59258461--59258627 Score: 253
Period size: 90 Copynumber: 1.8 Consensus size: 90
59258451 GACCACCGCT
*
59258461 GGTTTTGCAGTACCGAATTTTGCAGTCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
1 GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
59258526 GTAATTAAACACACCAACATTTGCA
66 GTAATTAAACACACCAACATTTGCA
* * * * * *
59258551 GGTTTTGCTGTACTGAATTTTGCAATCTTATGATTGTCATGGTTAGATTTGTGAAAATGATGGCT
1 GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTC-TGGCTAGATATGTGAAAACGATGGCT
*
59258616 TGTAATTTAACA
65 TGTAATTAAACA
59258628 AATTTTTTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
90 34 0.50
91 34 0.50
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (90 bp):
GGTTTTGCAGTACCGAATTTTGCAATCTCATGATTGTCTGGCTAGATATGTGAAAACGATGGCTT
GTAATTAAACACACCAACATTTGCA
Found at i:59267968 original size:22 final size:22
Alignment explanation
Indices: 59267927--59267968 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
59267917 AATAAAAATA
* *
59267927 TGCTATTTTTTTATTGTTTTAC
1 TGCTATTTTCTTATTATTTTAC
*
59267949 TGCTATTTTCTTGTTATTTT
1 TGCTATTTTCTTATTATTTT
59267969 CTTACTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (22 bp):
TGCTATTTTCTTATTATTTTAC
Found at i:59276239 original size:23 final size:24
Alignment explanation
Indices: 59276185--59276239 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 24
59276175 TTAAAAATAA
*
59276185 AAAAATAGAAATAGAAAATTAAAATT
1 AAAAA-AG-AATAGAAAATTAAAATG
59276211 AAAAAAGAATA-AAAATTAAAA-G
1 AAAAAAGAATAGAAAATTAAAATG
59276233 AATAAAA
1 AA-AAAA
59276240 AATTTTGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 14 0.52
24 4 0.15
25 2 0.07
26 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAAAAGAATAGAAAATTAAAATG
Found at i:59276241 original size:17 final size:17
Alignment explanation
Indices: 59276205--59276240 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
59276195 ATAGAAAATT
59276205 AAAATTAAAAAAGAATA
1 AAAATTAAAAAAGAATA
59276222 AAAATT--AAAAGAATA
1 AAAATTAAAAAAGAATA
59276237 AAAA
1 AAAA
59276241 ATTTTGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.68
17 6 0.32
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATTAAAAAAGAATA
Found at i:59277593 original size:11 final size:11
Alignment explanation
Indices: 59277579--59277622 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
59277569 AGATAAATAT
59277579 TATTTTATTAA
1 TATTTTATTAA
*
59277590 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
59277603 TATTTTATTAT
1 TATTTTATTAA
59277614 TATTTTATT
1 TATTTTATT
59277623 TAGTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:59279702 original size:21 final size:21
Alignment explanation
Indices: 59279661--59279807 Score: 73
Period size: 21 Copynumber: 7.0 Consensus size: 21
59279651 TAGCTCTCAC
* * *
59279661 GAGTTTCTG-TTAACTCATAT
1 GAGTTTCAGTTTAACCCTTAT
59279681 GAGTTTCAGTTTAACCCTTAT
1 GAGTTTCAGTTTAACCCTTAT
* * * * * *
59279702 GGGTTTCCGTTCAGCTCTTTT
1 GAGTTTCAGTTTAACCCTTAT
* *
59279723 GAGCTTCAATTTAACCCTTAT
1 GAGTTTCAGTTTAACCCTTAT
* * * * *
59279744 GGGTTTCCGTTCAGCTCTTAT
1 GAGTTTCAGTTTAACCCTTAT
* *
59279765 GAGCTTCCA-TTCAACCCTTAT
1 GAG-TTTCAGTTTAACCCTTAT
* * * *
59279786 GGGTTTCTGTTTAGCACTTAT
1 GAGTTTCAGTTTAACCCTTAT
59279807 G
1 G
59279808 TGCATCTGTG
Statistics
Matches: 89, Mismatches: 35, Indels: 5
0.69 0.27 0.04
Matches are distributed among these distances:
20 11 0.12
21 75 0.84
22 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
GAGTTTCAGTTTAACCCTTAT
Found at i:59279737 original size:42 final size:42
Alignment explanation
Indices: 59279678--59279807 Score: 188
Period size: 42 Copynumber: 3.1 Consensus size: 42
59279668 TGTTAACTCA
* *
59279678 TATGAGTTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
*
59279720 TTTGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
* * * * *
59279762 TATGAGCTTCCATTCAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
59279804 TATG
1 TATG
59279808 TGCATCTGTG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
TATGAGCTTCAATTTAACCCTTATGGGTTTCCGTTCAGCTCT
Found at i:59292796 original size:16 final size:16
Alignment explanation
Indices: 59292775--59292806 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59292765 ATTAGAGAAA
59292775 ATCCTTCGACAAACCT
1 ATCCTTCGACAAACCT
*
59292791 ATCCTTTGACAAACCT
1 ATCCTTCGACAAACCT
59292807 TCAGTAGTAA
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:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (16 bp):
ATCCTTCGACAAACCT
Found at i:59297315 original size:23 final size:24
Alignment explanation
Indices: 59297271--59297316 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
59297261 TTTCTCACAT
* **
59297271 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
59297295 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
59297317 AATGCACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:59297439 original size:17 final size:18
Alignment explanation
Indices: 59297414--59297483 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 18
59297404 AACAAACAAT
59297414 TCAAATATT-AATTCATA
1 TCAAATATTCAATTCATA
* * *
59297431 TCAATTATTCAATTTAATTCCT
1 TCAAATATTCAA-TTCA-T--A
59297453 TCAAATATT-AATTCATA
1 TCAAATATTCAATTCATA
*
59297470 TCAATTATTCAATT
1 TCAAATATTCAATT
59297484 TAATTCCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 16 0.40
18 6 0.15
19 4 0.10
20 4 0.10
21 2 0.05
22 8 0.20
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (18 bp):
TCAAATATTCAATTCATA
Found at i:59297462 original size:39 final size:39
Alignment explanation
Indices: 59297413--59297490 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
59297403 CAACAAACAA
59297413 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
1 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
59297452 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
1 TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
59297491 CACTCATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (39 bp):
TTCAAATATTAATTCATATCAATTATTCAATTTAATTCC
Found at i:59298260 original size:14 final size:17
Alignment explanation
Indices: 59298241--59298278 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
59298231 ATTTATTTCT
59298241 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
59298255 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
59298272 TAATATA
1 TAATATA
59298279 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:59298286 original size:12 final size:11
Alignment explanation
Indices: 59298258--59298301 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
59298248 ATATTTATAA
59298258 TATAATTAATT
1 TATAATTAATT
*
59298269 TAATAATATACTT
1 T-ATAAT-TAATT
59298282 TATAATTAATT
1 TATAATTAATT
59298293 TATATATTA
1 TATA-ATTA
59298302 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:59298305 original size:20 final size:23
Alignment explanation
Indices: 59298253--59298315 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
59298243 ATATAATATT
59298253 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
59298275 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
59298300 TATATAAATAAATAAT
1 TATATATATAATTAAT
59298316 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:59298317 original size:20 final size:20
Alignment explanation
Indices: 59298270--59298318 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
59298260 TAATTAATTT
*
59298270 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
59298290 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
59298310 AATAATATA
1 AATAATATA
59298319 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:59299278 original size:112 final size:110
Alignment explanation
Indices: 59299083--59299283 Score: 262
Period size: 112 Copynumber: 1.8 Consensus size: 110
59299073 CCGTGTGACT
* * * *
59299083 CACACGGCCTGGGCACATGCTCGTGTGCTTACTCGTGTGGTCCTAAATCACAAACAGTGAGTTAT
1 CACACAGCCTGGACACACGCTCGTGTGCTTACTCGTGTGGTCCTAAATCACAAACAGTGAGTTAC
* *
59299148 TCGACCTAGATACATGCCCATGTGAACCCTGCACTAACATGGCCA
66 ACGACCTAGACACATGCCCATGTGAACCCTGCACTAACATGGCCA
* * *
59299193 CACACAGCCTGGACACACGCTCGTGTGCCTTGCTTGTGTGG-CTTCAAATCA-ATGAACAGTGAG
1 CACACAGCCTGGACACACGCTCGTGTG-CTTACTCGTGTGGTCCT-AAATCACA--AACAGTGAG
*
59299256 TTACACGACCTAGACACATGCCCGTGTG
62 TTACACGACCTAGACACATGCCCATGTG
59299284 CCTGGCCGTG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
110 27 0.35
111 17 0.22
112 33 0.43
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (110 bp):
CACACAGCCTGGACACACGCTCGTGTGCTTACTCGTGTGGTCCTAAATCACAAACAGTGAGTTAC
ACGACCTAGACACATGCCCATGTGAACCCTGCACTAACATGGCCA
Found at i:59316854 original size:13 final size:12
Alignment explanation
Indices: 59316833--59316931 Score: 67
Period size: 12 Copynumber: 7.9 Consensus size: 12
59316823 TGCAAGAGAT
*
59316833 AAAAGCTTAATTG
1 AAAAACTTAA-TG
59316846 AAAAACTTAATG
1 AAAAACTTAATG
*
59316858 ATTAAAAACTTGATG
1 ---AAAAACTTAATG
* *
59316873 GAAAACTTTATG
1 AAAAACTTAATG
*
59316885 AAAAGACTTGATG
1 AAAA-ACTTAATG
59316898 AAAAACTTAA--
1 AAAAACTTAATG
*
59316908 AAAGAACTTGATG
1 AAA-AACTTAATG
*
59316921 CAAAACTTAAT
1 AAAAACTTAAT
59316932 AACAAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 27 0.39
13 22 0.32
15 11 0.16
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:59316877 original size:12 final size:12
Alignment explanation
Indices: 59316856--59316928 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
59316846 AAAAACTTAA
*
59316856 TGATTAAAAACT
1 TGATGAAAAACT
*
59316868 TGATGGAAAACT
1 TGATGAAAAACT
*
59316880 TTATGAAAAGACT
1 TGATGAAAA-ACT
59316893 TGATGAAAAACT
1 TGATGAAAAACT
*
59316905 T-A-AAAAGAACT
1 TGATGAAA-AACT
*
59316916 TGATGCAAAACT
1 TGATGAAAAACT
59316928 T
1 T
59316929 AATAACAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:59316902 original size:25 final size:25
Alignment explanation
Indices: 59316844--59316928 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
59316834 AAAGCTTAAT
* *
59316844 TGAAAAACTTAATGATTAAAAACTTGA
1 TGAAAAACTTTATGA--AAAGACTTGA
*
59316871 TGGAAAACTTTATGAAAAGACTTGA
1 TGAAAAACTTTATGAAAAGACTTGA
59316896 TGAAAAAC-TTA--AAAAGAACTTGA
1 TGAAAAACTTTATGAAAAG-ACTTGA
*
59316919 TGCAAAACTT
1 TGAAAAACTT
59316929 AATAACAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 5 0.10
23 13 0.25
24 4 0.08
25 16 0.31
27 13 0.25
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.27
Consensus pattern (25 bp):
TGAAAAACTTTATGAAAAGACTTGA
Found at i:59316929 original size:23 final size:23
Alignment explanation
Indices: 59316864--59316930 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
59316854 AATGATTAAA
*
59316864 AACTTGATGGAAAACTTTATGAAAAG
1 AACTTGATGAAAAAC-TTA--AAAAG
59316890 -ACTTGATGAAAAACTTAAAAAG
1 AACTTGATGAAAAACTTAAAAAG
*
59316912 AACTTGATGCAAAACTTAA
1 AACTTGATGAAAAACTTAA
59316931 TAACAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 5 0.13
23 17 0.45
24 3 0.08
25 13 0.34
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (23 bp):
AACTTGATGAAAAACTTAAAAAG
Found at i:59316988 original size:14 final size:13
Alignment explanation
Indices: 59316954--59316995 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
59316944 CTTGGTAATT
59316954 AAAAACTTGAT-A
1 AAAAACTTGATGA
59316966 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
59316980 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
59316994 AA
1 AA
59316996 GAAAACACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:59318405 original size:16 final size:16
Alignment explanation
Indices: 59318384--59318424 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
59318374 GTTTAACTGC
* *
59318384 AAAATAAGATAAGATA
1 AAAATAAAATAAAATA
59318400 AAAATAAAATAAAAT-
1 AAAATAAAATAAAATA
59318415 AAAATAAAAT
1 AAAATAAAAT
59318425 GTGCGTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:59318408 original size:5 final size:5
Alignment explanation
Indices: 59318384--59318424 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
59318374 GTTTAACTGC
* *
59318384 AAAAT AAGAT AAGAT AAAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
59318425 GTGCGTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:59318410 original size:21 final size:21
Alignment explanation
Indices: 59318384--59318423 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59318374 GTTTAACTGC
* *
59318384 AAAATAAGATAAGATAAAAAT
1 AAAATAAAATAAAATAAAAAT
59318405 AAAATAAAATAAAATAAAA
1 AAAATAAAATAAAATAAAA
59318424 TGTGCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATAAAATAAAATAAAAAT
Found at i:59325206 original size:13 final size:12
Alignment explanation
Indices: 59325185--59325283 Score: 67
Period size: 12 Copynumber: 7.9 Consensus size: 12
59325175 TGCAAGAGAT
*
59325185 AAAAGCTTAATTG
1 AAAAACTTAA-TG
59325198 AAAAACTTAATG
1 AAAAACTTAATG
*
59325210 ATTAAAAACTTGATG
1 ---AAAAACTTAATG
* *
59325225 GAAAACTTTATG
1 AAAAACTTAATG
*
59325237 AAAAGACTTGATG
1 AAAA-ACTTAATG
59325250 AAAAACTTAA--
1 AAAAACTTAATG
*
59325260 AAAGAACTTGATG
1 AAA-AACTTAATG
*
59325273 CAAAACTTAAT
1 AAAAACTTAAT
59325284 AACAAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 27 0.39
13 22 0.32
15 11 0.16
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:59325229 original size:12 final size:12
Alignment explanation
Indices: 59325208--59325280 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
59325198 AAAAACTTAA
*
59325208 TGATTAAAAACT
1 TGATGAAAAACT
*
59325220 TGATGGAAAACT
1 TGATGAAAAACT
*
59325232 TTATGAAAAGACT
1 TGATGAAAA-ACT
59325245 TGATGAAAAACT
1 TGATGAAAAACT
*
59325257 T-A-AAAAGAACT
1 TGATGAAA-AACT
*
59325268 TGATGCAAAACT
1 TGATGAAAAACT
59325280 T
1 T
59325281 AATAACAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:59325254 original size:25 final size:25
Alignment explanation
Indices: 59325196--59325280 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
59325186 AAAGCTTAAT
* *
59325196 TGAAAAACTTAATGATTAAAAACTTGA
1 TGAAAAACTTTATGA--AAAGACTTGA
*
59325223 TGGAAAACTTTATGAAAAGACTTGA
1 TGAAAAACTTTATGAAAAGACTTGA
59325248 TGAAAAAC-TTA--AAAAGAACTTGA
1 TGAAAAACTTTATGAAAAG-ACTTGA
*
59325271 TGCAAAACTT
1 TGAAAAACTT
59325281 AATAACAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 5 0.10
23 13 0.25
24 4 0.08
25 16 0.31
27 13 0.25
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.27
Consensus pattern (25 bp):
TGAAAAACTTTATGAAAAGACTTGA
Found at i:59325281 original size:23 final size:23
Alignment explanation
Indices: 59325216--59325282 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
59325206 AATGATTAAA
*
59325216 AACTTGATGGAAAACTTTATGAAAAG
1 AACTTGATGAAAAAC-TTA--AAAAG
59325242 -ACTTGATGAAAAACTTAAAAAG
1 AACTTGATGAAAAACTTAAAAAG
*
59325264 AACTTGATGCAAAACTTAA
1 AACTTGATGAAAAACTTAA
59325283 TAACAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 5 0.13
23 17 0.45
24 3 0.08
25 13 0.34
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (23 bp):
AACTTGATGAAAAACTTAAAAAG
Found at i:59325340 original size:14 final size:13
Alignment explanation
Indices: 59325306--59325347 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
59325296 CTTGGTAATT
59325306 AAAAACTTGAT-A
1 AAAAACTTGATGA
59325318 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
59325332 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
59325346 AA
1 AA
59325348 GAAAACACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:59331602 original size:11 final size:11
Alignment explanation
Indices: 59331588--59331617 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59331578 ATTGTTTGAT
59331588 TTTTACATAAA
1 TTTTACATAAA
*
59331599 TTTTACAGAAA
1 TTTTACATAAA
59331610 TTTTACAT
1 TTTTACAT
59331618 TCTTCTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (11 bp):
TTTTACATAAA
Done.