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 140 of 205
Found at i:42494415 original size:22 final size:22
Alignment explanation
Indices: 42494390--42494438 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
42494380 TGTTCAGATA
42494390 AGATGCAGAACAAATCA-AATAC
1 AGATGCAGAACAAATCAGAAT-C
*
42494412 AGATGCAGAACAGATCAGAATC
1 AGATGCAGAACAAATCAGAATC
42494434 AGATG
1 AGATG
42494439 TAGTTTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (22 bp):
AGATGCAGAACAAATCAGAATC
Found at i:42502047 original size:14 final size:15
Alignment explanation
Indices: 42502019--42502048 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42502009 TCTACGAGCC
42502019 TCCACATAGCTTGCT
1 TCCACATAGCTTGCT
42502034 TCCACATA-CTTGCT
1 TCCACATAGCTTGCT
42502048 T
1 T
42502049 TGGAAGGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (15 bp):
TCCACATAGCTTGCT
Found at i:42506415 original size:27 final size:27
Alignment explanation
Indices: 42506385--42506562 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42506375 ATATTGAGTC
* * * *
42506385 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42506412 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42506439 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42506467 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42506494 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42506521 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42506548 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42506563 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42506524 original size:82 final size:81
Alignment explanation
Indices: 42506406--42506561 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42506396 TGCTATATAA
* *
42506406 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42506471 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42506488 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42506552 CACTTAGTGC
65 CACTTAGTGC
42506562 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42507067 original size:12 final size:12
Alignment explanation
Indices: 42507050--42507075 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42507040 ATGGCATACT
42507050 TATGTATATATA
1 TATGTATATATA
42507062 TATGTATATATA
1 TATGTATATATA
42507074 TA
1 TA
42507076 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:42514530 original size:27 final size:27
Alignment explanation
Indices: 42514500--42514677 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42514490 ATATTGAGTC
* * * *
42514500 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42514527 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42514554 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42514582 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42514609 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42514636 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42514663 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42514678 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42514639 original size:82 final size:81
Alignment explanation
Indices: 42514521--42514676 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42514511 TGCTATATAA
* *
42514521 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42514586 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42514603 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42514667 CACTTAGTGC
65 CACTTAGTGC
42514677 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42517514 original size:25 final size:25
Alignment explanation
Indices: 42517486--42517537 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
42517476 TAGGTTTCAA
42517486 TTCCCATTCA-TTCACATATCTTGTT
1 TTCCCATTCATTTC-CATATCTTGTT
42517511 TTCCCATTCATTTCCATATCTTGTT
1 TTCCCATTCATTTCCATATCTTGTT
42517536 TT
1 TT
42517538 GCCTGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (25 bp):
TTCCCATTCATTTCCATATCTTGTT
Found at i:42522615 original size:21 final size:21
Alignment explanation
Indices: 42522591--42522661 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
42522581 GTTCTATGGT
42522591 ATCATGATGAAGATGAGTAAG
1 ATCATGATGAAGATGAGTAAG
* * **
42522612 ATCATGGCTGAAAGATG-CTATTC
1 ATCAT-GATG-AAGATGAGTA-AG
* *
42522635 ATCATGATAAATATGAGTAAG
1 ATCATGATGAAGATGAGTAAG
42522656 ATCATG
1 ATCATG
42522662 GCTGAAAGAC
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
21 16 0.44
22 9 0.25
23 11 0.31
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCATGATGAAGATGAGTAAG
Found at i:42522628 original size:23 final size:23
Alignment explanation
Indices: 42522600--42522670 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
42522590 TATCATGATG
42522600 AAGATGAGTAAGATCATGGCTGA
1 AAGATGAGTAAGATCATGGCTGA
* ** *
42522623 AAGATG-CTATTCATCAT-GAT-A
1 AAGATGAGTA-AGATCATGGCTGA
*
42522644 AATATGAGTAAGATCATGGCTGA
1 AAGATGAGTAAGATCATGGCTGA
42522667 AAGA
1 AAGA
42522671 CTCCATGACA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 11 0.32
22 8 0.24
23 15 0.44
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (23 bp):
AAGATGAGTAAGATCATGGCTGA
Found at i:42532894 original size:24 final size:23
Alignment explanation
Indices: 42532789--42532941 Score: 111
Period size: 24 Copynumber: 6.7 Consensus size: 23
42532779 ACAATATATA
*
42532789 ATAAATTTGAAATAATAATACAT-
1 ATAAATTTTAAATAAT-ATACATG
* * **
42532812 ATAAAATTTAAA-AATTTTGATG
1 ATAAATTTTAAATAATATACATG
* *
42532834 AT-AATTCTAGAATAATCATACGTG
1 ATAAATTTTA-AATAAT-ATACATG
*** *
42532858 ATAAATCCAAAATAATAGTACATA
1 ATAAATTTTAAATAATA-TACATG
42532882 ATAAATTTTAAAT-AT-TA-ATG
1 ATAAATTTTAAATAATATACATG
42532902 ATAAATTTTAAATAAATATACATG
1 ATAAATTTTAAAT-AATATACATG
*
42532926 ATAAATTTAAAATAAT
1 ATAAATTTTAAATAAT
42532942 GTTACGATGA
Statistics
Matches: 100, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
20 15 0.15
21 10 0.10
22 9 0.09
23 21 0.21
24 40 0.40
25 5 0.05
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (23 bp):
ATAAATTTTAAATAATATACATG
Found at i:42532904 original size:44 final size:44
Alignment explanation
Indices: 42532856--42532939 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
42532846 TAATCATACG
*
42532856 TGATAAATCCAAAAT-AATAGTACATAATAAATTTTAAATATTAA
1 TGATAAATCCAAAATAAATA-TACATAATAAATTTAAAATATTAA
*** *
42532900 TGATAAATTTTAAATAAATATACATGATAAATTTAAAATA
1 TGATAAATCCAAAATAAATATACATAATAAATTTAAAATA
42532940 ATGTTACGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 30 0.88
45 4 0.12
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (44 bp):
TGATAAATCCAAAATAAATATACATAATAAATTTAAAATATTAA
Found at i:42532938 original size:68 final size:69
Alignment explanation
Indices: 42532789--42532941 Score: 170
Period size: 68 Copynumber: 2.2 Consensus size: 69
42532779 ACAATATATA
* *
42532789 ATAAATTTGAAATAATAATACATATAAAATTTAAAAATTTTGATGATAATTCTAGAATAATCATA
1 ATAAATTTAAAATAATAATACATATAAAATTTAAAAATTATGATGATAATTCTAGAATAATCATA
*
42532854 CGTG
66 CATG
** * * * *
42532858 ATAAATCCAAAATAATAGTACATAATAAATTTTAAATATTA--ATGATAAATTTTA-AATAAAT-
1 ATAAATTTAAAATAATAATACAT-ATAAAATTTAAAAATTATGATGAT-AATTCTAGAAT-AATC
42532919 ATACATG
63 ATACATG
42532926 ATAAATTTAAAATAAT
1 ATAAATTTAAAATAAT
42532942 GTTACGATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
68 28 0.40
69 28 0.40
70 14 0.20
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATATAAAATTTAAAAATTATGATGATAATTCTAGAATAATCATA
CATG
Found at i:42533808 original size:24 final size:25
Alignment explanation
Indices: 42533750--42533811 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
42533740 CTCAATGAGT
42533750 AAACAAACAAAGAAAAGAATTAAAAA
1 AAACAAA-AAAGAAAAGAATTAAAAA
* * *
42533776 AAACGAAAAAGAAAATAATAAAAAA
1 AAACAAAAAAGAAAAGAATTAAAAA
*
42533801 AGAAAAAAAAA
1 A-AACAAAAAA
42533812 CTCAGATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.06
Consensus pattern (25 bp):
AAACAAAAAAGAAAAGAATTAAAAA
Found at i:42534477 original size:21 final size:21
Alignment explanation
Indices: 42534461--42534502 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42534451 TTTTTATTAC
42534461 ATAATTATTAAAATTTATAAA
1 ATAATTATTAAAATTTATAAA
* *
42534482 ATAATTATTAATATTTTTAAA
1 ATAATTATTAAAATTTATAAA
42534503 TTTTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATTATTAAAATTTATAAA
Found at i:42536644 original size:26 final size:24
Alignment explanation
Indices: 42536602--42536670 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
42536592 TTTTTCTGAT
* *
42536602 TTAAAACAAAATAAAATGTTATTAA
1 TTAAAACAAACTAAATTG-TATTAA
42536627 TTAAAAGCAAACTCAAATTGTATTAA
1 TTAAAA-CAAACT-AAATTGTATTAA
* *
42536653 ATATAATCAAACTAAATT
1 TTA-AAACAAACTAAATT
42536671 TAATGAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 11 0.30
26 19 0.51
27 7 0.19
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (24 bp):
TTAAAACAAACTAAATTGTATTAA
Found at i:42540485 original size:18 final size:18
Alignment explanation
Indices: 42540429--42540472 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
42540419 TGGTCTCGGC
*
42540429 GGTTTAGGTGGGGCAGGA
1 GGTTTAGGTGGAGCAGGA
*
42540447 GGTTTAGGTGGACCAGGA
1 GGTTTAGGTGGAGCAGGA
42540465 GGTTTAGG
1 GGTTTAGG
42540473 CGGTGCAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.07, G:0.50, T:0.25
Consensus pattern (18 bp):
GGTTTAGGTGGAGCAGGA
Found at i:42542782 original size:33 final size:33
Alignment explanation
Indices: 42542736--42542810 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
42542726 TTTAATTTAT
*
42542736 ATTATTAAATATTTATATTTAGTCATATAAAAA
1 ATTATTAATTATTTATATTTAGTCATATAAAAA
*
42542769 ATTATTAATTATTTATATTTAGTCATATAATAA
1 ATTATTAATTATTTATATTTAGTCATATAAAAA
*
42542802 ACTATTAAT
1 ATTATTAAT
42542811 ATAATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (33 bp):
ATTATTAATTATTTATATTTAGTCATATAAAAA
Found at i:42542886 original size:15 final size:13
Alignment explanation
Indices: 42542861--42542900 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
42542851 TTTCAATTTT
*
42542861 ATTTTAATAATAA
1 ATTTAAATAATAA
42542874 ATTTTAAAATAATAA
1 A-TTT-AAATAATAA
42542889 ATTTAAATAATA
1 ATTTAAATAATA
42542901 TTCTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 9 0.38
14 6 0.25
15 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTAAATAATAA
Found at i:42542953 original size:15 final size:15
Alignment explanation
Indices: 42542933--42542989 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
42542923 ATTCAATATT
42542933 AATATTTTAATAATA
1 AATATTTTAATAATA
42542948 AATATTTATTACAGTAATA
1 AATA-TT-TTA-A-TAATA
*
42542967 AATATATTAATAATA
1 AATATTTTAATAATA
*
42542982 AATGTTTT
1 AATATTTT
42542990 GTAGTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 15 0.43
16 3 0.09
17 6 0.17
18 2 0.06
19 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:42543763 original size:15 final size:13
Alignment explanation
Indices: 42543731--42543756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42543721 TCCAGTAAGT
42543731 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
42543744 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
42543757 AATTTTTATT
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):
TTTTTTTTTTCAA
Found at i:42564756 original size:88 final size:86
Alignment explanation
Indices: 42564662--42564919 Score: 346
Period size: 84 Copynumber: 3.0 Consensus size: 86
42564652 TTTTCTTTTC
*
42564662 TTTTTTTTTTTCACTCAATTGAGTACTTTAACTTTCATAATGTATAAAAAATCCCTCAAACTTTT
1 TTTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATGTATAAAAAA-CCCTCAAACTTTT
*
42564727 TCAAAAAAAAAAATTAAGCATCA
65 TCAAAAAAAAAAATTAAGC-CCA
42564750 TTTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATG-ATAAAAAACCCTCAAAC--TTT
1 TTTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATGTATAAAAAACCCTCAAACTTTTT
*
42564812 -AAAAAAAAATAATTAAGCCCC
66 CAAAAAAAAA-AATTAAGCCCA
* * *
42564833 TGCTTTTTTTTGCACTCAATTGGGTACTTTAGA-TTTCATAATGTATAAAAAAAAACCTCAAACT
1 T-TTTTTTTTTGCACTCAATTGAGTACTTTA-ACTTTCATAATGTAT--AAAAAACCCTCAAACT
**
42564897 TTTTCAAAAAAAGCAATTAAGCC
62 TTTTCAAAAAAAAAAATTAAGCC
42564920 TCTGCCTTTT
Statistics
Matches: 153, Mismatches: 8, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
83 11 0.07
84 48 0.31
85 3 0.02
86 9 0.06
87 22 0.14
88 41 0.27
89 12 0.08
90 7 0.05
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (86 bp):
TTTTTTTTTTGCACTCAATTGAGTACTTTAACTTTCATAATGTATAAAAAACCCTCAAACTTTTT
CAAAAAAAAAAATTAAGCCCA
Found at i:42564971 original size:89 final size:87
Alignment explanation
Indices: 42564753--42564974 Score: 197
Period size: 89 Copynumber: 2.6 Consensus size: 87
42564743 AGCATCATTT
** * *
42564753 TTTTTTTGCACTCAATTGAG-TACTTTA-ACTTTCATAATG-AT--AAAAAACCCTCAAACTTTA
1 TTTTTTTGCACTCAATTG-GCTACTTTAGA-TGCCAAAATGCATAAAAAAAAACCTCAAACTTTA
* *
42564813 AAAAAAAATAATTAAGCCCCTGCT
64 AAAAAAAACAATTAAGCCCCTGCC
* ** * * *
42564837 TTTTTTTGCACTCAATTGGGTACTTTAGATTTCATAATGTATAAAAAAAAACCTCAAACTTTTTC
1 TTTTTTTGCACTCAATTGGCTACTTTAGATGCCAAAATGCATAAAAAAAAACCTCAAAC--TTTA
* *
42564902 AAAAAAAGCAATTAAGCCTCTGCC
64 AAAAAAAACAATTAAGCCCCTGCC
* *
42564926 TTTTTTTGTACTCAATTGGCTA-TTT-GAACTGCCAAAATGCGTAAAAAAA
1 TTTTTTTGCACTCAATTGGCTACTTTAG-A-TGCCAAAATGCATAAAAAAA
42564975 GTCATTTGAC
Statistics
Matches: 116, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 35 0.30
85 3 0.03
87 15 0.13
88 4 0.03
89 58 0.50
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (87 bp):
TTTTTTTGCACTCAATTGGCTACTTTAGATGCCAAAATGCATAAAAAAAAACCTCAAACTTTAAA
AAAAAACAATTAAGCCCCTGCC
Found at i:42565117 original size:10 final size:9
Alignment explanation
Indices: 42565078--42565130 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
42565068 ACATGTGGCA
*
42565078 AAAAATGAT
1 AAAAATTAT
42565087 AAAAA--AT
1 AAAAATTAT
*
42565094 AAAAATCAAT
1 AAAAAT-TAT
*
42565104 AAAAGTTAT
1 AAAAATTAT
42565113 AAAAATTAT
1 AAAAATTAT
42565122 AAAAATTAT
1 AAAAATTAT
42565131 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.18
9 24 0.63
10 7 0.18
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (9 bp):
AAAAATTAT
Found at i:42565123 original size:18 final size:19
Alignment explanation
Indices: 42565092--42565210 Score: 59
Period size: 20 Copynumber: 6.3 Consensus size: 19
42565082 ATGATAAAAA
*
42565092 ATAAAAATCAATAAAAGTT
1 ATAAAAATCAATAAAAATT
*
42565111 ATAAAAAT-TATAAAAATT
1 ATAAAAATCAATAAAAATT
** * *
42565129 ATTAAATTTTAATAAAAA-A
1 A-TAAAAATCAATAAAAATT
* *
42565148 ATAAAACAT-ACTTAAAATTT
1 ATAAAA-ATCA-ATAAAAATT
** *
42565168 ATAAAAAAAAGAAAAAAATT
1 ATAAAAATCA-ATAAAAATT
*
42565188 ATAAAAATC-GTAAAAA-T
1 ATAAAAATCAATAAAAATT
42565205 ATAAAA
1 ATAAAA
42565211 TATATAGTAA
Statistics
Matches: 74, Mismatches: 20, Indels: 14
0.69 0.19 0.13
Matches are distributed among these distances:
17 7 0.09
18 19 0.26
19 21 0.28
20 27 0.36
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
ATAAAAATCAATAAAAATT
Found at i:42565151 original size:28 final size:27
Alignment explanation
Indices: 42565087--42565176 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 27
42565077 AAAAAATGAT
* * *
42565087 AAAAAATAAAAATCAATAAAAGTTATA
1 AAAAAATAAAAATTATTAAAATTTATA
* *
42565114 AAAATTATAAAAATTATTAAATTTTAATA
1 AAAA-AATAAAAATTATTAAAATTT-ATA
42565143 AAAAAATAAAACA-TACTTAAAATTTATA
1 AAAAAATAAAA-ATTA-TTAAAATTTATA
42565171 AAAAAA
1 AAAAAA
42565177 AGAAAAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.08
28 32 0.62
29 16 0.31
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAAAATAAAAATTATTAAAATTTATA
Found at i:42565192 original size:29 final size:29
Alignment explanation
Indices: 42565113--42565193 Score: 69
Period size: 30 Copynumber: 2.7 Consensus size: 29
42565103 TAAAAGTTAT
* *
42565113 AAAAATTATAAAAATTATTAAATTTTAATA
1 AAAAAATA-AAAAATTATAAAATTTTAATA
*
42565143 AAAAAATAAAACA-TACTTAAAATTTATAA-A
1 AAAAAATAAAAAATTA--TAAAATTT-TAATA
42565173 AAAAAGA-AAAAAATTATAAAA
1 AAAAA-ATAAAAAATTATAAAA
42565194 ATCGTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
28 2 0.05
29 9 0.21
30 25 0.60
31 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (29 bp):
AAAAAATAAAAAATTATAAAATTTTAATA
Found at i:42565504 original size:9 final size:9
Alignment explanation
Indices: 42565492--42565653 Score: 73
Period size: 9 Copynumber: 17.4 Consensus size: 9
42565482 TTTTTATGCA
42565492 TTTTATAATTT
1 TTTTATAA--T
*
42565503 TTTTATGAT
1 TTTTATAAT
42565512 TTTTATAAT
1 TTTTATAAT
* *
42565521 ATTCTACAAT
1 -TTTTATAAT
*
42565531 TTCT-T--T
1 TTTTATAAT
42565537 TTTTATATAT
1 TTTTATA-AT
*
42565547 TTTTATGAT
1 TTTTATAAT
*
42565556 TTTTATACT
1 TTTTATAAT
*
42565565 TTTTCTAAT
1 TTTTATAAT
*
42565574 TTTAATAAAT
1 TTTTAT-AAT
* *
42565584 TTTAAATATT
1 TTT-TATAAT
*
42565594 TTTTATTAAAA
1 TTTTA-T-AAT
*
42565605 TTTAATAATT
1 TTTTATAA-T
*
42565615 TTTTATAAA
1 TTTTATAAT
*
42565624 TTTTATTGAT
1 TTTTA-TAAT
42565634 TTTTAT--T
1 TTTTATAAT
42565641 TTTTATAAT
1 TTTTATAAT
42565650 TTTT
1 TTTT
42565654 TGTCACATGT
Statistics
Matches: 115, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
6 4 0.03
7 8 0.07
9 47 0.41
10 41 0.36
11 15 0.13
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:42565505 original size:20 final size:20
Alignment explanation
Indices: 42565480--42565520 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
42565470 ATTAAATGAC
42565480 TTTTTTTATGCA-TTTTATAA
1 TTTTTTTATG-ATTTTTATAA
42565500 TTTTTTTATGATTTTTATAA
1 TTTTTTTATGATTTTTATAA
42565520 T
1 T
42565521 ATTCTACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTTATGATTTTTATAA
Found at i:42565603 original size:21 final size:21
Alignment explanation
Indices: 42565573--42565628 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
42565563 CTTTTTCTAA
*
42565573 TTTTAATAAATTTTAAAT-AT
1 TTTTTATAAATTTTAAATAAT
*
42565593 TTTTTATTAAAATTT-AATAAT
1 TTTTTA-TAAATTTTAAATAAT
42565614 TTTTTATAAATTTTA
1 TTTTTATAAATTTTA
42565629 TTGATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTATAAATTTTAAATAAT
Found at i:42565611 original size:20 final size:22
Alignment explanation
Indices: 42565573--42565628 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
42565563 CTTTTTCTAA
* *
42565573 TTTTAATAAATTTTAAAT-ATT
1 TTTTATTAAAATTTAAATAATT
42565594 TTTTATTAAAATTT-AATAATT
1 TTTTATTAAAATTTAAATAATT
*
42565615 TTTTA-TAAATTTTA
1 TTTTATTAAAATTTA
42565629 TTGATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATTAAAATTTAAATAATT
Found at i:42567632 original size:17 final size:17
Alignment explanation
Indices: 42567612--42567644 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42567602 AAAATAAGAA
*
42567612 AAAAAAAGTGTTTTAGG
1 AAAAAAAGTATTTTAGG
42567629 AAAAAAAGTATTTTAG
1 AAAAAAAGTATTTTAG
42567645 TATGATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (17 bp):
AAAAAAAGTATTTTAGG
Found at i:42569508 original size:35 final size:34
Alignment explanation
Indices: 42569358--42569586 Score: 221
Period size: 35 Copynumber: 6.7 Consensus size: 34
42569348 CTGCAAACAT
* * *
42569358 ATTTGGACATCCTTATAACATGCGAAACAA-C-C
1 ATTTGGACAACATTATAACATGCAAAACAACCAC
* * ** * * *
42569390 ATTAGAACAACATTGCAACATACCAAAAGCAGCCGC
1 ATTTGGACAACATTATAACAT-GCAAAA-CAACCAC
* * **
42569426 CTTTGGACAACATTA-AACATACAAAACAATAAC
1 ATTTGGACAACATTATAACATGCAAAACAACCAC
*
42569459 ATTTGGACAACATTATAACATGTAAAAGCAACCAC
1 ATTTGGACAACATTATAACATGCAAAA-CAACCAC
*
42569494 ATTTGGACACCATTATAACATGCAAAACAACCAC
1 ATTTGGACAACATTATAACATGCAAAACAACCAC
*
42569528 ATTTGGACAACATTATAACATGTAAAAACAACCAC
1 ATTTGGACAACATTATAACATG-CAAAACAACCAC
* * *
42569563 ATTTGGACACCGTTGTAACATGCA
1 ATTTGGACAACATTATAACATGCA
42569587 TACCGCCATT
Statistics
Matches: 159, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
32 15 0.09
33 21 0.13
34 45 0.28
35 66 0.42
36 12 0.08
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (34 bp):
ATTTGGACAACATTATAACATGCAAAACAACCAC
Found at i:42569572 original size:69 final size:68
Alignment explanation
Indices: 42569358--42569586 Score: 257
Period size: 69 Copynumber: 3.4 Consensus size: 68
42569348 CTGCAAACAT
* * * ** **
42569358 ATTTGGACATCC-TTATAACATGCGAAACAAC-CATTAGAACAACATTGCAACATACCAAAAGCA
1 ATTTGGACA-CCATTATAACATGCAAAACAACACATTTGGACAACATTATAACAT-GTAAAAGCA
* *
42569421 GCCGC
64 ACCAC
* * * *
42569426 CTTTGGACAACATTA-AACATACAAAACAATAACATTTGGACAACATTATAACATGTAAAAGCAA
1 ATTTGGACACCATTATAACATGCAAAACAA-CACATTTGGACAACATTATAACATGTAAAAGCAA
42569490 CCAC
65 CCAC
*
42569494 ATTTGGACACCATTATAACATGCAAAACAACCACATTTGGACAACATTATAACATGTAAAAACAA
1 ATTTGGACACCATTATAACATGCAAAACAA-CACATTTGGACAACATTATAACATGTAAAAGCAA
42569559 CCAC
65 CCAC
* *
42569563 ATTTGGACACCGTTGTAACATGCA
1 ATTTGGACACCATTATAACATGCA
42569587 TACCGCCATT
Statistics
Matches: 136, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
67 13 0.10
68 34 0.25
69 89 0.65
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (68 bp):
ATTTGGACACCATTATAACATGCAAAACAACACATTTGGACAACATTATAACATGTAAAAGCAAC
CAC
Found at i:42569995 original size:17 final size:17
Alignment explanation
Indices: 42569967--42569999 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42569957 TTCAGAACTG
42569967 CTCCTAGCTTCTATCGTT
1 CTCCTAGCTTCT-TCGTT
42569985 CTCCT-GCTTCTTCGT
1 CTCCTAGCTTCTTCGT
42570000 GCTACAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.06, C:0.36, G:0.12, T:0.45
Consensus pattern (17 bp):
CTCCTAGCTTCTTCGTT
Found at i:42570127 original size:15 final size:15
Alignment explanation
Indices: 42570107--42570138 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42570097 CATTTAATAT
*
42570107 TTCCATGTATTTACA
1 TTCCATGCATTTACA
42570122 TTCCATGCATTTACA
1 TTCCATGCATTTACA
42570137 TT
1 TT
42570139 TTTTTTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (15 bp):
TTCCATGCATTTACA
Found at i:42571349 original size:43 final size:43
Alignment explanation
Indices: 42571252--42571684 Score: 277
Period size: 43 Copynumber: 10.1 Consensus size: 43
42571242 GCATCGTAAC
* *
42571252 GCATCATCGGATAAACCGAAA-TAACTATACT-GCAAACATAGT
1 GCATCATCGGATAAACC-AAAGTAACTATACTGGCACACACAGT
* * *
42571294 ACATCATCGGATATACCAAAGTAAGTATACTGGCACACACAGT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
* * * *
42571337 GCATCATTGGATAAACCGAAGCAACTATATTGGCACACACAGT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
* * * * * * *
42571380 GTATCATCGGATATACCGAATTAACCATACTGGCATACACAAT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
* * * *
42571423 ACATCATCGGATAAACCGAAA-CAACTATACAGGCATACACAGT
1 GCATCATCGGATAAACC-AAAGTAACTATACTGGCACACACAGT
** * *
42571466 GCATCATCAAATATACCGAAGTAACTATACTGGCACACACTA-T
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACAC-AGT
* *** * * *
42571509 GCATCATCAGATAAATTGGAA-CAACTATATTGACACACACAGT
1 GCATCATCGGATAAA-CCAAAGTAACTATACTGGCACACACAGT
* * * ** * * *
42571552 GCTTTATC--AAAAACTGAAGAAACTATACTAGCACATACAGT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
*** * * * *
42571593 GCATCATCGGATAAATTGAGGCAACTATACTGTCACACACAAT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
* * * * * * * * * *
42571636 ACATTATCAGATATATCGAAGTAACTATACTAGAACACAAAAT
1 GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
42571679 GCATCA
1 GCATCA
42571685 ACAAATAGAC
Statistics
Matches: 304, Mismatches: 77, Indels: 19
0.76 0.19 0.05
Matches are distributed among these distances:
40 3 0.01
41 30 0.10
42 27 0.09
43 238 0.78
44 6 0.02
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (43 bp):
GCATCATCGGATAAACCAAAGTAACTATACTGGCACACACAGT
Found at i:42571420 original size:86 final size:85
Alignment explanation
Indices: 42571252--42571684 Score: 395
Period size: 86 Copynumber: 5.1 Consensus size: 85
42571242 GCATCGTAAC
* * * * *
42571252 GCATCATCGGATAAACCGAAATAACTATACT-GCAAACATAGTACATCATCGGATATACCAAAGT
1 GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
*
42571316 AAGTATACTGGCACACACAGT
66 AACTATACTGGCACACACA-T
* * * * *
42571337 GCATCATTGGATAAACCGAAGCAACTATATTGGCACACACAGTGTATCATCGGATATACCGAATT
1 GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
* *
42571402 AACCATACTGGCATACACAAT
66 AACTATACTGGCACACAC-AT
* * * **
42571423 ACATCATCGGATAAACCGAAACAACTATACAGGCATACACAGTGCATCATCAAATATACCGAAGT
1 GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
42571488 AACTATACTGGCACACACTAT
66 AACTATACTGGCACACAC-AT
* ** * * * * * * * * *
42571509 GCATCATCAGATAAATTGGAACAACTATATTGACACACACAGTGCTTTATC--AAAAACTGAAGA
1 GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
* *
42571572 AACTATACTAGCACATACAGT
66 AACTATACTGGCACACACA-T
** ** * * * * * *
42571593 GCATCATCGGATAAATTGAGGCAACTATACTGTCACACACAATACATTATCAGATATATCGAAGT
1 GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
* * *
42571658 AACTATACTAGAACACAAAAT
66 AACTATACTGGCACAC-ACAT
42571679 GCATCA
1 GCATCA
42571685 ACAAATAGAC
Statistics
Matches: 282, Mismatches: 60, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
83 1 0.00
84 67 0.24
85 27 0.10
86 184 0.65
87 3 0.01
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (85 bp):
GCATCATCGGATAAACCGAAACAACTATACTGGCACACACAGTGCATCATCGGATATACCGAAGT
AACTATACTGGCACACACAT
Found at i:42571484 original size:129 final size:128
Alignment explanation
Indices: 42571254--42571523 Score: 328
Period size: 129 Copynumber: 2.1 Consensus size: 128
42571244 ATCGTAACGC
* * * * * *
42571254 ATCATCGGATAAACCGAAATAACTATACTGCAAACATAGTACATCATCGGATATACCAAAGTAAG
1 ATCATCGGATAAACCGAAATAACCATACTGCAAACACAATACATCATCGGATAAACCAAAGCAAC
* *** *
42571319 TATACTGGCACACACAGTGCATCATTGGATAAACCGAAGCAACTATATTGGCACACACAGTGT
66 TATACAGGCACACACAGTGCATCATCAAATAAACCGAAGCAACTATACTGGCACACACAGTGT
* * *
42571382 ATCATCGGATATACCGAATTAACCATACTGGCATACACAATACATCATCGGATAAACCGAAA-CA
1 ATCATCGGATAAACCGAAATAACCATACT-GCAAACACAATACATCATCGGATAAACC-AAAGCA
* * *
42571446 ACTATACAGGCATACACAGTGCATCATCAAATATACCGAAGTAACTATACTGGCACACACTA-TG
64 ACTATACAGGCACACACAGTGCATCATCAAATAAACCGAAGCAACTATACTGGCACACAC-AGTG
*
42571510 C
128 T
*
42571511 ATCATCAGATAAA
1 ATCATCGGATAAA
42571524 TTGGAACAAC
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
128 26 0.22
129 89 0.75
130 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.21
Consensus pattern (128 bp):
ATCATCGGATAAACCGAAATAACCATACTGCAAACACAATACATCATCGGATAAACCAAAGCAAC
TATACAGGCACACACAGTGCATCATCAAATAAACCGAAGCAACTATACTGGCACACACAGTGT
Found at i:42577495 original size:21 final size:21
Alignment explanation
Indices: 42577463--42577503 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42577453 GAACATCTGG
42577463 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
42577484 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
42577504 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:42587396 original size:15 final size:13
Alignment explanation
Indices: 42587363--42587405 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 13
42587353 CACACCAATC
42587363 ACAGATACAAAAT
1 ACAGATACAAAAT
42587376 ACAGATACAGAAAT
1 ACAGATACA-AAAT
42587390 AACAGATACAATAAT
1 -ACAGATACAA-AAT
42587405 A
1 A
42587406 TCATGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
15 12 0.44
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (13 bp):
ACAGATACAAAAT
Found at i:42590049 original size:23 final size:22
Alignment explanation
Indices: 42590022--42590085 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 22
42590012 ATGCATTTCT
42590022 TAAATAATAAAAAAATTATTTA
1 TAAATAATAAAAAAATTATTTA
* *
42590044 TAAAATCATCAAAAATATTATTTA
1 T-AAATAAT-AAAAAAATTATTTA
42590068 TAAATAAATAAAACAAAT
1 TAAAT-AATAAAA-AAAT
42590086 GGATAAGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 14 0.41
24 19 0.56
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATAATAAAAAAATTATTTA
Found at i:42594582 original size:23 final size:23
Alignment explanation
Indices: 42594556--42594599 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
42594546 GTAAAGCATT
*
42594556 TGTGGCGTATTATGTGATGCCTA
1 TGTGGCGTATTATGTAATGCCTA
*
42594579 TGTGGCGTATTCTGTAATGCC
1 TGTGGCGTATTATGTAATGCC
42594600 CTTGTGGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.39
Consensus pattern (23 bp):
TGTGGCGTATTATGTAATGCCTA
Found at i:42594605 original size:23 final size:22
Alignment explanation
Indices: 42594555--42594606 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
42594545 TGTAAAGCAT
*
42594555 TTGTGGCGTATTATGTGATGCC
1 TTGTGGCGTATTATGTAATGCC
*
42594577 TATGTGGCGTATTCTGTAATGCCC
1 T-TGTGGCGTATTATGTAATG-CC
42594601 TTGTGG
1 TTGTGG
42594607 TGAAATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.85
24 3 0.12
ACGTcount: A:0.13, C:0.15, G:0.31, T:0.40
Consensus pattern (22 bp):
TTGTGGCGTATTATGTAATGCC
Found at i:42600388 original size:25 final size:27
Alignment explanation
Indices: 42600360--42600412 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
42600350 TTTGACTTCT
*
42600360 TTAAGCATTCTT-TTACT-TTAACATA
1 TTAAGCATTCTTCTCACTGTTAACATA
**
42600385 TTAAGTTTTCTTCTCACTGTTAACATA
1 TTAAGCATTCTTCTCACTGTTAACATA
42600412 T
1 T
42600413 CCAGCCCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 4 0.17
27 9 0.39
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (27 bp):
TTAAGCATTCTTCTCACTGTTAACATA
Found at i:42607435 original size:17 final size:17
Alignment explanation
Indices: 42607401--42607440 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42607391 TATTTTTATA
42607401 AAATTAAAAATATAATT
1 AAATTAAAAATATAATT
* * *
42607418 ATATTAAAAATGTTATT
1 AAATTAAAAATATAATT
42607435 AAATTA
1 AAATTA
42607441 TATATTATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAATTAAAAATATAATT
Found at i:42607710 original size:21 final size:21
Alignment explanation
Indices: 42607686--42607730 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42607676 TTACAGCTAT
*
42607686 ATTACATTACAACTCTATTCC
1 ATTACAATACAACTCTATTCC
* * *
42607707 ATTACAATCCTATTCTATTCC
1 ATTACAATACAACTCTATTCC
42607728 ATT
1 ATT
42607731 GAACCAAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACAATACAACTCTATTCC
Found at i:42607721 original size:16 final size:16
Alignment explanation
Indices: 42607659--42607713 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
42607649 TGAATTACTG
42607659 ATTACAACGT-TATTCC
1 ATTACAAC-TCTATTCC
* * *
42607675 ATTACAGCTATATTAC
1 ATTACAACTCTATTCC
42607691 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
42607707 ATTACAA
1 ATTACAA
42607714 TCCTATTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:42612502 original size:27 final size:27
Alignment explanation
Indices: 42612472--42612565 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
42612462 AATGAGAGCC
* *
42612472 TTTGTGGCAAATCATAAAATAAAAGCT
1 TTTGTGGCGAATCATGAAATAAAAGCT
*
42612499 TTTGTGGCGAATCATGAAATGAAAA-CC
1 TTTGTGGCGAATCATGAAAT-AAAAGCT
* * *
42612526 TTTATGGTGAATCATGAAATGAAAGCT
1 TTTGTGGCGAATCATGAAATAAAAGCT
*
42612553 TTTGTGGAGAATC
1 TTTGTGGCGAATC
42612566 TTAAAAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.05
27 49 0.88
28 4 0.07
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (27 bp):
TTTGTGGCGAATCATGAAATAAAAGCT
Found at i:42612528 original size:54 final size:54
Alignment explanation
Indices: 42612460--42612565 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
42612450 GTCAGGAAAG
* * * *
42612460 GAAATGAGAGCCTTTGTGGCAAATCATAAAATAAAAGCTTTTGTGGCGAATCAT
1 GAAATGAAAACCTTTATGGCAAATCATAAAATAAAAGCTTTTGTGGAGAATCAT
** * *
42612514 GAAATGAAAACCTTTATGGTGAATCATGAAATGAAAGCTTTTGTGGAGAATC
1 GAAATGAAAACCTTTATGGCAAATCATAAAATAAAAGCTTTTGTGGAGAATC
42612566 TTAAAAAGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (54 bp):
GAAATGAAAACCTTTATGGCAAATCATAAAATAAAAGCTTTTGTGGAGAATCAT
Found at i:42615189 original size:39 final size:39
Alignment explanation
Indices: 42615135--42615381 Score: 291
Period size: 39 Copynumber: 6.3 Consensus size: 39
42615125 GCTATTGGGA
* *
42615135 GTACCAAAGCACAACAAGGGCACGTAAGTGCGTTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
*
42615174 GTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
** *
42615213 GTACCAAAGTACAAC-AGGAGCACACAAGTGCATTTAGGG
1 GTACCAAAGTACAACAAGG-GCACGTAAGTGCATTCAGGG
** * * *
42615252 GTACTGAAGTGCAAC-AGAGGCACATAAATGCATTCAGGG
1 GTACCAAAGTACAACAAG-GGCACGTAAGTGCATTCAGGG
* **
42615291 GTACCAAAGTACAACAGGGGCGTGTAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
** *
42615330 GTACTGAAGTACAACAAGGGCAGGTAAGTGCATTCAGGG
1 GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
* *
42615369 GTATCGAAGTACA
1 GTACCAAAGTACA
42615382 CCAGTTTTCT
Statistics
Matches: 177, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
38 2 0.01
39 173 0.98
40 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (39 bp):
GTACCAAAGTACAACAAGGGCACGTAAGTGCATTCAGGG
Found at i:42615191 original size:19 final size:19
Alignment explanation
Indices: 42615169--42615230 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
42615159 TAAGTGCGTT
42615169 CAGGGGTACCAAAGTACAA
1 CAGGGGTACCAAAGTACAA
* ** * *
42615188 CAGGGGCACGTAAGTGCATT
1 CAGGGGTACCAAAGTACA-A
42615208 CAGGGGTACCAAAGTACAA
1 CAGGGGTACCAAAGTACAA
42615227 CAGG
1 CAGG
42615231 AGCACACAAG
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.21, G:0.31, T:0.13
Consensus pattern (19 bp):
CAGGGGTACCAAAGTACAA
Found at i:42615378 original size:117 final size:117
Alignment explanation
Indices: 42615153--42615371 Score: 323
Period size: 117 Copynumber: 1.9 Consensus size: 117
42615143 GCACAACAAG
* * *
42615153 GGCACGTAAGTGCGTTCAGGGGTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGGTACC
1 GGCACATAAATGCATTCAGGGGTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGGTACC
*
42615218 AAAGTACAACAGGAGCACACAAGTGCATTTAGGGGTACTGAAGTGCAACAGA
66 AAAGTACAACAGGAGCACACAAGTGCATTCAGGGGTACTGAAGTGCAACAGA
** *
42615270 GGCACATAAATGCATTCAGGGGTACCAAAGTACAACAGGGGCGTGTAAGTGCATTCAGGGGTACT
1 GGCACATAAATGCATTCAGGGGTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGGTACC
* ***
42615335 GAAGTACAACAAGG-GCAGGTAAGTGCATTCAGGGGTA
66 AAAGTACAAC-AGGAGCACACAAGTGCATTCAGGGGTA
42615372 TCGAAGTACA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
117 87 0.97
118 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.32, T:0.17
Consensus pattern (117 bp):
GGCACATAAATGCATTCAGGGGTACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGGTACC
AAAGTACAACAGGAGCACACAAGTGCATTCAGGGGTACTGAAGTGCAACAGA
Found at i:42622491 original size:20 final size:20
Alignment explanation
Indices: 42622468--42622530 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
42622458 CCCTTGTTGT
42622468 ACTTCGGTACCCCTAAATGC
1 ACTTCGGTACCCCTAAATGC
* * * *
42622488 ACTTAC-ATGCCCCT-ATTGT
1 ACTT-CGGTACCCCTAAATGC
42622507 ACTTCGGTACCCCTAAATGC
1 ACTTCGGTACCCCTAAATGC
42622527 ACTT
1 ACTT
42622531 ATGTACGCCT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 17 0.53
21 1 0.03
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (20 bp):
ACTTCGGTACCCCTAAATGC
Found at i:42622491 original size:39 final size:39
Alignment explanation
Indices: 42622428--42622666 Score: 289
Period size: 39 Copynumber: 6.1 Consensus size: 39
42622418 AAAACTATTC
* *
42622428 TACTTCGGTACCCCTGAATTCACTTACGTGCCCTTGTTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
* * *
42622467 TACTTCGGTACCCCTAAATGCACTTACATGCCCCTATTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
* * * *
42622506 TACTTCGGTACCCCTAAATGCACTTATGTACGCCTGTTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
* * * * * *
42622545 TCCTTTGGTACCACTGAATGTACTTGCGTGCCCCTATTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
* * * *
42622584 TACTTCAGTACCCCTGAATACACTTAGGTGCCCTTGTTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
* *
42622623 TACTTCAGTACCCCTGAATGCACTTACGTGCCCATGTTG
1 TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
42622662 TACTT
1 TACTT
42622667 TAGTAATCTT
Statistics
Matches: 167, Mismatches: 33, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 167 1.00
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (39 bp):
TACTTCGGTACCCCTGAATGCACTTACGTGCCCCTGTTG
Found at i:42622519 original size:19 final size:20
Alignment explanation
Indices: 42622464--42622598 Score: 66
Period size: 19 Copynumber: 6.9 Consensus size: 20
42622454 CGTGCCCTTG
42622464 TTGTACTTCGGTACCCCTAA
1 TTGTACTTCGGTACCCCTAA
* * * *
42622484 ATGCACTTAC-ATGCCCCT-A
1 TTGTACTT-CGGTACCCCTAA
42622503 TTGTACTTCGGTACCCCTAA
1 TTGTACTTCGGTACCCCTAA
* * ** * *
42622523 ATGCACTTATGTACGCCT-G
1 TTGTACTTCGGTACCCCTAA
* * *
42622542 TTGTCCTTTGGTACCACTGAA
1 TTGTACTTCGGTACCCCT-AA
*
42622563 -TGTACTT-GCGTGCCCCT-A
1 TTGTACTTCG-GTACCCCTAA
*
42622581 TTGTACTTCAGTACCCCT
1 TTGTACTTCGGTACCCCT
42622599 GAATACACTT
Statistics
Matches: 80, Mismatches: 27, Indels: 17
0.65 0.22 0.14
Matches are distributed among these distances:
18 2 0.03
19 39 0.49
20 38 0.47
21 1 0.01
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.34
Consensus pattern (20 bp):
TTGTACTTCGGTACCCCTAA
Found at i:42623899 original size:26 final size:26
Alignment explanation
Indices: 42623863--42623912 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
42623853 AAAAAAATTT
*
42623863 CCTTTTTCTAAAAATTTTCATATGTG
1 CCTTTTTCTAAAAAATTTCATATGTG
42623889 CCTTTTTCTAAAAAATTTCATATG
1 CCTTTTTCTAAAAAATTTCATATG
42623913 CTTTCGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (26 bp):
CCTTTTTCTAAAAAATTTCATATGTG
Found at i:42624395 original size:75 final size:75
Alignment explanation
Indices: 42624309--42624456 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
42624299 AAAGGAAAAC
* * *
42624309 CAAGAGTATTCCCTTATTAATAGAGCAA-ACAAATGGAAATTTAGAAATATGAATTATATTCTTT
1 CAAGAGTATTCCCATATTAATAGAG-AAGACAAATGGAAAGTTAGAAAAATGAATTATATTCTTT
42624373 CCAAAAGAATA
65 CCAAAAGAATA
*
42624384 CAAGATTATTCCCATATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
1 CAAGAGTATTCCCATATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
*
42624449 GAAAAGAA
66 CAAAAGAA
42624457 CATTAATTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
74 2 0.03
75 65 0.97
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (75 bp):
CAAGAGTATTCCCATATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATGAATTATATTCTTTC
CAAAAGAATA
Found at i:42624635 original size:138 final size:134
Alignment explanation
Indices: 42624435--42624845 Score: 437
Period size: 128 Copynumber: 3.1 Consensus size: 134
42624425 TAGAAAAATG
* * *
42624435 AATTATATTC-TTTCGAAAAGAACATTAATTTC-TGTCTTTTATAATTTGA-CTAAAATTAATTA
1 AATTATATTCTTTTC-AAAAGAATATTAATTTCATGTCTTTTATATTTTGATC-GAAATTAATTA
* * *
42624497 ATATAACTGTTTATATTAACAATTTCGATAGAATATATACAATTAATATTTTGTACGAATCAAAT
64 ATATAACTGTTAATATTAA-AA-TTCGGTA-AATATATACAATTAATATTTTGTAAGAATCAAAT
*
42624562 TTATATACT
126 TCATATACT
* *
42624571 AATTATATTCTTTTCAAAAGAATACTATTTTCTATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTC-ATGTCTTTTATATTTTGATCGAAATTAATTAA
* *
42624636 TATAA---TTGA-A-T-AAATTCGGT-AATATATATAATTAATATTTTGTAAGAATCAAATTCAT
65 TATAACTGTTAATATTAAAATTCGGTAAATATATACAATTAATATTTTGTAAGAATCAAATTCAT
*
42624694 ATATT
130 ATACT
* ** * * *
42624699 AATTACATTCTTTAAAAAAGAATATTAATTTCCATGTCTTTTATATTTTTATTGACATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTT-CATGTCTTTTATATTTTGATCGAAATTAATTAA
* * ***
42624764 TATAACTGTTAATATTAATAAATTCGGTAAAATATATACAAATAATATTTTGTATGAAAGGAATT
65 TATAACTGTTAATATT-A-AAATTCGGT-AAATATATACAATTAATATTTTGTAAGAATCAAATT
*
42624829 CATATATT
127 CATATACT
*
42624837 AATTTTATT
1 AATTATATT
42624846 TATGTTCTCT
Statistics
Matches: 232, Mismatches: 28, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
128 99 0.43
129 1 0.00
130 5 0.02
131 5 0.02
132 2 0.01
133 2 0.01
134 1 0.00
135 3 0.01
136 33 0.14
137 4 0.02
138 76 0.33
139 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (134 bp):
AATTATATTCTTTTCAAAAGAATATTAATTTCATGTCTTTTATATTTTGATCGAAATTAATTAAT
ATAACTGTTAATATTAAAATTCGGTAAATATATACAATTAATATTTTGTAAGAATCAAATTCATA
TACT
Found at i:42626760 original size:12 final size:12
Alignment explanation
Indices: 42626743--42626781 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
42626733 GACACGGGCG
42626743 TGTCCTAGCCCA
1 TGTCCTAGCCCA
42626755 TGTCCTAGCCCA
1 TGTCCTAGCCCA
42626767 TGTCC-ATGCCCA
1 TGTCCTA-GCCCA
42626779 TGT
1 TGT
42626782 AACAGTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.15, C:0.38, G:0.18, T:0.28
Consensus pattern (12 bp):
TGTCCTAGCCCA
Found at i:42633938 original size:183 final size:183
Alignment explanation
Indices: 42633630--42633989 Score: 630
Period size: 183 Copynumber: 2.0 Consensus size: 183
42633620 TGAGCCATTG
*
42633630 GGTTCGTTCGTACGAACTCGGTAAACCACTTATTAATCATCTGGAAGAAGGCTTCCTTAGCCTCT
1 GGTTCGTTCGTACGAACTCGGTAAACCACTCATTAATCATCTGGAAGAAGGCTTCCTTAGCCTCT
* * **
42633695 GCTCCCCGGTCCTCAGATATGGGCTTACTACCACTCGTCGCTGCTCTGTAAACAGAGGCTTATGC
66 CCTCCCCGGTCCTCAAATATGGGCTTACTACCACTCACCGCTGCTCTGTAAACAGAGGCTTATGC
*
42633760 GTTACTTTCAACCTCATCTAAATTGGCTCGGTTGGATGACATTATCTCTATCA
131 GTTACTTTCAACCTCATCTAAATTAGCTCGGTTGGATGACATTATCTCTATCA
*
42633813 GGTTCGTTCGTACGAACTCGGTAAACCACTCATTCATCATCTGGAAGAAGGCTTCCTTAGCCTCT
1 GGTTCGTTCGTACGAACTCGGTAAACCACTCATTAATCATCTGGAAGAAGGCTTCCTTAGCCTCT
* * *
42633878 CCTCCCCGGTCCTCAAATATGGGCTTGCTACCACTCACCGCTGCTTTGTGAACAGAGGCTTATGC
66 CCTCCCCGGTCCTCAAATATGGGCTTACTACCACTCACCGCTGCTCTGTAAACAGAGGCTTATGC
42633943 GTTACTTTCAACCTCATCTAAATTAGCTCGGTTGGATGACATTATCT
131 GTTACTTTCAACCTCATCTAAATTAGCTCGGTTGGATGACATTATCT
42633990 ATATGAAACC
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 167 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (183 bp):
GGTTCGTTCGTACGAACTCGGTAAACCACTCATTAATCATCTGGAAGAAGGCTTCCTTAGCCTCT
CCTCCCCGGTCCTCAAATATGGGCTTACTACCACTCACCGCTGCTCTGTAAACAGAGGCTTATGC
GTTACTTTCAACCTCATCTAAATTAGCTCGGTTGGATGACATTATCTCTATCA
Found at i:42646016 original size:17 final size:18
Alignment explanation
Indices: 42645984--42646022 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
42645974 TCTATAACAA
42645984 AAAATACAAGATGTTTTAC
1 AAAATACAAGATGTTTT-C
42646003 AAAATA-AA-ATGTTTTC
1 AAAATACAAGATGTTTTC
42646019 AAAA
1 AAAA
42646023 GGTAAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 2 0.10
19 6 0.30
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (18 bp):
AAAATACAAGATGTTTTC
Found at i:42646763 original size:28 final size:28
Alignment explanation
Indices: 42646731--42646886 Score: 163
Period size: 28 Copynumber: 5.6 Consensus size: 28
42646721 TGAAGGACGT
* *
42646731 CTTTGTGGAAATCTCTGTTAAAGGAAAC
1 CTTTGTGGAGATCTCTGTTAAAGGAAGC
* * *
42646759 CTTTGTGGTGATCTCTATTAAAGGAAGT
1 CTTTGTGGAGATCTCTGTTAAAGGAAGC
*
42646787 CTTTGTGGTGATCTCTGTTAAAGGAAGC
1 CTTTGTGGAGATCTCTGTTAAAGGAAGC
* *
42646815 CTTTGTGGAAATCTTTG-TAAAGGAAGC
1 CTTTGTGGAGATCTCTGTTAAAGGAAGC
* * *
42646842 CTTTGT-GATGATCTCTATTAAAAGAAAC
1 CTTTGTGGA-GATCTCTGTTAAAGGAAGC
* **
42646870 ATTTGTGGCTATCTCTG
1 CTTTGTGGAGATCTCTG
42646887 AAAAAGGGAA
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
26 2 0.02
27 21 0.20
28 82 0.77
29 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (28 bp):
CTTTGTGGAGATCTCTGTTAAAGGAAGC
Found at i:42646809 original size:56 final size:55
Alignment explanation
Indices: 42646723--42646885 Score: 186
Period size: 55 Copynumber: 2.9 Consensus size: 55
42646713 ACACTAGATG
* **
42646723 AAGGACGTCTTTGTGGAAATCTCTGTTAAAGGAAACCTTTGTGGTGATCTCTAT-TA
1 AAGGAAGTCTTTGTGGTGATCTCTGTTAAAGGAAACCTTTGTGGT-ATCTCT-TGTA
* *
42646779 AAGGAAGTCTTTGTGGTGATCTCTGTTAAAGGAAGCCTTTGTGGAAATCT-TTGTA
1 AAGGAAGTCTTTGTGGTGATCTCTGTTAAAGGAAACCTTTGTGG-TATCTCTTGTA
* * * * *
42646834 AAGGAAGCCTTTGTGATGATCTCTATTAAAAGAAACATTTGTGGCTATCTCT
1 AAGGAAGTCTTTGTGGTGATCTCTGTTAAAGGAAACCTTTGTGG-TATCTCT
42646886 GAAAAAGGGA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
54 1 0.01
55 45 0.49
56 45 0.49
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (55 bp):
AAGGAAGTCTTTGTGGTGATCTCTGTTAAAGGAAACCTTTGTGGTATCTCTTGTA
Found at i:42646875 original size:83 final size:84
Alignment explanation
Indices: 42646731--42646886 Score: 228
Period size: 83 Copynumber: 1.9 Consensus size: 84
42646721 TGAAGGACGT
* * *
42646731 CTTTGTGGAAATCTCTGTTAAAGGAAACCTTTGTGGTGATCTCTATTAAAGGAAGTCTTTGTGG-
1 CTTTGTGGAAATCTCTGTTAAAGGAAACCTTTGTGATGATCTCTATTAAAAGAAGACTTTGTGGC
42646795 TGATCTCTGTTAAAGGAAGC
66 T-ATCTCTGTTAAAGGAAGC
* *
42646815 CTTTGTGGAAATCTTTG-TAAAGGAAGCCTTTGTGATGATCTCTATTAAAAGAA-ACATTTGTGG
1 CTTTGTGGAAATCTCTGTTAAAGGAAACCTTTGTGATGATCTCTATTAAAAGAAGAC-TTTGTGG
42646878 CTATCTCTG
65 CTATCTCTG
42646887 AAAAAGGGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
82 1 0.02
83 47 0.72
84 17 0.26
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (84 bp):
CTTTGTGGAAATCTCTGTTAAAGGAAACCTTTGTGATGATCTCTATTAAAAGAAGACTTTGTGGC
TATCTCTGTTAAAGGAAGC
Found at i:42651605 original size:24 final size:24
Alignment explanation
Indices: 42651578--42651623 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42651568 TTAAAACTAC
42651578 TTCTAAAGAAAACTC-AAGAGAAAA
1 TTCTAAA-AAAACTCAAAGAGAAAA
* *
42651602 TTCTTAAATAACTCAAAGAGAA
1 TTCTAAAAAAACTCAAAGAGAA
42651624 TTTTCACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (24 bp):
TTCTAAAAAAACTCAAAGAGAAAA
Found at i:42668737 original size:26 final size:26
Alignment explanation
Indices: 42668708--42668769 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
42668698 TAAAATACAA
42668708 GTTGAGAGGTAAATGATAATTTTATC
1 GTTGAGAGGTAAATGATAATTTTATC
42668734 GTTGAGAGGTAAATGATAATTTTATC
1 GTTGAGAGGTAAATGATAATTTTATC
*
42668760 ATTGAG-GGTA
1 GTTGAGAGGTA
42668770 TTTTGGTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (26 bp):
GTTGAGAGGTAAATGATAATTTTATC
Found at i:42678669 original size:21 final size:22
Alignment explanation
Indices: 42678645--42678688 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
42678635 AGAATGAAGC
* *
42678645 TTGATGGATGCTT-CGGGATGA
1 TTGAGGGATGCTTGAGGGATGA
42678666 TTGAGGGATGCTTGAGGGATGA
1 TTGAGGGATGCTTGAGGGATGA
42678688 T
1 T
42678689 GAATGAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.20, C:0.07, G:0.41, T:0.32
Consensus pattern (22 bp):
TTGAGGGATGCTTGAGGGATGA
Found at i:42678673 original size:11 final size:11
Alignment explanation
Indices: 42678659--42678688 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
42678649 TGGATGCTTC
42678659 GGGATGATTGA
1 GGGATGATTGA
*
42678670 GGGATGCTTGA
1 GGGATGATTGA
42678681 GGGATGAT
1 GGGATGAT
42678689 GAATGAAGGA
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:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (11 bp):
GGGATGATTGA
Found at i:42685437 original size:254 final size:254
Alignment explanation
Indices: 42684975--42685487 Score: 717
Period size: 254 Copynumber: 2.0 Consensus size: 254
42684965 CTTCATCCTC
* * * *
42684975 CAAAAGGTCAAGATCTAAGGCTTTCTCTAATGGATCTTCTTTAAAATTGCTTTCTATAGAAACCA
1 CAAAAGGTCAAGATCTAAGGCTTTCTCCAATGGATCTTCCTCAAAATTGCTTTCCATAGAAACCA
* * *
42685040 AGGTTTCTATATCTTCCATAACTGAACACTACTTTATCGGATCGGGAAATTTCATCACTTTAAGA
66 AGGTTTCTATATCTTCCATAACTGAACACTACTTTATAGGATCAGAAAATTTCATCACTTTAAGA
* * * *
42685105 ATTTTAAAGGTTAACTGATCATTTTAAACTCACATGGTGAGTTCTCCTTTCTACACATCAATTAA
131 ATGTTAAAGGTTAACTGATCATTTTAAACACACATGGTGAGTTCCCCTTTCTACACATAAATTAA
* * * *
42685170 CGTTCTTCCCGTGGCTAAGAAAGGTCTCCTAAGGATGATCGACACGTCCTTGTCTGCTT
196 AGTTCTTCCCGTGGCTAAGAAAGGTCTCCCAAGGATAATCGACACGTCCTTATCTGCTT
*
42685229 CAAAGGGTCAA-ACTCTAAGGCTTTCTCCAATGGATCTTCCTCAAAATTGCTTTCCATAGAAACC
1 CAAAAGGTCAAGA-TCTAAGGCTTTCTCCAATGGATCTTCCTCAAAATTGCTTTCCATAGAAACC
* * * *
42685293 AAGGTTTCTATTTCTTCCATAACTGAACACT-CTTCTGTTAGG-TTAGAAAATTTCATCGCTTTA
65 AAGGTTTCTATATCTTCCATAACTGAACACTACTT-T-ATAGGATCAGAAAATTTCATCACTTTA
* * * * * *
42685356 AGAATGTTAAAGGTTACCTGATCGTTTTGAACACGCATGGTGAGTTCCCCTTTTTGCACATAAAT
128 AGAATGTTAAAGGTTAACTGATCATTTTAAACACACATGGTGAGTTCCCCTTTCTACACATAAAT
* * *
42685421 TAAAGTTCTTCCCGTGGCTAAGAAAGGTCTCCCAAGGATAATTGGCACTTCCTTATCTGCTT
193 TAAAGTTCTTCCCGTGGCTAAGAAAGGTCTCCCAAGGATAATCGACACGTCCTTATCTGCTT
42685483 CAAAA
1 CAAAA
42685488 TCTAAAATAA
Statistics
Matches: 226, Mismatches: 30, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
253 4 0.02
254 219 0.97
255 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (254 bp):
CAAAAGGTCAAGATCTAAGGCTTTCTCCAATGGATCTTCCTCAAAATTGCTTTCCATAGAAACCA
AGGTTTCTATATCTTCCATAACTGAACACTACTTTATAGGATCAGAAAATTTCATCACTTTAAGA
ATGTTAAAGGTTAACTGATCATTTTAAACACACATGGTGAGTTCCCCTTTCTACACATAAATTAA
AGTTCTTCCCGTGGCTAAGAAAGGTCTCCCAAGGATAATCGACACGTCCTTATCTGCTT
Found at i:42685810 original size:33 final size:33
Alignment explanation
Indices: 42685767--42685832 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
42685757 TTTGTTCTGT
* * *
42685767 AGGAACGCACTGCACTCTTTTGTCAAGGCAACA
1 AGGAACGCACTACACTCATTTGTCAAGCCAACA
*
42685800 AGGAATGCACTACACTCATTTGTCAAGCCAACA
1 AGGAACGCACTACACTCATTTGTCAAGCCAACA
42685833 GTCTCATACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (33 bp):
AGGAACGCACTACACTCATTTGTCAAGCCAACA
Found at i:42690575 original size:22 final size:22
Alignment explanation
Indices: 42690558--42690600 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42690548 CTATGTTGTG
*
42690558 ACATTAATCATACCATGTTGCA
1 ACATCAATCATACCATGTTGCA
42690580 ACATCAATCATACCATGTTGC
1 ACATCAATCATACCATGTTGC
42690601 GATGTAGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (22 bp):
ACATCAATCATACCATGTTGCA
Found at i:42691317 original size:22 final size:22
Alignment explanation
Indices: 42691278--42691327 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
42691268 CATGTAAGTG
* *
42691278 AATTTTTAACCCAGTTTTCGTC
1 AATTTTTAACCCAGTTTTCATA
* * *
42691300 AATTTTTAATCTATTTTTCATA
1 AATTTTTAACCCAGTTTTCATA
42691322 AATTTT
1 AATTTT
42691328 ATGTTTTGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.54
Consensus pattern (22 bp):
AATTTTTAACCCAGTTTTCATA
Found at i:42698395 original size:110 final size:109
Alignment explanation
Indices: 42698240--42698695 Score: 603
Period size: 110 Copynumber: 4.2 Consensus size: 109
42698230 CTAACCAGAT
* *
42698240 TGGCAGATCATGATACATGAATGTGTGTAAGACCATATGGTTAAGACCCATGGCATGATATGTCT
1 TGGCAAATCACGATACATGAATGTGTGTAAGACCATATGGTTAAGACCCATGGCATGATATGTCT
* *
42698305 GTATTTATATTCATGGTGTAACATGCGATAGTGTATGAATCGAAA
66 GTATTTATATTCATGGTGTAGC-TTCGATAGTGTATGAATCGAAA
* * *
42698350 TGGCAAATCACGATACATGAATGTGTGTAAG-CTCATGTGGCTAAGACTCATGGCATGATATGTC
1 TGGCAAATCACGATACATGAATGTGTGTAAGAC-CATATGGTTAAGACCCATGGCATGATATGTC
*
42698414 TATATTTATATTCATGGTGTAGTCTTCGATAGTGTATGAATCGAAA
65 TGTATTTATATTCATGGTGTAG-CTTCGATAGTGTATGAATCGAAA
* * * * *
42698460 CGGCAAATCAAGGTACATGAATGTGTGTAAGACCATGTGGTTATA-ACCCATGGCATGATATATC
1 TGGCAAATCACGATACATGAATGTGTGTAAGACCATATGGTTA-AGACCCATGGCATGATATGTC
*
42698524 TGTATTTATATTCATGGTGTAGCCTTCGGTAGTGTATGAATCGAAA
65 TGTATTTATATTCATGGTGTAG-CTTCGATAGTGTATGAATCGAAA
* * * * * * * *
42698570 TGGTATATCACGATACTTGAATATGTGTAAAACCATATAGTTAAGACCCATGGTATGATATGTAT
1 TGGCAAATCACGATACATGAATGTGTGTAAGACCATATGGTTAAGACCCATGGCATGATATGTCT
* *
42698635 GTATTCATATTCATGGTGTAGCTTTCGATAGTGTATAAATC-AAA
66 GTATTTATATTCATGGTGTAGC-TTCGATAGTGTATGAATCGAAA
* *
42698679 TGGCAGATCATGATACA
1 TGGCAAATCACGATACA
42698696 CAAAATTATG
Statistics
Matches: 303, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
109 19 0.06
110 281 0.93
111 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (109 bp):
TGGCAAATCACGATACATGAATGTGTGTAAGACCATATGGTTAAGACCCATGGCATGATATGTCT
GTATTTATATTCATGGTGTAGCTTCGATAGTGTATGAATCGAAA
Found at i:42703755 original size:50 final size:50
Alignment explanation
Indices: 42703673--42703864 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
42703663 ATTTGGGTAA
42703673 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
*
42703723 AGAGGTCTCATGTAAGACCATGTCT-GGTACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGG-ACATGGCATTGGCACCGAGATG
** * * *
42703773 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
** * * *
42703823 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
42703865 GTACAAGAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.02
50 121 0.97
51 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATG
Found at i:42703898 original size:49 final size:50
Alignment explanation
Indices: 42703678--42703903 Score: 204
Period size: 50 Copynumber: 4.5 Consensus size: 50
42703668 GGTAAAGAGG
* * * * * **
42703678 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC
* * * * * * **
42703728 TCTCATGTAAGACCATGTCTGGTACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC
** * * *
42703778 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC
* * * *
42703828 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC
*
42703876 ATCCCATGTAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
42703904 AGCTTTGGCA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
48 3 0.02
49 29 0.19
50 118 0.79
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAAC
Found at i:42705910 original size:37 final size:37
Alignment explanation
Indices: 42705860--42705938 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42705850 TTATTACGAA
* * *
42705860 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
42705897 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
42705934 GTCTT
1 GTCTT
42705939 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42706144 original size:47 final size:47
Alignment explanation
Indices: 42706057--42706704 Score: 909
Period size: 47 Copynumber: 13.4 Consensus size: 47
42706047 CCTTTCGGGA
* * * * * * * * *
42706057 CTTATCACATTTTTTCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706104 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706151 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42706198 CTTATTACACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTA-T---CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42706249 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42706296 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706343 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42706390 CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAC----ACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706441 CTGATCACATATATACATACACTTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
42706492 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706541 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42706588 CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAC----ACTTTCACATTCATCACATCGGCCATTAGGC
* *
42706639 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42706686 CTTATCACACATATACACT
1 CTTATCACATATATACACT
42706705 CTCTTGGCTG
Statistics
Matches: 552, Mismatches: 33, Indels: 32
0.89 0.05 0.05
Matches are distributed among these distances:
47 328 0.59
48 1 0.00
49 51 0.09
50 1 0.00
51 163 0.30
53 4 0.01
55 4 0.01
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42706701 original size:98 final size:98
Alignment explanation
Indices: 42706109--42706702 Score: 970
Period size: 98 Copynumber: 6.1 Consensus size: 98
42706099 TCGGCCCTGT
42706109 CACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
42706172 CACATTCATCACATCGGCTATTAGGCCTTATTA
66 CACATTCATCACATCGGCTATTAGGCCTTATTA
* * *
42706205 CACACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTT
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
* *
42706270 CACATTCATCGCATCGGCCATTAGGCCTTA-T-
66 CACATTCATCACATCGGCTATTAGGCCTTATTA
42706301 CACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
42706364 CACATTCATCACATCGGCTATTAGGCCTTATTA
66 CACATTCATCACATCGGCTATTAGGCCTTATTA
* * * *
42706397 CATATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTGATCACATATATACATACA
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTAC--ATAT--ATACA
* *
42706462 CTTTCTCATTCATCACATCGGCCATTAGGCCTTA-T-
62 CTTTCACATTCATCACATCGGCTATTAGGCCTTATTA
42706497 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
42706562 CACATTCATCACATCGGCTATTAGGCCTTATTA
66 CACATTCATCACATCGGCTATTAGGCCTTATTA
* *
42706595 CATATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
1 CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
*
42706660 CACATTCATCACATCGGCTATTAGGCCTTATCA
66 CACATTCATCACATCGGCTATTAGGCCTTATTA
42706693 CACATATACA
1 CACATATACA
42706703 CTCTCTTGGC
Statistics
Matches: 462, Mismatches: 24, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
94 83 0.18
95 1 0.00
96 55 0.12
97 2 0.00
98 231 0.50
100 52 0.11
101 1 0.00
102 37 0.08
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (98 bp):
CACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTT
CACATTCATCACATCGGCTATTAGGCCTTATTA
Found at i:42711462 original size:20 final size:19
Alignment explanation
Indices: 42711399--42711758 Score: 141
Period size: 20 Copynumber: 18.0 Consensus size: 19
42711389 GATGGATAAT
*
42711399 AGGGGCACCAAAGTGCAATC
1 AGGGGCA-CGAAGTGCAATC
*
42711419 AGGAGCACGAATGTGCAATC
1 AGGGGCACGAA-GTGCAATC
42711439 AGGGGCACTGAAGTGCAAAT-
1 AGGGGCAC-GAAGTGC-AATC
* * *
42711459 AGGGTCACAGATGTGCATTC
1 AGGGGCAC-GAAGTGCAATC
* * * *
42711479 AGGCGTACTGAAGTACAAAC
1 AGGGGCAC-GAAGTGCAATC
*
42711499 AAGGGCACGTAAGTGCAATC
1 AGGGGCACG-AAGTGCAATC
* * *
42711519 TA-GGGTATCGAAGTACAAAC
1 -AGGGGCA-CGAAGTGCAATC
* *
42711539 AGGGGCATGTAAGTGCAATT
1 AGGGGCACG-AAGTGCAATC
** * *
42711559 AGGGTTATCGAAGTACAAAC
1 AGGGGCA-CGAAGTGCAATC
42711579 AGGGGCACGTAAGTGCAATC
1 AGGGGCACG-AAGTGCAATC
* * ** *
42711599 TA-GGGTACTAAAGTATAAAC
1 -AGGGGCAC-GAAGTGCAATC
*
42711619 AGGGGCATGTAAGTGCAATC
1 AGGGGCACG-AAGTGCAATC
* * * * *
42711639 AAGGGTATCAAAGTACAAAC
1 AGGGGCA-CGAAGTGCAATC
* *
42711659 AAGGGCATGTAAGTGCAATC
1 AGGGGCACG-AAGTGCAATC
* * * *
42711679 AGGCGTACCGAAGTACAAAC
1 AGGGGCA-CGAAGTGCAATC
42711699 AGGGGCACGTAAGTGCAATC
1 AGGGGCACG-AAGTGCAATC
* * *
42711719 AGGGGTATCGAAGTACAAAC
1 AGGGGCA-CGAAGTGCAATC
* *
42711739 AAGGGCACATAAGTGCAATC
1 AGGGGCAC-GAAGTGCAATC
42711759 TTTCAATAAT
Statistics
Matches: 241, Mismatches: 78, Indels: 42
0.67 0.22 0.12
Matches are distributed among these distances:
19 14 0.06
20 213 0.88
21 14 0.06
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.17
Consensus pattern (19 bp):
AGGGGCACGAAGTGCAATC
Found at i:42711515 original size:40 final size:39
Alignment explanation
Indices: 42711471--42711758 Score: 364
Period size: 40 Copynumber: 7.2 Consensus size: 39
42711461 GGTCACAGAT
* *
42711471 GTGCATTCAGGCGTA-CTGAAGTACAAACAAGGGCACGTAA
1 GTGCAATCAGG-GTATC-GAAGTACAAACAGGGGCACGTAA
*
42711511 GTGCAATCTAGGGTATCGAAGTACAAACAGGGGCATGTAA
1 GTGCAATC-AGGGTATCGAAGTACAAACAGGGGCACGTAA
*
42711551 GTGCAATTAGGGTTATCGAAGTACAAACAGGGGCACGTAA
1 GTGCAATCAGGG-TATCGAAGTACAAACAGGGGCACGTAA
* * *
42711591 GTGCAATCTAGGGTA-CTAAAGTATAAACAGGGGCATGTAA
1 GTGCAATC-AGGGTATC-GAAGTACAAACAGGGGCACGTAA
* * *
42711631 GTGCAATCAAGGGTATCAAAGTACAAACAAGGGCATGTAA
1 GTGCAATC-AGGGTATCGAAGTACAAACAGGGGCACGTAA
*
42711671 GTGCAATCAGGCGTACCGAAGTACAAACAGGGGCACGTAA
1 GTGCAATCAGG-GTATCGAAGTACAAACAGGGGCACGTAA
* *
42711711 GTGCAATCAGGGGTATCGAAGTACAAACAAGGGCACATAA
1 GTGCAATCA-GGGTATCGAAGTACAAACAGGGGCACGTAA
42711751 GTGCAATC
1 GTGCAATC
42711759 TTTCAATAAT
Statistics
Matches: 221, Mismatches: 19, Indels: 16
0.86 0.07 0.06
Matches are distributed among these distances:
39 8 0.04
40 202 0.91
41 11 0.05
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (39 bp):
GTGCAATCAGGGTATCGAAGTACAAACAGGGGCACGTAA
Found at i:42711644 original size:120 final size:120
Alignment explanation
Indices: 42711431--42711758 Score: 421
Period size: 120 Copynumber: 2.7 Consensus size: 120
42711421 GAGCACGAAT
* * * * * * * * *
42711431 GTGCAATCAGGGGCACTGAAGTGCAAATAGGGTCACAG-ATGTGCATTCAGGCGTACTGAAGTAC
1 GTGCAATCAGGCGTACCGAAGTACAAACAGGGGCAC-GTAAGTGCAATCAGGGGTACTGAAGTAC
* * *
42711495 AAACAAGGGCACGTAAGTGCAATCTAGGGTATCGAAGTACAAACAGGGGCATGTAA
65 AAACAAGGGCACGTAAGTGCAATCAAGGGTATCAAAGTACAAACAAGGGCATGTAA
* * *
42711551 GTGCAATTAGG-GTTATCGAAGTACAAACAGGGGCACGTAAGTGCAATCTA-GGGTACTAAAGTA
1 GTGCAATCAGGCG-TACCGAAGTACAAACAGGGGCACGTAAGTGCAATC-AGGGGTACTGAAGTA
* * *
42711614 TAAACAGGGGCATGTAAGTGCAATCAAGGGTATCAAAGTACAAACAAGGGCATGTAA
64 CAAACAAGGGCACGTAAGTGCAATCAAGGGTATCAAAGTACAAACAAGGGCATGTAA
42711671 GTGCAATCAGGCGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTA-TCGAAGTAC
1 GTGCAATCAGGCGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACT-GAAGTAC
*
42711735 AAACAAGGGCACATAAGTGCAATC
65 AAACAAGGGCACGTAAGTGCAATC
42711759 TTTCAATAAT
Statistics
Matches: 178, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
119 4 0.02
120 172 0.97
121 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (120 bp):
GTGCAATCAGGCGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTACTGAAGTACA
AACAAGGGCACGTAAGTGCAATCAAGGGTATCAAAGTACAAACAAGGGCATGTAA
Found at i:42714766 original size:24 final size:23
Alignment explanation
Indices: 42714739--42714783 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
42714729 GGTTTACAAA
42714739 TTTAAATCATAGAAAAAAAACATT
1 TTTAAATCATA-AAAAAAAACATT
** *
42714763 TTTATTTTATAAAAAAAAACA
1 TTTAAATCATAAAAAAAAACA
42714784 ACAGTTACGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TTTAAATCATAAAAAAAAACATT
Found at i:42722093 original size:18 final size:18
Alignment explanation
Indices: 42722072--42722111 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42722062 GATTGAGAGT
* * *
42722072 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
42722090 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
42722108 GAAA
1 GAAA
42722112 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:42723723 original size:19 final size:19
Alignment explanation
Indices: 42723699--42723735 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42723689 TGAAGGCAAG
42723699 GCCCAAT-AAGGAAATTCCA
1 GCCCAATCAA-GAAATTCCA
42723718 GCCCAATCAAGAAATTCC
1 GCCCAATCAAGAAATTCC
42723736 TACATACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (19 bp):
GCCCAATCAAGAAATTCCA
Found at i:42732208 original size:20 final size:22
Alignment explanation
Indices: 42732183--42732228 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
42732173 TTAATCGATG
42732183 GTCGTCA-CATCCC-TTTCATA
1 GTCGTCACCATCCCTTTTCATA
42732203 GTCGTCACCATCCCTTTTCATA
1 GTCGTCACCATCCCTTTTCATA
42732225 GTCG
1 GTCG
42732229 ATAGTCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.35
Consensus pattern (22 bp):
GTCGTCACCATCCCTTTTCATA
Found at i:42732244 original size:29 final size:29
Alignment explanation
Indices: 42732200--42732339 Score: 122
Period size: 29 Copynumber: 4.8 Consensus size: 29
42732190 CATCCCTTTC
* * *
42732200 ATAGTCGTCACCATCCCTTTTCATAGTCG
1 ATAGTCATAACCATCCCTTTTCATAATCG
* * *
42732229 ATAGTCGA-AACTATCCCTTATCATAATCA
1 ATAGTC-ATAACCATCCCTTTTCATAATCG
* * * *
42732258 ATGGTCATCACCATCCCTTTTCATAGTTG
1 ATAGTCATAACCATCCCTTTTCATAATCG
* *
42732287 ATGGTCATCACCATCCCTTTTCATAATCG
1 ATAGTCATAACCATCCCTTTTCATAATCG
* *
42732316 ATAGTCA-AAGCTATCACTTTTCAT
1 ATAGTCATAA-CCATCCCTTTTCAT
42732340 TGGTCGATGA
Statistics
Matches: 89, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
28 2 0.02
29 87 0.98
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (29 bp):
ATAGTCATAACCATCCCTTTTCATAATCG
Found at i:42733881 original size:21 final size:21
Alignment explanation
Indices: 42733856--42733896 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42733846 ATGAGAATCA
42733856 TACAAATACAATGATGAAATT
1 TACAAATACAATGATGAAATT
*
42733877 TACAAGTACAATGATGAAAT
1 TACAAATACAATGATGAAAT
42733897 CACAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (21 bp):
TACAAATACAATGATGAAATT
Found at i:42738500 original size:140 final size:140
Alignment explanation
Indices: 42738248--42738530 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
42738238 TGATGGGAAG
* *
42738248 TACATTACACGTATTCTTAAAGTAAATTTTGTCTGGTTTTGTAGTTGTTTTTTCTATAAACTTTC
1 TACATTACACATATTCTTAAAGTAAATTTTGTCTGGTTTTGTAGTTGTTTTTGCTATAAACTTTC
42738313 TGTGTAAAAGCAAAATCACAATTTGATTAATTTGAAGAAATGACAGAATTGTAACATCAATTCCT
66 TGTGTAAAAGCAAAATCACAATTTGATTAATTTGAAGAAATGACAGAATTGTAACATCAATTCCT
42738378 ACGAAGACAC
131 ACGAAGACAC
42738388 TACATTACACATATTCTTAAAGTAAATTTTGTCTGGTTTTGTAGTTGTTTTTGCTATAAACTTTC
1 TACATTACACATATTCTTAAAGTAAATTTTGTCTGGTTTTGTAGTTGTTTTTGCTATAAACTTTC
*
42738453 TGTGTAAAAGTAAAATCACAATTTGATTAATTTGAAGAAATGACAGAATTGTAACATCAATTCCT
66 TGTGTAAAAGCAAAATCACAATTTGATTAATTTGAAGAAATGACAGAATTGTAACATCAATTCCT
*
42738518 TCGAAGACAC
131 ACGAAGACAC
42738528 TAC
1 TAC
42738531 TTTGATTTTA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (140 bp):
TACATTACACATATTCTTAAAGTAAATTTTGTCTGGTTTTGTAGTTGTTTTTGCTATAAACTTTC
TGTGTAAAAGCAAAATCACAATTTGATTAATTTGAAGAAATGACAGAATTGTAACATCAATTCCT
ACGAAGACAC
Found at i:42741941 original size:41 final size:41
Alignment explanation
Indices: 42741884--42742020 Score: 186
Period size: 41 Copynumber: 3.4 Consensus size: 41
42741874 CTTTCGGGAA
* * *
42741884 TTTAGCGGCGTTTTTGGAGAAGTGCCTCTAATGCTCCGGGC
1 TTTAGCGGCGTTTTTGGAGAAGCGCCACTAATGCTCAGGGC
* * *
42741925 TTTAGCGGCGTTTTTGGAGAAACGCCGCTAATGTTCAGGGC
1 TTTAGCGGCGTTTTTGGAGAAGCGCCACTAATGCTCAGGGC
* **
42741966 TTTAGCGGCGTTTTTGGAAAAGCGCCACTAATGCTCAATGC
1 TTTAGCGGCGTTTTTGGAGAAGCGCCACTAATGCTCAGGGC
42742007 -TTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
42742021 TAAAAAGCGC
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 14 0.16
41 71 0.84
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAGAAGCGCCACTAATGCTCAGGGC
Found at i:42742460 original size:14 final size:15
Alignment explanation
Indices: 42742433--42742461 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42742423 AGGTTTATAT
42742433 ATTATGGAATTAGGG
1 ATTATGGAATTAGGG
42742448 ATTATGG-ATTAGGG
1 ATTATGGAATTAGGG
42742462 GTTCTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (15 bp):
ATTATGGAATTAGGG
Found at i:42742515 original size:14 final size:14
Alignment explanation
Indices: 42742496--42742526 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42742486 AGGGGTTAGG
42742496 GTTAGAGATTAAGA
1 GTTAGAGATTAAGA
*
42742510 GTTAGAGATTTAGA
1 GTTAGAGATTAAGA
42742524 GTT
1 GTT
42742527 TATAGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (14 bp):
GTTAGAGATTAAGA
Found at i:42742702 original size:21 final size:21
Alignment explanation
Indices: 42742678--42742723 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42742668 TAAATAAGGT
42742678 TTAGGGG-TCAGTAGTTAGGGG
1 TTAGGGGTTCA-TAGTTAGGGG
* *
42742699 TTAGGGGTTTATGGTTAGGGG
1 TTAGGGGTTCATAGTTAGGGG
42742720 TTAG
1 TTAG
42742724 AGCTTAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.17, C:0.02, G:0.46, T:0.35
Consensus pattern (21 bp):
TTAGGGGTTCATAGTTAGGGG
Found at i:42744071 original size:16 final size:17
Alignment explanation
Indices: 42744044--42744081 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
42744034 TAGGTTTTTA
42744044 TTTCTATTTGGGGTTCT
1 TTTCTATTTGGGGTTCT
42744061 TTTCT-TTTGGGGTTCT
1 TTTCTATTTGGGGTTCT
42744077 TTTCT
1 TTTCT
42744082 GGGTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.03, C:0.13, G:0.21, T:0.63
Consensus pattern (17 bp):
TTTCTATTTGGGGTTCT
Found at i:42747725 original size:27 final size:27
Alignment explanation
Indices: 42747695--42747750 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
42747685 AATTTCGAGG
*
42747695 TTTACAATTTT-TAATTTTTATTAATTA
1 TTTAC-ATTTTCTAACTTTTATTAATTA
* *
42747722 TTTACGTTTTCTCACTTTTATTAATTA
1 TTTACATTTTCTAACTTTTATTAATTA
42747749 TT
1 TT
42747751 ATTATTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTACATTTTCTAACTTTTATTAATTA
Found at i:42748055 original size:43 final size:42
Alignment explanation
Indices: 42747938--42748162 Score: 190
Period size: 43 Copynumber: 5.3 Consensus size: 42
42747928 GATATGTTTT
* ** * *
42747938 TAGCGGCGTTTTTGCAAGAAGTGTCGCTAAAGGT-TTGTTCTA
1 TAGCGGCGTTTGTGCAA-AAACGCCGCTAAAGGTCATGTTCTA
* * *
42747980 TAGCGGCGTTTGTGATAAAAAGCGCCGTTAAAGGTCATGTTCTT
1 TAGCGGCGTTTGTG-CAAAAA-CGCCGCTAAAGGTCATGTTCTA
* *
42748024 TAGCGGCGTTTGTGACAAAAATGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTG-CAAAAACGCCGCTAAAGGTCATGTTCTA
* * *
42748067 TAGTGGCGTTTGTGGGAAAAGA-GCCGCTAAAGGGCATGGTT-TA
1 TAGCGGCGTTTGT-GCAAAA-ACGCCGCTAAAGGTCAT-GTTCTA
* * *
42748110 TAGCGGCATTTGTGGAAAAGCGCCGCTAAAGGTCATGACTT-T-
1 TAGCGGCGTTTGTGCAAAAACGCCGCTAAAGGTCATG--TTCTA
42748152 TAGCGGCGTTT
1 TAGCGGCGTTT
42748163 ATTTCTAAAA
Statistics
Matches: 152, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 45 0.30
43 76 0.50
44 30 0.20
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTGTGCAAAAACGCCGCTAAAGGTCATGTTCTA
Found at i:42748056 original size:86 final size:84
Alignment explanation
Indices: 42747931--42748146 Score: 245
Period size: 86 Copynumber: 2.5 Consensus size: 84
42747921 TCTGCATGAT
* * * *
42747931 ATGTTTTTAGCGGCGTTTTTGCAAGAAGTGTCGCTAAAGGT-TTGTTCTATAGCGGCGTTTGTGA
1 ATGTTTTTAGCGGCGTTTGTGCAA-AAGTGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTG-
* * * *
42747995 TAAAAAGCGCCGTTAAAGGTC
64 GAAAAAGAGCCGCTAAAGGGC
* *
42748016 ATGTTCTTTAGCGGCGTTTGTGACAAAAATGCCGCTAAAGGTCATGGTCTATAGTGGCGTTTGTG
1 ATGTT-TTTAGCGGCGTTTGTG-CAAAAGTGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTG
*
42748081 GGAAAAGAGCCGCTAAAGGGC
64 GAAAAAGAGCCGCTAAAGGGC
* * * *
42748102 ATGGTTTATAGCGGCATTTGTGGAAAAGCGCCGCTAAAGGTCATG
1 AT-GTTTTTAGCGGCGTTTGTGCAAAAGTGCCGCTAAAGGTCATG
42748147 ACTTTTAGCG
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
85 25 0.23
86 61 0.55
87 25 0.23
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (84 bp):
ATGTTTTTAGCGGCGTTTGTGCAAAAGTGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGA
AAAAGAGCCGCTAAAGGGC
Found at i:42748140 original size:42 final size:43
Alignment explanation
Indices: 42747962--42748162 Score: 205
Period size: 43 Copynumber: 4.7 Consensus size: 43
42747952 CAAGAAGTGT
* *
42747962 CGCTAAAGGT--TTGTTCTATAGCGGCGTTTGTGATAAAAAGCGC
1 CGCTAAAGGTCATGGTT-TATAGCGGCGTTTGTGA-GAAAAGCGC
* * * **
42748005 CGTTAAAGGTCAT-GTTCTTTAGCGGCGTTTGTGACAAAAATGC
1 CGCTAAAGGTCATGGTT-TATAGCGGCGTTTGTGAGAAAAGCGC
* * * *
42748048 CGCTAAAGGTCATGGTCTATAGTGGCGTTTGTGGGAAAAGAGC
1 CGCTAAAGGTCATGGTTTATAGCGGCGTTTGTGAGAAAAGCGC
* *
42748091 CGCTAAAGGGCATGGTTTATAGCGGCATTTGTG-GAAAAGCGC
1 CGCTAAAGGTCATGGTTTATAGCGGCGTTTGTGAGAAAAGCGC
*
42748133 CGCTAAAGGTCATGACTTT-TAGCGGCGTTT
1 CGCTAAAGGTCATG-GTTTATAGCGGCGTTT
42748163 ATTTCTAAAA
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
42 31 0.23
43 79 0.59
44 22 0.17
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (43 bp):
CGCTAAAGGTCATGGTTTATAGCGGCGTTTGTGAGAAAAGCGC
Found at i:42754364 original size:20 final size:19
Alignment explanation
Indices: 42754339--42754419 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 19
42754329 GTTGGAGTCT
42754339 GAATCGAGTTAAACAACAAA
1 GAATCGA-TTAAACAACAAA
* * *
42754359 GAATCGATTCAAAGAATAAT
1 GAATCGATT-AAACAACAAA
*
42754379 GAATCGATTAAATAAGCAAA
1 GAATCGATTAAACAA-CAAA
42754399 GAATCGATTTAAGACAACAAA
1 GAATCGA-TTAA-ACAACAAA
42754420 CAATTTATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.14
20 32 0.64
21 8 0.16
22 3 0.06
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (19 bp):
GAATCGATTAAACAACAAA
Found at i:42756503 original size:16 final size:16
Alignment explanation
Indices: 42756466--42756505 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42756456 TTAATAAAAT
* *
42756466 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42756482 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42756498 TAAAATTA
1 TAAAATTA
42756506 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42756575 original size:66 final size:67
Alignment explanation
Indices: 42756494--42756636 Score: 261
Period size: 68 Copynumber: 2.1 Consensus size: 67
42756484 AAATTAATTG
42756494 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
42756558 GA
66 GA
*
42756560 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
42756625 TGA
65 TGA
42756628 TTAGTAAAA
1 TTAGTAAAA
42756637 CAAACATGAT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 26 0.36
68 47 0.64
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:42756611 original size:9 final size:9
Alignment explanation
Indices: 42756578--42756605 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
42756568 TTTATCAAAT
42756578 TATTAATTG
1 TATTAATTG
42756587 TATTAATTG
1 TATTAATTG
42756596 TATTAATTG
1 TATTAATTG
42756605 T
1 T
42756606 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:42761549 original size:27 final size:26
Alignment explanation
Indices: 42761490--42761552 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
42761480 GGACTTTGTT
* *
42761490 TTAATTATAATAAAAATAATTAATAT
1 TTAATTTTAATAAAAATAATTAATAA
*
42761516 TTTATTTTAATAAAAATAATTGAATAA
1 TTAATTTTAATAAAAATAATT-AATAA
42761543 TTAATTTTAA
1 TTAATTTTAA
42761553 AAATATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TTAATTTTAATAAAAATAATTAATAA
Found at i:42763514 original size:20 final size:20
Alignment explanation
Indices: 42763477--42763513 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42763467 CCCAAATTAT
*
42763477 TTTTTTTCTTTTTCTTTTTG
1 TTTTTTTCTTCTTCTTTTTG
42763497 TTTTTTTC-TC-TCTTTTT
1 TTTTTTTCTTCTTCTTTTT
42763514 TATGCTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 1 0.06
20 8 0.50
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (20 bp):
TTTTTTTCTTCTTCTTTTTG
Found at i:42764558 original size:9 final size:10
Alignment explanation
Indices: 42764544--42764586 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
42764534 ATTAATATCC
42764544 AAAT-AAGTA
1 AAATAAAGTA
*
42764553 AAATAAAATA
1 AAATAAAGTA
42764563 AAATAAAGTAA
1 AAATAAAGT-A
42764574 TAAATAAAGTA
1 -AAATAAAGTA
42764585 AA
1 AA
42764587 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:42764580 original size:17 final size:17
Alignment explanation
Indices: 42764557--42764613 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
42764547 TAAGTAAAAT
*
42764557 AAAATAAAATAAAGTAA
1 AAAATAAAATAAAGAAA
* *
42764574 TAAATAAAGTAAAGAAA
1 AAAATAAAATAAAGAAA
42764591 AAAATAAAAATAAA-AATA
1 AAAAT-AAAATAAAGAA-A
42764609 AAAAT
1 AAAAT
42764614 TGGGTTGCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAATAAAATAAAGAAA
Found at i:42764598 original size:12 final size:12
Alignment explanation
Indices: 42764552--42764613 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
42764542 CCAAATAAGT
42764552 AAAAT-AAAAT-
1 AAAATAAAAATA
*
42764562 AAAAT-AAAGTA
1 AAAATAAAAATA
*
42764573 ATAAAT-AAAGTA
1 A-AAATAAAAATA
42764585 AAGAA-AAAAATA
1 AA-AATAAAAATA
42764597 AAAATAAAAATA
1 AAAATAAAAATA
42764609 AAAAT
1 AAAAT
42764614 TGGGTTGCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
10 9 0.20
11 4 0.09
12 32 0.71
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:42765211 original size:19 final size:19
Alignment explanation
Indices: 42765187--42765225 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
42765177 CAATTATGTC
42765187 AATACGATTTACGCTCAAG
1 AATACGATTTACGCTCAAG
*
42765206 AATACGATTTATGCTCAAG
1 AATACGATTTACGCTCAAG
42765225 A
1 A
42765226 TTTCGCTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (19 bp):
AATACGATTTACGCTCAAG
Found at i:42769336 original size:22 final size:20
Alignment explanation
Indices: 42769287--42769327 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
42769277 CACAATAGGC
42769287 TTGTCTTGAGACAATTTGCTA
1 TTGTCTTGAGAC-ATTTGCTA
42769308 TATGTCTTGAGACATTTGCT
1 T-TGTCTTGAGACATTTGCT
42769328 CGGTTGTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (20 bp):
TTGTCTTGAGACATTTGCTA
Found at i:42774265 original size:22 final size:21
Alignment explanation
Indices: 42774232--42774289 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
42774222 GACAATAGGC
*
42774232 TTGTCTCAAGACAATATGCT-A
1 TTGTCTCGAGACAAT-TGCTCA
42774253 TATGTCTCGAGACAATTGCTCGA
1 T-TGTCTCGAGACAATTGCTC-A
*
42774276 TTTTCTCGAGACAA
1 TTGTCTCGAGACAA
42774290 GGCTCCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 5 0.16
22 25 0.78
23 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (21 bp):
TTGTCTCGAGACAATTGCTCA
Found at i:42774924 original size:68 final size:68
Alignment explanation
Indices: 42774812--42774944 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 68
42774802 TTAATAAAAA
* *
42774812 TAATAAATTAAGGAAATTTATTTTAATAAGGACTTGAACATTAATTATAAAATATTTTATTAATA
1 TAATAAATTAAGGAAATTTACTTTAATAAGGACTTGAACATTAATGATAAAATATTTTATTAATA
42774877 TTT
66 TTT
* * ** * *
42774880 TAATAAATTAAGGAATTTTACTTTAATAAGGA-TTCTAATGTTAATGGTAATATATTTTATTAAT
1 TAATAAATTAAGGAAATTTACTTTAATAAGGACTT-GAACATTAATGATAAAATATTTTATTAAT
42774944 A
65 A
42774945 CATCATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 2 0.04
68 54 0.96
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (68 bp):
TAATAAATTAAGGAAATTTACTTTAATAAGGACTTGAACATTAATGATAAAATATTTTATTAATA
TTT
Found at i:42786714 original size:20 final size:21
Alignment explanation
Indices: 42786689--42786728 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42786679 AAGACCACTT
42786689 ACTTT-GGTATCGCGATATCC
1 ACTTTGGGTATCGCGATATCC
*
42786709 ACTTTGGGTATCGTGATATC
1 ACTTTGGGTATCGCGATATC
42786729 TACCTTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (21 bp):
ACTTTGGGTATCGCGATATCC
Found at i:42789005 original size:22 final size:22
Alignment explanation
Indices: 42788979--42789056 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
42788969 CTCGTTAACA
42788979 AATTTATTCATTTTTTATAGAC
1 AATTTATTCATTTTTTATAGAC
*
42789001 AATTTATT-AATTTTTATAGAC
1 AATTTATTCATTTTTTATAGAC
*
42789022 AATTTATTCATTTTGTATAGAC
1 AATTTATTCATTTTTTATAGAC
42789044 AATTTATTCATTT
1 AATTTATTCATTT
42789057 ATTCATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
21 20 0.38
22 32 0.62
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (22 bp):
AATTTATTCATTTTTTATAGAC
Found at i:42791964 original size:40 final size:40
Alignment explanation
Indices: 42791920--42792002 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
42791910 AGACTAACAG
*
42791920 AAGAAAAGGAAACAATACTAAACGTGTTTTTCATACTTTC
1 AAGAAAAGGAAACAATACTAAACGTGTCTTTCATACTTTC
42791960 AAGAAAAGGAAACAATACTAAACGTGTCTTTCATACTTTC
1 AAGAAAAGGAAACAATACTAAACGTGTCTTTCATACTTTC
42792000 AAG
1 AAG
42792003 CAATAACGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (40 bp):
AAGAAAAGGAAACAATACTAAACGTGTCTTTCATACTTTC
Found at i:42792243 original size:31 final size:29
Alignment explanation
Indices: 42792183--42792244 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
42792173 ATGTGGGGTG
**
42792183 TTATATAAAAATTTTAATTTTGTGTAATT
1 TTATATAAAAATTTTAATTTAATGTAATT
* *
42792212 TTATATATAAGATTTTAATTTAATTTAAATT
1 TTATATA-AAAATTTTAATTTAATGT-AATT
42792243 TT
1 TT
42792245 TAAAGAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.26
30 14 0.52
31 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (29 bp):
TTATATAAAAATTTTAATTTAATGTAATT
Found at i:42792626 original size:7 final size:7
Alignment explanation
Indices: 42792614--42792654 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
42792604 TTAGAATAAT
42792614 TTTAAAA
1 TTTAAAA
42792621 TTTAAAA
1 TTTAAAA
42792628 TTTAAAA
1 TTTAAAA
42792635 TTTAAAA
1 TTTAAAA
42792642 TTTAAAA
1 TTTAAAA
42792649 TATTAA
1 T-TTAA
42792655 TAACTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 29 0.88
8 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:42792756 original size:19 final size:17
Alignment explanation
Indices: 42792728--42792762 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
42792718 TATAATTTTT
42792728 AAATAATTTTATTCATTA
1 AAATAATTTTA-TCATTA
42792746 AAATAATTTTTATCATT
1 AAATAA-TTTTATCATT
42792763 TTCTCCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATAATTTTATCATTA
Found at i:42796130 original size:21 final size:21
Alignment explanation
Indices: 42796099--42796154 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
42796089 TACAGCCTAA
* *
42796099 CCACACAGGCGTGTCCTAAAG
1 CCACACGGGCGTGTCCCAAAG
*
42796120 CCACGCGGGCGTGTCCCAAAG
1 CCACACGGGCGTGTCCCAAAG
*
42796141 CCACATGGGCGTGT
1 CCACACGGGCGTGT
42796155 GACCCCTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.14
Consensus pattern (21 bp):
CCACACGGGCGTGTCCCAAAG
Found at i:42804101 original size:47 final size:47
Alignment explanation
Indices: 42804039--42804133 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
42804029 TTTAGTATGA
*
42804039 AATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATTTTACC
1 AATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATTTGACC
42804086 AATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATTTGACC
1 AATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATTTGACC
42804133 A
1 A
42804134 GTTTTAAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (47 bp):
AATTGTTTTGGAATATTAATGAGGAGGTCTTAAATAGCAATTTGACC
Found at i:42809235 original size:21 final size:21
Alignment explanation
Indices: 42809209--42809253 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
42809199 AAGGTAGTGG
42809209 GAAAAATATCTACCGTTGGTT
1 GAAAAATATCTACCGTTGGTT
42809230 GAAAAATATCTACCGTTGGTT
1 GAAAAATATCTACCGTTGGTT
42809251 GAA
1 GAA
42809254 TTTTCCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (21 bp):
GAAAAATATCTACCGTTGGTT
Done.