Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 193 of 198
Found at i:59953854 original size:2 final size:2
Alignment explanation
Indices: 59953847--59953881 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59953837 AACAGAGGTA
59953847 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
59953882 TTGGTTGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:59957430 original size:12 final size:12
Alignment explanation
Indices: 59957415--59957447 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
59957405 GGATTCAAAT
59957415 TGGAACTGGAAC
1 TGGAACTGGAAC
59957427 TGGAACTGGAAC
1 TGGAACTGGAAC
59957439 TGGAACTGG
1 TGGAACTGG
59957448 GATTCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.36, T:0.18
Consensus pattern (12 bp):
TGGAACTGGAAC
Found at i:59958996 original size:22 final size:22
Alignment explanation
Indices: 59958956--59958998 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59958946 ATTAATGTTT
* *
59958956 AATTTGATATTTAATTTTTTTC
1 AATTTGATACTTAAGTTTTTTC
*
59958978 AATTTGATACTTGAGTTTTTT
1 AATTTGATACTTAAGTTTTTT
59958999 TTTATCTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (22 bp):
AATTTGATACTTAAGTTTTTTC
Found at i:59962768 original size:26 final size:26
Alignment explanation
Indices: 59962712--59962768 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
59962702 AAAGATTCTT
**
59962712 CAAAATTAAATGGCATTTTACAAAAA
1 CAAAATTAAATGAAATTTTACAAAAA
* *
59962738 AAAAATTAAATTAAATTTTA-AAAATA
1 CAAAATTAAATGAAATTTTACAAAA-A
59962764 CAAAA
1 CAAAA
59962769 AAATTATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (26 bp):
CAAAATTAAATGAAATTTTACAAAAA
Found at i:59962788 original size:30 final size:31
Alignment explanation
Indices: 59962754--59962817 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
59962744 TAAATTAAAT
59962754 TTTAAAAA-TACAAAAAAATTATAAAAAT-TA
1 TTTAAAAAGTACAAAAAAA-TATAAAAATATA
* *
59962784 TTTAAAAAGTACTAAAATATATAAAAATATA
1 TTTAAAAAGTACAAAAAAATATAAAAATATA
59962815 TTT
1 TTT
59962818 TTTAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (31 bp):
TTTAAAAAGTACAAAAAAATATAAAAATATA
Found at i:59963549 original size:2 final size:2
Alignment explanation
Indices: 59963542--59963590 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
59963532 GCATACATAC
59963542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59963584 AT AT AT A
1 AT AT AT A
59963591 ATGACAGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59973273 original size:36 final size:36
Alignment explanation
Indices: 59973233--59973301 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
59973223 AGCCTAATCA
* * *
59973233 AGCAAGCTCAAGTAGTTCGCTTTTTATCTCAAATTC
1 AGCAAGATCAAGCAGTTCACTTTTTATCTCAAATTC
*
59973269 AGCAAGATCAAGCATTTCACTTTTTATCTCAAA
1 AGCAAGATCAAGCAGTTCACTTTTTATCTCAAA
59973302 ACTTTAGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
AGCAAGATCAAGCAGTTCACTTTTTATCTCAAATTC
Found at i:59978911 original size:25 final size:25
Alignment explanation
Indices: 59978884--59978930 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
59978874 ATTTTATAAT
*
59978884 TTTTAT-ATATATGTATTCATATTC
1 TTTTATAATATATGTACTCATATTC
*
59978908 TTTTATAATATGTGTACTCATAT
1 TTTTATAATATATGTACTCATAT
59978931 AATTTTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTTATAATATATGTACTCATATTC
Found at i:59978936 original size:25 final size:25
Alignment explanation
Indices: 59978878--59978936 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
59978868 TTATACATTT
*
59978878 TATAATTTTTATATATATGTATTCA
1 TATAATTTTTATATATATGTACTCA
*
59978903 TAT--TCTTTTATAATATGTGTACTCA
1 TATAAT-TTTTAT-ATATATGTACTCA
59978928 TATAATTTT
1 TATAATTTT
59978937 CCAAGTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.04
24 6 0.21
25 17 0.61
26 3 0.11
27 1 0.04
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (25 bp):
TATAATTTTTATATATATGTACTCA
Found at i:59981429 original size:22 final size:24
Alignment explanation
Indices: 59981404--59981448 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
59981394 ATTTCTAAAC
59981404 AAAATAT-AAAA-ATATTTTATTT
1 AAAATATGAAAAGATATTTTATTT
*
59981426 AAAATTTGAAAATGATATTTTAT
1 AAAATATGAAAA-GATATTTTAT
59981449 GAATTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 4 0.21
25 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAATATGAAAAGATATTTTATTT
Found at i:59984625 original size:34 final size:34
Alignment explanation
Indices: 59984582--59984650 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
59984572 ATTGTGAAGT
59984582 TAAAAAATTCTACCACCAACGTATCGAATAACAA
1 TAAAAAATTCTACCACCAACGTATCGAATAACAA
59984616 TAAAAAATTCTACCACCAACGTATCGAATAACAA
1 TAAAAAATTCTACCACCAACGTATCGAATAACAA
59984650 T
1 T
59984651 GTATATAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (34 bp):
TAAAAAATTCTACCACCAACGTATCGAATAACAA
Found at i:59984951 original size:27 final size:28
Alignment explanation
Indices: 59984921--59984974 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
59984911 AAAATTACAT
59984921 TTTAA-CTTTTCAAAA-ATAAAAAAAATA
1 TTTAATCTTTT-AAAAGATAAAAAAAATA
*
59984948 TTTAATCTTTTAAAAGATAATAAAAAT
1 TTTAATCTTTTAAAAGATAAAAAAAAT
59984975 CATAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTAATCTTTTAAAAGATAAAAAAAATA
Found at i:59990940 original size:28 final size:29
Alignment explanation
Indices: 59990856--59990943 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 29
59990846 AGAGATTAAC
59990856 TTGGACAAAAAAAA-TTCAAACTCTAATG
1 TTGGACAAAAAAAAGTTCAAACTCTAATG
* **** ***
59990884 TGGGAACAATTGCCAAGTTCAAGGACTAAT-
1 TTGG-ACAA-AAAAAAGTTCAAACTCTAATG
59990914 TTGGACAAAAAAAAGTTCAAACTCTAATG
1 TTGGACAAAAAAAAGTTCAAACTCTAATG
59990943 T
1 T
59990944 AAGAATAATT
Statistics
Matches: 40, Mismatches: 16, Indels: 7
0.63 0.25 0.11
Matches are distributed among these distances:
28 16 0.40
29 9 0.22
30 5 0.12
31 10 0.25
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (29 bp):
TTGGACAAAAAAAAGTTCAAACTCTAATG
Found at i:59990954 original size:59 final size:59
Alignment explanation
Indices: 59990852--59991168 Score: 334
Period size: 59 Copynumber: 5.4 Consensus size: 59
59990842 TATTAGAGAT
* *
59990852 TAACTTGGACAAAAAAAA-TTCAAACTCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
* * * ** * * *
59990910 TAATTTGGACAAAAAAAAGTTCAAACTCTAATGTAAGAATAATTGTCAAGTTCGAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
* * * * *
59990969 TAACTTGAACAAAAAAAAATTCAGGCCCCAATGTGGGAACAATTGCCAAGTTTAGAGG-C
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCA-AGGAC
* * * * ** * *
59991028 TAACTTGGA-TAAAAAATGTTCAAGCCCCAATGTGGGAAAAATTGTTAAGTTCAGGGAT
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
* * * ** * *
59991086 TAATTTGAATATTAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGAC
1 TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
59991145 TAACTTGGACAAAAAAAAGTTCAA
1 TAACTTGGACAAAAAAAAGTTCAA
59991169 CCTTCAATGT
Statistics
Matches: 206, Mismatches: 49, Indels: 7
0.79 0.19 0.03
Matches are distributed among these distances:
57 2 0.01
58 60 0.29
59 141 0.68
60 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (59 bp):
TAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGGGAACAATTGCCAAGTTCAAGGAC
Found at i:59991079 original size:117 final size:117
Alignment explanation
Indices: 59990852--59991168 Score: 370
Period size: 117 Copynumber: 2.7 Consensus size: 117
59990842 TATTAGAGAT
* * * * *
59990852 TAACTTGGAC-AAAAAAAATTCAAACTCTAATGTGGGAACAATTGCCAAGTTCAAGGACTAATTT
1 TAACTTGAACAAAAAAAAATTCAAGCCCTAATGTGGGAACAATTGCCAAGTTTAAGGACTAACTT
* * *
59990916 GGACAAAAAAAAGTTCAAACTCTAATGTAAGAATAATTGTCAAGTTC-GAGGAC
66 GGA-AAAAAAAAGTTCAAACCCCAATGTAAGAAAAATTGTCAAGTTCAG-GGAC
* *
59990969 TAACTTGAACAAAAAAAAATTCAGGCCCCAATGTGGGAACAATTGCCAAGTTTAGAGG-CTAACT
1 TAACTTGAACAAAAAAAAATTCAAGCCCTAATGTGGGAACAATTGCCAAGTTTA-AGGACTAACT
* * * ** * *
59991033 TGGATAAAAAATGTTCAAGCCCCAATGTGGGAAAAATTGTTAAGTTCAGGGAT
65 TGGAAAAAAAAAGTTCAAACCCCAATGTAAGAAAAATTGTCAAGTTCAGGGAC
* * ** * *
59991086 TAATTTGAATATTAAAAAGTTCAAGCCCTAATGTGAGAACAATTGCCAAGTTTAAGGACTAACTT
1 TAACTTGAACAAAAAAAAATTCAAGCCCTAATGTGGGAACAATTGCCAAGTTTAAGGACTAACTT
59991151 GGACAAAAAAAAGTTCAA
66 GGA-AAAAAAAAGTTCAA
59991169 CCTTCAATGT
Statistics
Matches: 168, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
116 3 0.02
117 102 0.61
118 60 0.36
119 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (117 bp):
TAACTTGAACAAAAAAAAATTCAAGCCCTAATGTGGGAACAATTGCCAAGTTTAAGGACTAACTT
GGAAAAAAAAAGTTCAAACCCCAATGTAAGAAAAATTGTCAAGTTCAGGGAC
Found at i:60017762 original size:18 final size:19
Alignment explanation
Indices: 60017723--60017775 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
60017713 TATCACTATT
*
60017723 TTTACAAATTAAATACACTA
1 TTTA-AAATTAAATACAATA
60017743 -TTAAAATTGAAATA-AATA
1 TTTAAAATT-AAATACAATA
60017761 TTTAAAATATAAATA
1 TTTAAAAT-TAAATA
60017776 ATGTTACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.28
19 20 0.69
20 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
TTTAAAATTAAATACAATA
Found at i:60018711 original size:181 final size:180
Alignment explanation
Indices: 60018276--60018795 Score: 684
Period size: 182 Copynumber: 2.9 Consensus size: 180
60018266 AAATGTTATT
* ** * *
60018276 TTTTTAGAGAGATAATTATGAAACTTTAAAATATTAGTATTTTATAGACAGTAAAATAAACATTA
1 TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGT-CTTTATAGACCGTAAAATAAACATTA
60018341 AGGAAACCTTGGTCATAAAAAATATATACATTTTTAAACAATTTT-CAAATTAAGAATTCTTGAT
65 AGGAAACCTTGGTCATAAAAAATATATACATTTTTAAAC-ATTTTCCAAATTAAGAATTCTTGAT
* * *
60018405 CCAAAACCTGAATTAACAATATTCACGTGTAAAAAAATTACACGAAATATCA
129 CCAAAACCCGAATTAACAATACTCACGTGTAAAAAAATGACACGAAATATCA
* * * * *
60018457 TTTTTGAGAGGGATAATCATGGACCTCAAAAATGTTAATCTTTATAGACCGTAAAATAAACATTA
1 TTTTT-AGAGAGATAATCATGAAACTCAAAAATATTAGTCTTTATAGACCGTAAAATAAACATTA
* * * *
60018522 AGGAAACCTTGGTCATAAAAAATATATATATTTTTAAACATTTTCCAAATTAAGGATTTTTAATC
65 AGGAAACCTTGGTCATAAAAAATATATACATTTTTAAACATTTTCCAAATTAAGAATTCTTGATC
* * ** *
60018587 CAAAACCCAAATTAACAATACTCACGTGTAAAAGATATGACTGGAAATGTCA
130 CAAAACCCGAATTAACAATACTCACGTGTAAAA-AAATGACACGAAATATCA
* * * *
60018639 GTTTTTAGAAAGATAATCATGAATCTCAAAAATATTAGTCTTCATAGACCGTAAAATGAACATTA
1 -TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGTCTTTATAGACCGTAAAATAAACATTA
* * * * *
60018704 A-GAAACCTTAGTCATAAAAAAAATATACATTTTTTAAACCTTTTCGAAATTAAGAAATCTTGAT
65 AGGAAACCTTGGTCATAAAAAATATATACA-TTTTTAAACATTTTCCAAATTAAGAATTCTTGAT
*
60018768 TCAAAACCCGAATTAACAATACTCACGT
129 CCAAAACCCGAATTAACAATACTCACGT
60018796 ATAAGTGTAA
Statistics
Matches: 293, Mismatches: 41, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
180 5 0.02
181 139 0.47
182 144 0.49
183 5 0.02
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (180 bp):
TTTTTAGAGAGATAATCATGAAACTCAAAAATATTAGTCTTTATAGACCGTAAAATAAACATTAA
GGAAACCTTGGTCATAAAAAATATATACATTTTTAAACATTTTCCAAATTAAGAATTCTTGATCC
AAAACCCGAATTAACAATACTCACGTGTAAAAAAATGACACGAAATATCA
Found at i:60025129 original size:23 final size:21
Alignment explanation
Indices: 60025058--60025144 Score: 115
Period size: 21 Copynumber: 4.1 Consensus size: 21
60025048 CATGATCAGT
60025058 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* *
60025078 AAACGACACA-CAAGATGCCTG
1 ATACGACACATAAAG-TGCCTG
60025099 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
60025120 ACGTACGACACATAAAGTGCCTG
1 A--TACGACACATAAAGTGCCTG
60025143 AT
1 AT
60025145 CAGCAAAGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.20
21 23 0.39
22 3 0.05
23 21 0.36
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:60025143 original size:44 final size:41
Alignment explanation
Indices: 60025058--60025144 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 41
60025048 CATGATCAGT
*
60025058 ATACGACACATAAGTGCCTGAAACGACACACAAGATGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACAAAAGATGCCTG
*
60025099 ATACGACACATAAAGTGCCTGACGTACGACACATAAAG-TGCCTG
1 ATACGACACAT-AAGTGCCTGA--AACGACACA-AAAGATGCCTG
60025143 AT
1 AT
60025145 CAGCAAAGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 11 0.28
42 10 0.25
44 16 0.40
45 3 0.08
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACAAAAGATGCCTG
Found at i:60026319 original size:14 final size:17
Alignment explanation
Indices: 60026300--60026337 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
60026290 ATTTATTTCT
60026300 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
60026314 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
60026331 TAATATA
1 TAATATA
60026338 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:60026355 original size:11 final size:11
Alignment explanation
Indices: 60026317--60026355 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
60026307 ATATTTATAA
60026317 TATAATTAATT
1 TATAATTAATT
*
60026328 TAATAATATACTT
1 T-ATAAT-TAATT
60026341 TATAATTAATT
1 TATAATTAATT
60026352 TATA
1 TATA
60026356 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:60026377 original size:21 final size:20
Alignment explanation
Indices: 60026329--60026378 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
60026319 TAATTAATTT
*
60026329 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* * *
60026349 ATTTATATATTTATATAAATA
1 AATAATATACTT-TATAAATA
60026370 AATAATATA
1 AATAATATA
60026379 AAAATCTAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:60031401 original size:54 final size:54
Alignment explanation
Indices: 60031317--60031421 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
60031307 CCTGTTGAGA
*
60031317 ATTCAGATCACTGTGTTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACCCTC
1 ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACCCTC
* **
60031371 ATTCAGATCACTGTATTCACCCTGCTGAGTTTTGGTGTGAACAGTAGTACC
1 ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACC
60031422 AACAGACTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (54 bp):
ATTCAGATCACTGTATTCACCCTGCCGAGTTTCAGTGTGAACAGTAGTACCCTC
Found at i:60038542 original size:28 final size:28
Alignment explanation
Indices: 60038510--60038578 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
60038500 TTTTCACAAA
60038510 TTTAAAATTTAATCCCTATATTTTTAA-T
1 TTTAAAATTTAAT-CCTATATTTTTAATT
** * *
60038538 TTTAAGAATTTAATGTTTTTTTTTTAATT
1 TTTAA-AATTTAATCCTATATTTTTAATT
60038567 TTTAAAATTTAA
1 TTTAAAATTTAA
60038579 GTTTAACTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 21 0.60
29 14 0.40
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAAAATTTAATCCTATATTTTTAATT
Found at i:60045065 original size:19 final size:19
Alignment explanation
Indices: 60045041--60045079 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
60045031 ACACCATATG
60045041 TTCCAAAGATAACAAGGAA
1 TTCCAAAGATAACAAGGAA
60045060 TTCCAAAGATAACAAGGAA
1 TTCCAAAGATAACAAGGAA
60045079 T
1 T
60045080 ACAGACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (19 bp):
TTCCAAAGATAACAAGGAA
Found at i:60057278 original size:11 final size:11
Alignment explanation
Indices: 60057262--60057289 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
60057252 ACCTGCCATC
60057262 TTTTTTTTTCT
1 TTTTTTTTTCT
60057273 TTTTTTTTTCT
1 TTTTTTTTTCT
60057284 TTTTTT
1 TTTTTT
60057290 GCAGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:60057958 original size:20 final size:20
Alignment explanation
Indices: 60057909--60057981 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
60057899 AAACTTAAAA
*
60057909 TTTATTTTTTAATTCTTTTAT
1 TTTATTTTTTTA-TCTTTTAT
**
60057930 TTTCCTTTTTTATCTTTTAT
1 TTTATTTTTTTATCTTTTAT
* * * *
60057950 ATTATTTTTCTCTCTTTTTT
1 TTTATTTTTTTATCTTTTAT
60057970 TTGTATTTTTTT
1 TT-TATTTTTTT
60057982 CATTCTTCTA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.12, C:0.10, G:0.01, T:0.77
Consensus pattern (20 bp):
TTTATTTTTTTATCTTTTAT
Found at i:60074071 original size:36 final size:36
Alignment explanation
Indices: 60074022--60074208 Score: 191
Period size: 36 Copynumber: 5.2 Consensus size: 36
60074012 TGCACCTGGT
* *
60074022 GGTGGAGGAGGCACAGCAGGACCTTTCGGTGGAGGA
1 GGTGGAGGGGGCACAGCAGGACCTTTCGGTGGAGGG
* *
60074058 GGTGGAGGGGGCACAGCATGACCTTTCAGTGGAGGG
1 GGTGGAGGGGGCACAGCAGGACCTTTCGGTGGAGGG
* * *
60074094 GGTGGAGGGGGCACCGCAGAACCTTTCGGTGGAGGT
1 GGTGGAGGGGGCACAGCAGGACCTTTCGGTGGAGGG
* ** * *
60074130 GGAGGAGGGGGTGCAGTAGGAGCTTTTCGGGTGGAGGG
1 GGTGGAGGGGGCACAGCAGGA-CCTTTC-GGTGGAGGG
* * * *
60074168 GGTGGA-GGGGCGCTGGAGG-GCTTT-GGTGGAGGG
1 GGTGGAGGGGGCACAGCAGGACCTTTCGGTGGAGGG
60074201 GGTGGAGG
1 GGTGGAGG
60074209 AGCTTTTTGG
Statistics
Matches: 125, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
33 15 0.12
34 1 0.01
35 3 0.02
36 78 0.62
37 15 0.12
38 13 0.10
ACGTcount: A:0.17, C:0.13, G:0.53, T:0.17
Consensus pattern (36 bp):
GGTGGAGGGGGCACAGCAGGACCTTTCGGTGGAGGG
Found at i:60074195 original size:24 final size:23
Alignment explanation
Indices: 60074168--60074233 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 23
60074158 GGGTGGAGGG
60074168 GGTGGAGGGGCGCTGGAGG-GCTTT
1 GGTGGAGGGG-G-TGGAGGAGCTTT
60074192 GGTGGAGGGGGTGGAGGAGCTTTTT
1 GGTGGAGGGGGTGGAGGAGC--TTT
*
60074217 GGAGGAGGGGGTGGAGG
1 GGTGGAGGGGGTGGAGG
60074234 GGGCGCTGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 6 0.16
23 3 0.08
24 10 0.26
25 19 0.50
ACGTcount: A:0.12, C:0.06, G:0.62, T:0.20
Consensus pattern (23 bp):
GGTGGAGGGGGTGGAGGAGCTTT
Found at i:60074210 original size:25 final size:25
Alignment explanation
Indices: 60074182--60074247 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
60074172 GAGGGGCGCT
*
60074182 GGAGGGCTTTGGTGGAGGGGGTGGA
1 GGAGGGCTTTGGAGGAGGGGGTGGA
***
60074207 GGAGCTTTTTGGAGGAGGGGGTGGA
1 GGAGGGCTTTGGAGGAGGGGGTGGA
**
60074232 GG-GGGCGCTGGAGGAG
1 GGAGGGCTTTGGAGGAG
60074248 CTTTTGGTAG
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.14, C:0.06, G:0.62, T:0.18
Consensus pattern (25 bp):
GGAGGGCTTTGGAGGAGGGGGTGGA
Found at i:60074215 original size:59 final size:61
Alignment explanation
Indices: 60074133--60074269 Score: 190
Period size: 59 Copynumber: 2.2 Consensus size: 61
60074123 TGGAGGTGGA
*
60074133 GGAGGGGGTGCAGTAGGAGCTTTTCGGGTGGAGGGGGTGGA-GGGGCGCTGGAGG-GC-TTTGGT
1 GGAGGGGGTG--G-AGGAGCTTTT-GGGAGGAGGGGGTGGAGGGGGCGCTGGAGGAGCTTTTGGT
*
60074195 GGAGGGGGTGGAGGAGCTTTTTGGAGGAGGGGGTGGAGGGGGCGCTGGAGGAGCTTTTGGT
1 GGAGGGGGTGGAGGAGCTTTTGGGAGGAGGGGGTGGAGGGGGCGCTGGAGGAGCTTTTGGT
*
60074256 AGAGGGGGTGGAGG
1 GGAGGGGGTGGAGG
60074270 GGGCGCTGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
58 14 0.20
59 23 0.33
60 3 0.04
61 19 0.28
62 10 0.14
ACGTcount: A:0.13, C:0.07, G:0.60, T:0.20
Consensus pattern (61 bp):
GGAGGGGGTGGAGGAGCTTTTGGGAGGAGGGGGTGGAGGGGGCGCTGGAGGAGCTTTTGGT
Found at i:60074221 original size:22 final size:24
Alignment explanation
Indices: 60074168--60074214 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
60074158 GGGTGGAGGG
60074168 GGTGGAGGGGCGCTGGAGGGCTTT
1 GGTGGAGGGGCGCTGGAGGGCTTT
60074192 GGTGGAGGGG-G-TGGAGGAGCTTT
1 GGTGGAGGGGCGCTGGAGG-GCTTT
60074215 TTGGAGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 6 0.27
24 10 0.45
ACGTcount: A:0.11, C:0.09, G:0.60, T:0.21
Consensus pattern (24 bp):
GGTGGAGGGGCGCTGGAGGGCTTT
Found at i:60074234 original size:96 final size:96
Alignment explanation
Indices: 60074124--60074306 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
60074114 ACCTTTCGGT
* * * *
60074124 GGAGGTGGAGGAGGGGGTGCAGTAGGAGCTTTTCGGGTGGAGGGGGTGGA-GGGGCGCTGGAGG-
1 GGAGGGGGAGGAGGGGGCGCAGGAGGAGCTTTT--GGTAGAGGGGGTGGAGGGGGCGCTGGAGGA
60074187 GC-TTTGGTGGAGGGGGTGGAGGAGCTTTTTGGA
64 GCTTTTGGTGGA-GGGGTGGAGGAGCTTTTTGGA
* *
60074220 GGAGGGGGTGGAGGGGGCGCTGGAGGAGCTTTTGGTAGAGGGGGTGGAGGGGGCGCTGGAGGAGC
1 GGAGGGGGAGGAGGGGGCGCAGGAGGAGCTTTTGGTAGAGGGGGTGGAGGGGGCGCTGGAGGAGC
60074285 TTTTGGTGGAGGGGTGGAGGAG
66 TTTTGGTGGAGGGGTGGAGGAG
60074307 GAATAGAACC
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 14 0.18
95 13 0.17
96 42 0.54
97 9 0.12
ACGTcount: A:0.14, C:0.07, G:0.60, T:0.19
Consensus pattern (96 bp):
GGAGGGGGAGGAGGGGGCGCAGGAGGAGCTTTTGGTAGAGGGGGTGGAGGGGGCGCTGGAGGAGC
TTTTGGTGGAGGGGTGGAGGAGCTTTTTGGA
Found at i:60074261 original size:36 final size:36
Alignment explanation
Indices: 60074192--60074304 Score: 164
Period size: 36 Copynumber: 3.2 Consensus size: 36
60074182 GGAGGGCTTT
60074192 GGTGGA-GGGG-G-TGGAGGAGCTTTTTGG-AGGAGGG
1 GGTGGAGGGGGCGCTGGAGGAGC-TTTTGGTA-GAGGG
60074226 GGTGGAGGGGGCGCTGGAGGAGCTTTTGGTAGAGGG
1 GGTGGAGGGGGCGCTGGAGGAGCTTTTGGTAGAGGG
*
60074262 GGTGGAGGGGGCGCTGGAGGAGCTTTTGGTGGA-GG
1 GGTGGAGGGGGCGCTGGAGGAGCTTTTGGTAGAGGG
60074297 GGTGGAGG
1 GGTGGAGG
60074305 AGGAATAGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
34 6 0.08
35 14 0.19
36 44 0.59
37 10 0.14
ACGTcount: A:0.13, C:0.06, G:0.61, T:0.19
Consensus pattern (36 bp):
GGTGGAGGGGGCGCTGGAGGAGCTTTTGGTAGAGGG
Found at i:60074452 original size:12 final size:12
Alignment explanation
Indices: 60074435--60074460 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60074425 GACAACCATT
60074435 GGAGGTGGTGGC
1 GGAGGTGGTGGC
60074447 GGAGGTGGTGGC
1 GGAGGTGGTGGC
60074459 GG
1 GG
60074461 TTGGTTTGGC
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:0.08, C:0.08, G:0.69, T:0.15
Consensus pattern (12 bp):
GGAGGTGGTGGC
Found at i:60074527 original size:12 final size:12
Alignment explanation
Indices: 60074501--60074543 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
60074491 GCTGAAGGAT
* *
60074501 GGTGGATGCAAG
1 GGTGGAGGCAGG
* *
60074513 GGTGGGGGTAGG
1 GGTGGAGGCAGG
60074525 GGTGGAGGCAGG
1 GGTGGAGGCAGG
60074537 GGTGGAG
1 GGTGGAG
60074544 ATGGCGATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.65, T:0.14
Consensus pattern (12 bp):
GGTGGAGGCAGG
Found at i:60074837 original size:3 final size:3
Alignment explanation
Indices: 60074831--60074860 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
60074821 AGGAGGAGGA
*
60074831 GGT GGT GGT GGT GGC GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
60074861 CCAGGAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.67, T:0.30
Consensus pattern (3 bp):
GGT
Found at i:60081458 original size:31 final size:29
Alignment explanation
Indices: 60081423--60081497 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
60081413 AATGGCTCAA
*
60081423 TGACTAAAATGTTACAACACGATAACATAAG
1 TGACTAAAATGTAACAACAC-A-AACATAAG
***
60081454 TGACTAAAATGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACAACACAAACATAAG
*
60081483 TGACTAAAACGTAAC
1 TGACTAAAATGTAAC
60081498 CTGAAGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 22 0.56
30 1 0.03
31 16 0.41
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (29 bp):
TGACTAAAATGTAACAACACAAACATAAG
Found at i:60088578 original size:110 final size:110
Alignment explanation
Indices: 60088442--60088666 Score: 423
Period size: 110 Copynumber: 2.0 Consensus size: 110
60088432 TTTTTTTACT
*
60088442 TAGTTTTGTTCTAGAAGAAGACTGTCTTTATATTAGCTTCTTGAACAGAGTGTTGATTTCCTATA
1 TAGTTTTGTTCTAGAAGAAGACTGTCTTTATATTAGCTTCTTGAACAGAGTGTTGATTTCCAATA
*
60088507 CTTTTCTAGTCCAGGAGTTGGGCTACTGATGTTATTATAATTCCC
66 CTTTTCTAGTCCAGGAGTTGGGCTACTGATGCTATTATAATTCCC
60088552 TAGTTTTGTTCTAGAAGAAGACTGTCTTTATATTAGCTTCTTGAACAGAGTGTTGATTTCCAATA
1 TAGTTTTGTTCTAGAAGAAGACTGTCTTTATATTAGCTTCTTGAACAGAGTGTTGATTTCCAATA
*
60088617 CTTTTCTAGTCCAGGAGTTGGGCTACTGATGCTATTATAATTCCT
66 CTTTTCTAGTCCAGGAGTTGGGCTACTGATGCTATTATAATTCCC
60088662 TAGTT
1 TAGTT
60088667 AGCCAGACAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (110 bp):
TAGTTTTGTTCTAGAAGAAGACTGTCTTTATATTAGCTTCTTGAACAGAGTGTTGATTTCCAATA
CTTTTCTAGTCCAGGAGTTGGGCTACTGATGCTATTATAATTCCC
Found at i:60097642 original size:192 final size:193
Alignment explanation
Indices: 60097305--60097655 Score: 501
Period size: 192 Copynumber: 1.8 Consensus size: 193
60097295 CGGTTATTAT
* * * * *
60097305 ATTTCTGGATCAATTTAGGTTTGTGTTCTTTTTGGTTTTGATCATTAGGGTTTTTCGGGTTGAAT
1 ATTTCTGGATCAATTTAGGCTAGTGCTCTTTTTGGTTTTAATCATTAGGGTTTTTCAGGTTGAAT
* * * * * * *
60097370 CATCTTTGGGTTCATATCATTTCGGATCCTTTTGTGTTTGGAACATCTTGGATTCGAATTCTTTT
66 AATCTTTGGATTCATATAATTTCGGATCATTTTATGTTTGGAACATCTTGGATTAGAATTATTTT
*
60097435 CAGGTTTGGTTGAGCCAGTTTGGGTTATTGCCATTTGATTACCAGGTCCATTTGTTTTTTGAA
131 CAGGTTCGGTTGAGCCAGTTTGGGTTATTGCCATTTGATTACCAGGTCCATTTGTTTTTTGAA
* * *
60097498 ATTTCTGGATCAGTTTAGGCTAG-GCTCATTTTTTGTTTTAATCATTAGGGTTTTTCAGGTTGGA
1 ATTTCTGGATCAATTTAGGCTAGTGCTC-TTTTTGGTTTTAATCATTAGGGTTTTTCAGGTTGAA
*
60097562 TAATC-TTGGATTCATATAATTTTGGATCATTTTATGTTTGGAACAT-TTGGAATTAGAATTATT
65 TAATCTTTGGATTCATATAATTTCGGATCATTTTATGTTTGGAACATCTTGG-ATTAGAATTATT
*
60097625 TTCGGGTTCGGTTGAGCCAGTTTGGGTTATT
129 TTCAGGTTCGGTTGAGCCAGTTTGGGTTATT
60097656 CCCTTTTCAT
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
191 4 0.03
192 78 0.57
193 56 0.41
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (193 bp):
ATTTCTGGATCAATTTAGGCTAGTGCTCTTTTTGGTTTTAATCATTAGGGTTTTTCAGGTTGAAT
AATCTTTGGATTCATATAATTTCGGATCATTTTATGTTTGGAACATCTTGGATTAGAATTATTTT
CAGGTTCGGTTGAGCCAGTTTGGGTTATTGCCATTTGATTACCAGGTCCATTTGTTTTTTGAA
Found at i:60098955 original size:22 final size:22
Alignment explanation
Indices: 60098927--60098972 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
60098917 CTGTACTCTT
60098927 TGAAAAATTGGAATTTAGTCCC
1 TGAAAAATTGGAATTTAGTCCC
60098949 TGAAAAATTGGAATTTAGTCCC
1 TGAAAAATTGGAATTTAGTCCC
60098971 TG
1 TG
60098973 TGCTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (22 bp):
TGAAAAATTGGAATTTAGTCCC
Found at i:60099190 original size:13 final size:13
Alignment explanation
Indices: 60099172--60099237 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
60099162 AGTTCTTTAT
60099172 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
60099185 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
60099198 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
*
60099211 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
60099224 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
60099237 T
1 T
60099238 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:60104077 original size:14 final size:14
Alignment explanation
Indices: 60104058--60104085 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60104048 TATCTTTTAT
60104058 AAATTGAACAAAAC
1 AAATTGAACAAAAC
60104072 AAATTGAACAAAAC
1 AAATTGAACAAAAC
60104086 CCAACTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AAATTGAACAAAAC
Found at i:60110696 original size:6 final size:6
Alignment explanation
Indices: 60110685--60110722 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
60110675 TTTTACTTAC
60110685 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATATAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT A
60110723 CATATAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:60122998 original size:21 final size:21
Alignment explanation
Indices: 60122974--60123013 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
60122964 AACAAAATAT
60122974 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
60122995 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
60123014 AAATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:60123489 original size:2 final size:2
Alignment explanation
Indices: 60123482--60123531 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
60123472 TAAATATTAA
60123482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60123524 AT AT AT AT
1 AT AT AT AT
60123532 GTATGTATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60124139 original size:17 final size:18
Alignment explanation
Indices: 60124099--60124146 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
60124089 TCAAATTAAA
60124099 TAAATTATTAAAAATGTAT
1 TAAATT-TTAAAAATGTAT
*
60124118 AAAATTTTAAAAAT-TAT
1 TAAATTTTAAAAATGTAT
*
60124135 TAAATTATAAAA
1 TAAATTTTAAAA
60124147 TATGATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
18 8 0.31
19 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATTTTAAAAATGTAT
Found at i:60130828 original size:4 final size:4
Alignment explanation
Indices: 60130819--60130873 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
60130809 CGAGCACGCG
*
60130819 CATA CATA CATA CATA CATA CATA CATA CTTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
60130867 CATA CAT
1 CATA CAT
60130874 GAAAAGGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:60133421 original size:18 final size:18
Alignment explanation
Indices: 60133398--60133432 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
60133388 TATAGTAAAA
60133398 TTATATAAAAATATTATT
1 TTATATAAAAATATTATT
*
60133416 TTATATAAAGATATTAT
1 TTATATAAAAATATTAT
60133433 ACTAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTATATAAAAATATTATT
Found at i:60140832 original size:39 final size:40
Alignment explanation
Indices: 60140788--60140874 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
60140778 ACGTGTTAGT
* *
60140788 AAATCGCGTCCACGTCAGCGCGA-TTACTTACGTGGCAA-C
1 AAATCGCGTCCACGTAAGCGCGATTTACTAACGTGG-AAGC
* *
60140827 AAATCGCATCCACGTAAGCGCGATTTGCTAACGTGGAAGC
1 AAATCGCGTCCACGTAAGCGCGATTTACTAACGTGGAAGC
60140867 AAATCGCG
1 AAATCGCG
60140875 CTTACGTGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 23 0.56
40 18 0.44
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (40 bp):
AAATCGCGTCCACGTAAGCGCGATTTACTAACGTGGAAGC
Found at i:60146375 original size:9 final size:9
Alignment explanation
Indices: 60146361--60146388 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
60146351 TGAGTTTTCG
60146361 AATTCGAAT
1 AATTCGAAT
60146370 AATTCGAAT
1 AATTCGAAT
60146379 AATTCGAAT
1 AATTCGAAT
60146388 A
1 A
60146389 TCAAACTATA
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:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:60149059 original size:2 final size:2
Alignment explanation
Indices: 60149052--60149084 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60149042 TGTAACAAAC
60149052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60149085 AGATTACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60149408 original size:57 final size:57
Alignment explanation
Indices: 60149340--60149461 Score: 244
Period size: 57 Copynumber: 2.1 Consensus size: 57
60149330 AACTAGAAAG
60149340 GACATGATATTTTAGGTACTAATGTGAGGAAACGAGATAATTTATGGGTCAAATCGT
1 GACATGATATTTTAGGTACTAATGTGAGGAAACGAGATAATTTATGGGTCAAATCGT
60149397 GACATGATATTTTAGGTACTAATGTGAGGAAACGAGATAATTTATGGGTCAAATCGT
1 GACATGATATTTTAGGTACTAATGTGAGGAAACGAGATAATTTATGGGTCAAATCGT
60149454 GACATGAT
1 GACATGAT
60149462 CCGATTATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (57 bp):
GACATGATATTTTAGGTACTAATGTGAGGAAACGAGATAATTTATGGGTCAAATCGT
Found at i:60153680 original size:16 final size:16
Alignment explanation
Indices: 60153659--60153719 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
60153649 GTTAAAATAT
60153659 ATATTATAATATTATA
1 ATATTATAATATTATA
*
60153675 ATATTAT-ATCTTAAGTA
1 ATATTATAATATT-A-TA
60153692 TATATTATATATATTATA
1 -ATATTATA-ATATTATA
*
60153710 TTA-TATAATA
1 ATATTATAATA
60153720 AAACAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
15 7 0.19
16 12 0.32
17 4 0.11
18 9 0.24
19 1 0.03
20 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATTATAATATTATA
Found at i:60154123 original size:41 final size:40
Alignment explanation
Indices: 60154067--60154198 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 40
60154057 GACTTCGAAT
* *
60154067 CGATAAGACACTGGGTGTCAAATTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * *
60154108 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
60154145 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
*
60154185 CGATGAGGCACTGG
1 CGATGAGACACTGG
60154199 TTGCCAAACT
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 16 0.22
38 14 0.19
39 2 0.03
40 27 0.36
41 15 0.20
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:60160827 original size:29 final size:30
Alignment explanation
Indices: 60160780--60160839 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
60160770 GGACTCTTGG
*
60160780 AATTTAGTTTTTATATTTTTA-TTTTTAAA
1 AATTTAGTTTTTATATTTTTAGATTTTAAA
*
60160809 AATTTAG-TTTTATGGTTTTTAGATTTTAAA
1 AATTTAGTTTTTAT-ATTTTTAGATTTTAAA
60160839 A
1 A
60160840 TTGAGGTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 13 0.48
30 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (30 bp):
AATTTAGTTTTTATATTTTTAGATTTTAAA
Found at i:60161585 original size:2 final size:2
Alignment explanation
Indices: 60161578--60161613 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
60161568 ACTTTTCATG
60161578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60161614 TTTTTCTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60163692 original size:251 final size:251
Alignment explanation
Indices: 60163249--60163750 Score: 995
Period size: 251 Copynumber: 2.0 Consensus size: 251
60163239 CATTTTGGTC
60163249 ACTAAACTTCAAAGGTTACAAAATGATCACTGAACTATTCGAAAGTTTTCATTTAAGTCACTGAG
1 ACTAAACTTCAAAGGTTACAAAATGATCACTGAACTATTCGAAAGTTTTCATTTAAGTCACTGAG
60163314 TTGTTAAAATTGTTGTATAACCTTCTCTGTTCTCACCTCTAGCACCCATCAAAGGGGTAAACTTT
66 TTGTTAAAATTGTTGTATAACCTTCTCTGTTCTCACCTCTAGCACCCATCAAAGGGGTAAACTTT
60163379 CCCTCTTCTTCGAAAGTTTAGTTTTTTGTTTATTTCTTTATTTTTTATGAAATAACTTTGAATGT
131 CCCTCTTCTTCGAAAGTTTAGTTTTTTGTTTATTTCTTTATTTTTTATGAAATAACTTTGAATGT
60163444 CACGAATTTGTGAACCAAAATCCGAACAGTTTTCTTCTCTGATCTCTAACACCAAT
196 CACGAATTTGTGAACCAAAATCCGAACAGTTTTCTTCTCTGATCTCTAACACCAAT
60163500 ACTAAACTTCAAAGGTTACAAAATGATCACTGAACTATTCGAAAGTTTTCATTTAAGTCACTGAG
1 ACTAAACTTCAAAGGTTACAAAATGATCACTGAACTATTCGAAAGTTTTCATTTAAGTCACTGAG
60163565 TTGTTAAAATTGTTGTATAACCTTCTCTGTTCTCACCTCTAGCACCCATCAAAGGGGTAAACTTT
66 TTGTTAAAATTGTTGTATAACCTTCTCTGTTCTCACCTCTAGCACCCATCAAAGGGGTAAACTTT
*
60163630 CCCTCTTCTTCGAAAGTTTAGTTTTTTGTTTATTTCTTTATTTTTTTTGAAATAACTTTGAATGT
131 CCCTCTTCTTCGAAAGTTTAGTTTTTTGTTTATTTCTTTATTTTTTATGAAATAACTTTGAATGT
60163695 CACGAATTTGTGAACCAAAATCCGAACAGTTTTCTTCTCTGATCTCTAACACCAAT
196 CACGAATTTGTGAACCAAAATCCGAACAGTTTTCTTCTCTGATCTCTAACACCAAT
60163751 CATCAGATCA
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 250 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (251 bp):
ACTAAACTTCAAAGGTTACAAAATGATCACTGAACTATTCGAAAGTTTTCATTTAAGTCACTGAG
TTGTTAAAATTGTTGTATAACCTTCTCTGTTCTCACCTCTAGCACCCATCAAAGGGGTAAACTTT
CCCTCTTCTTCGAAAGTTTAGTTTTTTGTTTATTTCTTTATTTTTTATGAAATAACTTTGAATGT
CACGAATTTGTGAACCAAAATCCGAACAGTTTTCTTCTCTGATCTCTAACACCAAT
Found at i:60178413 original size:21 final size:21
Alignment explanation
Indices: 60178371--60178416 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
60178361 ATGTATGGTT
60178371 TATAAAATT-TTATATATGATA
1 TATAAAATTATT-TATATGATA
60178392 TATAAAATTATTTAT-TG-TA
1 TATAAAATTATTTATATGATA
60178411 TATAAA
1 TATAAA
60178417 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.33
20 2 0.08
21 12 0.50
22 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TATAAAATTATTTATATGATA
Found at i:60181431 original size:2 final size:2
Alignment explanation
Indices: 60181424--60181461 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
60181414 NNNNNNNTAG
60181424 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
60181462 ATAACAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60182081 original size:41 final size:40
Alignment explanation
Indices: 60181980--60182117 Score: 120
Period size: 41 Copynumber: 3.4 Consensus size: 40
60181970 CCTTGGACTT
* * * *
60181980 GAAGCAACCAGCAAATAACTTCGGAGCAAGTCTTTTCA-AG
1 GAAGCAACCAGCAAACAACCTCGGAGCAAG-CCTTCCACAG
** *
60182020 GAAGCAATGAGCAAAGAACCTCGGAGCAAGCCTTCCACATG
1 GAAGCAACCAGCAAACAACCTCGGAGCAAGCCTTCCACA-G
* * *
60182061 GAAGCAACCAGTAAACAACCTTGAAGCAAG-CTTCCCACACG
1 GAAGCAACCAGCAAACAACCTCGGAGCAAGCCTT-CCACA-G
60182102 GAAGCAGA-CAGCAAAC
1 GAAGCA-ACCAGCAAAC
60182118 CTTTGTAAGA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
39 5 0.06
40 30 0.38
41 44 0.55
42 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (40 bp):
GAAGCAACCAGCAAACAACCTCGGAGCAAGCCTTCCACAG
Found at i:60185043 original size:77 final size:77
Alignment explanation
Indices: 60184849--60185070 Score: 232
Period size: 76 Copynumber: 2.8 Consensus size: 77
60184839 CATGATGGTC
* * * * * * *
60184849 ACATAGCAACTTCATATGTACTTCAAATTCCATGGTTCCATATATGAAT-GTACAAGCAAATCAT
1 ACATAACAACTGCAAATGTACTTCAAGTTCCATGGTT-CA-ATTTGAATCAT-C-ATCAAATCAT
60184913 ATAACCATATGAACGT
62 ATAACCATATGAACGT
** * * * *
60184929 ACATAGTAACTTCAAATGTACTTCAAGTTCCATGGTTCCATTT-AATCCTCATTAAATCATATAA
1 ACATAACAACTGCAAATGTACTTCAAGTTCCATGGTTCAATTTGAATCATCATCAAATCATATAA
*
60184993 CCATATGAATGT
66 CCATATGAACGT
* * *
60185005 ACTTAACAACTGCATATGTTACTTCAAGTTCCATGGTTCAATTTGACTCATCATCAAATCATATA
1 ACATAACAACTGCAAATG-TACTTCAAGTTCCATGGTTCAATTTGAATCATCATCAAATCATATA
60185070 A
65 A
60185071 TTAACTACAT
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
76 36 0.30
77 28 0.23
78 22 0.18
79 1 0.01
80 34 0.28
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (77 bp):
ACATAACAACTGCAAATGTACTTCAAGTTCCATGGTTCAATTTGAATCATCATCAAATCATATAA
CCATATGAACGT
Found at i:60197918 original size:67 final size:68
Alignment explanation
Indices: 60197810--60197952 Score: 164
Period size: 67 Copynumber: 2.1 Consensus size: 68
60197800 GCATCATCAA
* * * * *
60197810 TTGGAATATATATTTTTAAGAAAATCTTTGTCTTCAATATTTTAA-TGGAAAC-AAGAGTATTAT
1 TTGGAATATATATATTTAAAAAAATATTTGACCTCAATATTTTAACT-GAAACTAAGAGTATTAT
60197873 CTAT
65 CTAT
**
60197877 TTGGAATATATATATTTAAAAAAATATTTGACCTCGTTATTTTAACTGAAACATTTAAGAGTATT
1 TTGGAATATATATATTTAAAAAAATATTTGACCTCAATATTTTAACTGAAAC---TAAGAGTATT
*
60197942 ATTTAT
63 ATCTAT
60197948 TTGGA
1 TTGGA
60197953 CTAATTAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
67 43 0.68
68 1 0.02
71 19 0.30
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (68 bp):
TTGGAATATATATATTTAAAAAAATATTTGACCTCAATATTTTAACTGAAACTAAGAGTATTATC
TAT
Found at i:60198473 original size:21 final size:18
Alignment explanation
Indices: 60198449--60198492 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
60198439 TTTTAAATCG
60198449 ATTAATAAAATTTCATTAATT
1 ATTAA-AAAATTTCA--AATT
*
60198470 ATTAAAAACTTTCAAATT
1 ATTAAAAAATTTCAAATT
60198488 ATTAA
1 ATTAA
60198493 CATGCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 8 0.36
21 5 0.23
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAAAAATTTCAAATT
Found at i:60202589 original size:27 final size:27
Alignment explanation
Indices: 60202541--60202595 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
60202531 TTCTTCCTCG
*
60202541 AGCATTTGAACTGAGTTAGAATCCTAA
1 AGCATTTGAACTGAATTAGAATCCTAA
* * *
60202568 AGCATTTGAATTGAATTTGAATCTTAA
1 AGCATTTGAACTGAATTAGAATCCTAA
60202595 A
1 A
60202596 ACCATCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (27 bp):
AGCATTTGAACTGAATTAGAATCCTAA
Found at i:60206943 original size:19 final size:20
Alignment explanation
Indices: 60206915--60206956 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
60206905 TTTAAATGTT
60206915 TTATTATTAA-AT-TATATTA
1 TTATTATTAATATATAT-TTA
*
60206934 TTATTCTTAATATATATTTA
1 TTATTATTAATATATATTTA
60206954 TTA
1 TTA
60206957 ACATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTATTAATATATATTTA
Found at i:60222532 original size:21 final size:21
Alignment explanation
Indices: 60222507--60222546 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60222497 CAATAACCAT
*
60222507 TTACATATACATAA-AAATAAA
1 TTACAT-TACACAACAAATAAA
60222528 TTACATTACACAACAAATA
1 TTACATTACACAACAAATA
60222547 CAATCCATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
TTACATTACACAACAAATAAA
Found at i:60225605 original size:10 final size:10
Alignment explanation
Indices: 60225590--60225616 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
60225580 TTGTTAGTAT
60225590 CATTAATGTC
1 CATTAATGTC
60225600 CATTAATGTC
1 CATTAATGTC
60225610 CATTAAT
1 CATTAAT
60225617 AATCAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (10 bp):
CATTAATGTC
Found at i:60227260 original size:32 final size:32
Alignment explanation
Indices: 60227219--60227283 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
60227209 GAGTTTAGCA
60227219 ACTAATAAATAATGTATAAAGGTAAAAAAGGC
1 ACTAATAAATAATGTATAAAGGTAAAAAAGGC
60227251 ACTAATAAATAATGTATAAAGGTAAAAAAGGC
1 ACTAATAAATAATGTATAAAGGTAAAAAAGGC
60227283 A
1 A
60227284 AGGTTGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (32 bp):
ACTAATAAATAATGTATAAAGGTAAAAAAGGC
Found at i:60227801 original size:17 final size:18
Alignment explanation
Indices: 60227779--60227815 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60227769 TCAAAAGCTA
60227779 TAATTT-AGTCATTGAAC
1 TAATTTAAGTCATTGAAC
*
60227796 TAATTTAAGTTATTGAAC
1 TAATTTAAGTCATTGAAC
60227814 TA
1 TA
60227816 TTCAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (18 bp):
TAATTTAAGTCATTGAAC
Found at i:60230411 original size:13 final size:13
Alignment explanation
Indices: 60230395--60230447 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
60230385 TTTAAACCAA
*
60230395 ACTTTTCGAAAGC
1 ACTTTTCAAAAGC
* *
60230408 ACTTTTCCATAGC
1 ACTTTTCAAAAGC
* *
60230421 ACTTTTTAAAATC
1 ACTTTTCAAAAGC
60230434 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
60230447 A
1 A
60230448 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:60230703 original size:28 final size:28
Alignment explanation
Indices: 60230647--60230705 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
60230637 TTCAACTAAA
*
60230647 TATATATATTTTTTATAAATACATTTAT
1 TATATATATTTTTTATAAATAAATTTAT
*
60230675 TATATA-ATTTTATTTTAAA-AAATTCTAT
1 TATATATATTTT-TTATAAATAAATT-TAT
60230703 TAT
1 TAT
60230706 TGCATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TATATATATTTTTTATAAATAAATTTAT
Found at i:60233304 original size:17 final size:17
Alignment explanation
Indices: 60233282--60233344 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
60233272 TGTAATATAC
60233282 TTTTTAATTAATTATTA
1 TTTTTAATTAATTATTA
**
60233299 TTTTTAAAAAACTGTAATATA
1 TTTTTAATTAA-T-T-AT-TA
60233320 TTTTTTAATTAATTATTA
1 -TTTTTAATTAATTATTA
60233338 TTTTTAA
1 TTTTTAA
60233345 CTTATTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 16 0.43
18 3 0.08
19 3 0.08
20 3 0.08
21 3 0.08
22 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTTAATTAATTATTA
Found at i:60233315 original size:39 final size:40
Alignment explanation
Indices: 60233264--60233344 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
60233254 AAACTTTTAA
60233264 AAAAAACCTGTAATATACTTTTTAATTAATTATTATTTTT
1 AAAAAACCTGTAATATACTTTTTAATTAATTATTATTTTT
*
60233304 AAAAAA-CTGTAATATATTTTTTAATTAATTATTATTTTT
1 AAAAAACCTGTAATATACTTTTTAATTAATTATTATTTTT
60233343 AA
1 AA
60233345 CTTATTTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 34 0.85
40 6 0.15
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (40 bp):
AAAAAACCTGTAATATACTTTTTAATTAATTATTATTTTT
Found at i:60242187 original size:18 final size:19
Alignment explanation
Indices: 60242159--60242196 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
60242149 GATAAAAAAT
60242159 AATTAAATAAACA-ATTAAA
1 AATTAAATAAA-ATATTAAA
60242178 AATT-AATAAAATATTAAA
1 AATTAAATAAAATATTAAA
60242196 A
1 A
60242197 TTTATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAATAAAATATTAAA
Found at i:60243689 original size:31 final size:31
Alignment explanation
Indices: 60243608--60243689 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
60243598 ACTATCTTAA
* * ***
60243608 AGTCACTAAACTATTAATAAATTTACATTTT
1 AGTCACTAAACTATTAAAAAAGTTACAAAAT
*
60243639 AGTCAC-ATAA-TTTTAAAAAAGTTACAAAAT
1 AGTCACTA-AACTATTAAAAAAGTTACAAAAT
60243669 AGTCACTAAACTATTAAAAAA
1 AGTCACTAAACTATTAAAAAA
60243690 TTTTCATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
30 23 0.56
31 18 0.44
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (31 bp):
AGTCACTAAACTATTAAAAAAGTTACAAAAT
Found at i:60243706 original size:31 final size:30
Alignment explanation
Indices: 60243608--60243707 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
60243598 ACTATCTTAA
*
60243608 AGTCACTAAACTATTAATAAATTTACATTTT
1 AGTCACTAAACTATTAAAAAATTTACA-TTT
* * **
60243639 AGTCAC-ATAA-TTTTAAAAAAGTTACAAAAT
1 AGTCACTA-AACTATTAAAAAATTTAC-ATTT
*
60243669 AGTCACTAAACTATTAAAAAATTTTCATTT
1 AGTCACTAAACTATTAAAAAATTTACATTT
60243699 AGATCACTA
1 AG-TCACTA
60243708 GGCTGCTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
30 26 0.48
31 28 0.52
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (30 bp):
AGTCACTAAACTATTAAAAAATTTACATTT
Found at i:60256533 original size:16 final size:16
Alignment explanation
Indices: 60256512--60256545 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
60256502 TTTGACATTG
60256512 AAAATTATAATATAAT
1 AAAATTATAATATAAT
*
60256528 AAAATTATCATATAAT
1 AAAATTATAATATAAT
60256544 AA
1 AA
60256546 CTATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATAATATAAT
Found at i:60259637 original size:11 final size:11
Alignment explanation
Indices: 60259621--60259645 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60259611 AAGGGGTGGA
60259621 AAAAGAGAAAT
1 AAAAGAGAAAT
60259632 AAAAGAGAAAT
1 AAAAGAGAAAT
60259643 AAA
1 AAA
60259646 CAAAGATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAGAGAAAT
Found at i:60260170 original size:22 final size:21
Alignment explanation
Indices: 60260145--60260193 Score: 89
Period size: 22 Copynumber: 2.3 Consensus size: 21
60260135 TTTTACTTAT
60260145 TATTATATTAAATTATCTAAA
1 TATTATATTAAATTATCTAAA
60260166 GTATTATATTAAATTATCTAAA
1 -TATTATATTAAATTATCTAAA
60260188 TATTAT
1 TATTAT
60260194 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TATTATATTAAATTATCTAAA
Found at i:60260279 original size:33 final size:31
Alignment explanation
Indices: 60260168--60260284 Score: 96
Period size: 33 Copynumber: 3.7 Consensus size: 31
60260158 TATCTAAAGT
* * *
60260168 ATTATATTAAATTATCTAAATA-TTATTTATT
1 ATTATATTAAATTATTTAAATATTTA-ATATC
* *
60260199 ATTATATTTAGCA-T-TTTAAATTATTTAATATT
1 ATTATA-TTA-AATTATTTAAA-TATTTAATATC
*
60260231 ATTCTATTAAATTATTTAAATATTTCATATATC
1 ATTATATTAAATTATTTAAATATTT-A-ATATC
*
60260264 ATTATATTAATTTATTTAAAT
1 ATTATATTAAATTATTTAAAT
60260285 TTATTTATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
30 1 0.01
31 20 0.29
32 22 0.31
33 27 0.39
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTATATTAAATTATTTAAATATTTAATATC
Found at i:60262372 original size:29 final size:29
Alignment explanation
Indices: 60262330--60262388 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
60262320 AAGCCATAGT
*
60262330 AAACCTCGAACTGGGCCAATAATCACGCC
1 AAACCTCAAACTGGGCCAATAATCACGCC
60262359 AAACCTCAAACTGGGCCAATAATCACGCC
1 AAACCTCAAACTGGGCCAATAATCACGCC
60262388 A
1 A
60262389 TGAGACAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.14
Consensus pattern (29 bp):
AAACCTCAAACTGGGCCAATAATCACGCC
Found at i:60267253 original size:29 final size:28
Alignment explanation
Indices: 60267211--60267271 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 28
60267201 ATTTTTATTT
60267211 TACTTTACTTTCATGTCTGAAGTTGTTAA
1 TACTTTACTTTCATGTCTGAAGTTGTT-A
60267240 TACTTTACTTTCATGTCTGAAGTTGTTA
1 TACTTTACTTTCATGTCTGAAGTTGTTA
60267268 TACT
1 TACT
60267272 GGCTTATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (28 bp):
TACTTTACTTTCATGTCTGAAGTTGTTA
Found at i:60277777 original size:3 final size:3
Alignment explanation
Indices: 60277771--60277816 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
60277761 CTACTACTAT
*
60277771 TGA TGA TGA TGA TGA TGG TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
60277817 AATGGGAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:60279032 original size:178 final size:175
Alignment explanation
Indices: 60278716--60279249 Score: 654
Period size: 178 Copynumber: 3.0 Consensus size: 175
60278706 ACAGTAACCC
* * *
60278716 TATGTTCATAGAATTCAGTGTATTGAGAGTCTACTTAGTCAACGGTCGTATTATCATATCATCCA
1 TATGTTCATAGAATTCGGTGTATTGAGAGTCTAC-TATTCAATGGTCGTA-TATCATATCATCCA
*
60278781 TCCATTATGTTTAGAAGGTTTTGTCATTGATATGGTGTGTTTTACCGTTGTTCTAAACCCCAGAG
64 TCCA-TA-GTTTAGAAGGTTTTG---TTGATATGGTGTGTTTTA-CTTTGTTCTAAACCCCAGAG
* *
60278846 TGATAACATATTGTTAAACACGTTGAGTGCTCTTGGCTTATAAGGTCTGTGCA
123 TGATAACATATTGTCAAACATGTTGAGTGCTCTTGGCTTATAAGGTCTGTGCA
* *
60278899 TATGTTCATAGAATTCGGTGTATTGAGAGTCTACTATTTAATGGACGTATCATCATATCATCCAT
1 TATGTTCATAGAATTCGGTGTATTGAGAGTCTACTATTCAATGGTCGTAT-ATCATATCATCCAT
60278964 CCATCACGTTTAGAAGGTTTTGTTGATATGGTGTGTTTTACTTTGTTCTAAACCCCAGAGTGATA
65 CCAT-A-GTTTAGAAGGTTTTGTTGATATGGTGTGTTTTACTTTGTTCTAAACCCCAGAGTGATA
* * * *
60279029 ACATATTGTCAAACATGTTGAGTGTTATTGGCTTAGAAGGTCTGTGTA
128 ACATATTGTCAAACATGTTGAGTGCTCTTGGCTTATAAGGTCTGTGCA
* * * * *
60279077 TATGTTCATAGAATTTGGTGTATTG-G-G---AGTATTCAATTGTCGCATTTCCATATCATCCAT
1 TATGTTCATAGAATTCGGTGTATTGAGAGTCTACTATTCAATGGTCGTATAT-CATATCATCCAT
* * *
60279137 -CAT-GTTTGGAAGGTTTTCTCATTGATATGGTGTGTTTTACTTTGTTCTAAGCCCCAGAGTGAT
65 CCATAGTTTAGAAGG-TTT-T-GTTGATATGGTGTGTTTTACTTTGTTCTAAACCCCAGAGTGAT
* *
60279200 AGCATATTGTCAAA-AGTGTTGA-TCGCTCTTGGCTTATAAGGTCCGTGCA
127 AACATATTGTCAAACA-TGTTGAGT-GCTCTTGGCTTATAAGGTCTGTGCA
60279249 T
1 T
60279250 GTGAACATTG
Statistics
Matches: 314, Mismatches: 29, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
169 9 0.03
170 3 0.01
171 3 0.01
172 85 0.27
173 25 0.08
176 1 0.00
177 1 0.00
178 90 0.29
179 18 0.06
181 2 0.01
182 44 0.14
183 33 0.11
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (175 bp):
TATGTTCATAGAATTCGGTGTATTGAGAGTCTACTATTCAATGGTCGTATATCATATCATCCATC
CATAGTTTAGAAGGTTTTGTTGATATGGTGTGTTTTACTTTGTTCTAAACCCCAGAGTGATAACA
TATTGTCAAACATGTTGAGTGCTCTTGGCTTATAAGGTCTGTGCA
Found at i:60281587 original size:132 final size:132
Alignment explanation
Indices: 60281342--60281983 Score: 760
Period size: 132 Copynumber: 5.0 Consensus size: 132
60281332 AACCCCACCT
* * * *
60281342 GCAGTGGCATTGGCAGCTCCT-CTGTTGGTAGAGCCCCTGTCTTCATCCCATGATGAGCTGCTTT
1 GCAGTGGCATTGGCAGCT-CTGCTGGTGGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTTT
* ** * * * * * *
60281406 TCGCTGGTGCCACGGTTCCACTTGCATTGCTGAAGGCTTGAGACCGAAGCCCATCTCCAGTGGTA
65 TTGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCAGTGGTA
60281471 GTG
130 GTG
* * * *
60281474 GCATTGGCAATAGCAGCTCTGCTGGTGGTAGAGCCCCAGTTTTCATCCCATGCTGGGCTGCTTTT
1 GCAGTGGCATTGGCAGCTCTGCTGGTGGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTTTT
* * * *
60281539 TGCTAGAGCCACAGTTCCACTTGTGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCGGCGGTAG
66 TGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCAGTGGTAG
60281604 TG
131 TG
* * * * * *
60281606 GTAGTGGCATTGGAAGCTCTGCTGGAGGTAGAGCCCCACTCTTCATCCCATTCTGGGTTGCTTTT
1 GCAGTGGCATTGGCAGCTCTGCTGGTGGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTTTT
*
60281671 TG-CAGGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAATCCCATCTGCAGTGGTA
66 TGCCA-GAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCAGTGGTA
60281735 GTG
130 GTG
* *
60281738 GCA---GC--T--C--CTCTG-T--TGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTT
1 GCAGTGGCATTGGCAGCTCTGCTGGTGGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTTTT
* *
60281791 TGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAATCCCATCTGCAGTGGTAG
66 TGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCAGTGGTAG
60281856 TG
131 TG
* * *
60281858 GCAGTGGCATTGGCAGCTCCT-CT-GTGGGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTT
1 GCAGTGGCATTGGCAGCT-CTGCTGGT-GGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTT
* ** **
60281921 TTTGCCGGAGCCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCAT-TGGCAGTG
64 TTTGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCT-GCAGTG
60281984 ACAGCATGTT
Statistics
Matches: 443, Mismatches: 50, Indels: 34
0.84 0.09 0.06
Matches are distributed among these distances:
120 102 0.23
121 2 0.00
122 1 0.00
123 7 0.02
125 1 0.00
127 2 0.00
129 4 0.01
130 3 0.01
131 5 0.01
132 316 0.71
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.27
Consensus pattern (132 bp):
GCAGTGGCATTGGCAGCTCTGCTGGTGGTAGAGCCCCAGTCTTCATCCCATGCTGGGCTGCTTTT
TGCCAGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCAGTGGTAG
TG
Found at i:60281807 original size:252 final size:252
Alignment explanation
Indices: 60281486--60281983 Score: 716
Period size: 252 Copynumber: 2.0 Consensus size: 252
60281476 ATTGGCAATA
* * * *
60281486 GCAGCTCTGCTGGTGGTAGAGCCCCAGTTTTCATCCCATGCTGGGCTGCTTTTTGCTAGAGCCAC
1 GCAGCTCTGCTGGTGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTTTGCCAGAGCCAC
* * * *
60281551 AGTTCCACTTGTGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCGGCGGTAGTGGTAGTGGCAT
66 AGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAAGCCCATCTGCAGCGGTAGTGGCAGTGGCAT
* * ** *
60281616 TGGAAGCT-CTGCTG-GAGGTAGAGCCCCACTCTTCATCCCATTCTGGGTTGCTTTTTGCAGGAG
131 TGGAAGCTCCT-CTGTG-GGCAGAGCCCCACGCTTCATCCCACGCTGGGCTGCTTTTTGCAGGAG
** ** *
60281679 CCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAATCCCATCT-GCAGTGGTAGTG
194 CCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCAT-TGGCAGTGGTAGTG
*
60281738 GCAGCTCCT-CTGTTGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTTTGCCAGAGCCA
1 GCAGCT-CTGCTGGTGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTTTGCCAGAGCCA
* *
60281802 CAGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAATCCCATCTGCAGTGGTAGTGGCAGTGGCA
65 CAGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAAGCCCATCTGCAGCGGTAGTGGCAGTGGCA
* * *
60281867 TTGGCAGCTCCTCTGTGGGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTTTTTGCCGGAGC
130 TTGGAAGCTCCTCTGTGGGCAGAGCCCCACGCTTCATCCCACGCTGGGCTGCTTTTTGCAGGAGC
60281932 CACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCATTGGCAGTG
195 CACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCATTGGCAGTG
60281984 ACAGCATGTT
Statistics
Matches: 218, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
251 1 0.00
252 212 0.97
253 5 0.02
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.27
Consensus pattern (252 bp):
GCAGCTCTGCTGGTGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTTTGCCAGAGCCAC
AGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAAGCCCATCTGCAGCGGTAGTGGCAGTGGCAT
TGGAAGCTCCTCTGTGGGCAGAGCCCCACGCTTCATCCCACGCTGGGCTGCTTTTTGCAGGAGCC
ACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCATTGGCAGTGGTAGTG
Found at i:60281934 original size:384 final size:384
Alignment explanation
Indices: 60281281--60281975 Score: 1025
Period size: 384 Copynumber: 1.8 Consensus size: 384
60281271 ATGCTGAGCA
* * *
60281281 GCTTTTTGCTGGAGCCGCAGTTTCACTTGCATTGCTCAAGGCTTGAGACTGAACCCCACCTGCAG
1 GCTTTTTGCAGGAGCCACAGTTCCACTTGCATTGCTCAAGGCTTGAGACTGAACCCCACCTGCAG
* * ** *
60281346 TGGCATTGGCAGCTCCTCTGTTGGTAGAGCCCCTGTCTTCATCCCATGATGAGCTGCTTTTCGCT
66 TGGCAGTGGCAGCTCCTCTGTTGGCAGAGCCCCACTCTTCATCCCATGATGAGCTGCTTTTCGCC
* * * * *
60281411 GGTGCCACGGTTCCACTTGCATTGCTGAAGGCTTGAGACCGAAGCCCATCTCCAGTGGTAGTGGC
131 AGAGCCACAGTTCCACTTGCATTGCTCAAAGCTTGAGACCGAAGCCCATCTCCAGTGGTAGTGGC
* * ** *
60281476 ATTGGCAATAGCAGCTCTGCTGGTGGTAGAGCCCCAGTTTTCATCCCATGCTGGGCTGCTTTTTG
196 AGTGGCAATAGCAGCTCTGCTGGTGGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTTTTTG
* ** **
60281541 CTAGAGCCACAGTTCCACTTGTGTTGCTCAAGGCTTGAGACTGAAGCCCATCTGCGGCGGTAGTG
261 CCAGAGCCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCATCTGCGGCGGTAGTG
60281606 GTAGTGGCATTGGAAGCTCTGCTGGAGGTAGAGCCCCACTCTTCATCCCATTCTGGGTT
326 GTAGTGGCATTGGAAGCTCTGCTGGAGGTAGAGCCCCACTCTTCATCCCATTCTGGGTT
* * *
60281665 GCTTTTTGCAGGAGCCACAGTTCCACTTGCGTTGCTCAAGGCTTGAGACTGAATCCCATCTGCAG
1 GCTTTTTGCAGGAGCCACAGTTCCACTTGCATTGCTCAAGGCTTGAGACTGAACCCCACCTGCAG
* * * *
60281730 TGGTAGTGGCAGCTCCTCTGTTGGCAGAGCCCCACTCTTCATCCCATGCTGGGCTGCTTTTTGCC
66 TGGCAGTGGCAGCTCCTCTGTTGGCAGAGCCCCACTCTTCATCCCATGATGAGCTGCTTTTCGCC
* * * *
60281795 AGAGCCACAGTTCCACTTGCGTTGCTCAAAGCTTGAGACTGAATCCCATCTGCAGTGGTAGTGGC
131 AGAGCCACAGTTCCACTTGCATTGCTCAAAGCTTGAGACCGAAGCCCATCTCCAGTGGTAGTGGC
* *
60281860 AGTGGCATTGGCAGCTCCT-CT-GTGGGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTTTT
196 AGTGGCAATAGCAGCT-CTGCTGGT-GGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTTTT
*
60281923 TGCCGGAGCCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCAT
259 TGCCAGAGCCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCAT
60281976 TGGCAGTGAC
Statistics
Matches: 272, Mismatches: 37, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
383 2 0.01
384 268 0.99
385 2 0.01
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (384 bp):
GCTTTTTGCAGGAGCCACAGTTCCACTTGCATTGCTCAAGGCTTGAGACTGAACCCCACCTGCAG
TGGCAGTGGCAGCTCCTCTGTTGGCAGAGCCCCACTCTTCATCCCATGATGAGCTGCTTTTCGCC
AGAGCCACAGTTCCACTTGCATTGCTCAAAGCTTGAGACCGAAGCCCATCTCCAGTGGTAGTGGC
AGTGGCAATAGCAGCTCTGCTGGTGGCAGAGCCCCAGGCTTCATCCCACGCTGGGCTGCTTTTTG
CCAGAGCCACAGTTCCACTTGAATTGCTCAACACTTGAGACTGAAGCCCATCTGCGGCGGTAGTG
GTAGTGGCATTGGAAGCTCTGCTGGAGGTAGAGCCCCACTCTTCATCCCATTCTGGGTT
Found at i:60286554 original size:21 final size:21
Alignment explanation
Indices: 60286528--60286573 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
60286518 CTATGATGGG
60286528 TGTCAAAACTGTCTAGTCTTA
1 TGTCAAAACTGTCTAGTCTTA
60286549 TGTCAAAACTGTCTAGTCTTA
1 TGTCAAAACTGTCTAGTCTTA
60286570 TGTC
1 TGTC
60286574 TTGACCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (21 bp):
TGTCAAAACTGTCTAGTCTTA
Found at i:60291862 original size:2 final size:2
Alignment explanation
Indices: 60291855--60291912 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
60291845 CAATCCCACC
60291855 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
60291897 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
60291913 GTTTTCTGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:60292561 original size:31 final size:31
Alignment explanation
Indices: 60292526--60292592 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
60292516 GTCCAATCTT
* * *
60292526 GTTCAAAGATCAAAATGGATCTAGTTGCTAA
1 GTTCAAAGACCAAAATAGATCTAGTTGCCAA
*
60292557 GTTCAATGACCAAAATAGATCTAGTTGCCAA
1 GTTCAAAGACCAAAATAGATCTAGTTGCCAA
60292588 GTTCA
1 GTTCA
60292593 TGGGCAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (31 bp):
GTTCAAAGACCAAAATAGATCTAGTTGCCAA
Found at i:60300071 original size:21 final size:22
Alignment explanation
Indices: 60300032--60300073 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
60300022 TTTTACTTTT
60300032 TTTTAATTTTTATATATTTTAG
1 TTTTAATTTTTATATATTTTAG
60300054 TTTT-ATTATTTA-ATATTTTA
1 TTTTAATT-TTTATATATTTTA
60300074 TAGTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTAATTTTTATATATTTTAG
Found at i:60300156 original size:24 final size:26
Alignment explanation
Indices: 60300122--60300176 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
60300112 TTGAGTGTTT
*
60300122 TATTTCTATAA-TATTAA-TTTTTCAA
1 TATTTCTATAATTATAAACTTTTT-AA
60300147 TATTT-TATAATTATAAACTTTTTAA
1 TATTTCTATAATTATAAACTTTTTAA
60300172 TATTT
1 TATTT
60300177 AGAATAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 17 0.63
26 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTCTATAATTATAAACTTTTTAA
Found at i:60302724 original size:19 final size:19
Alignment explanation
Indices: 60302700--60302738 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
60302690 CAAACCTAAA
60302700 TGAACCCTAATTTAATTAT
1 TGAACCCTAATTTAATTAT
60302719 TGAACCCTAATTTAATTAT
1 TGAACCCTAATTTAATTAT
60302738 T
1 T
60302739 AAGTTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
TGAACCCTAATTTAATTAT
Found at i:60313638 original size:31 final size:31
Alignment explanation
Indices: 60313600--60313660 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
60313590 TGATGAAATA
*
60313600 CAAGTTCAAAGACCAAAATGAACCTAATTGT
1 CAAGTTCAAAGAACAAAATGAACCTAATTGT
* * *
60313631 CAAGTTCAGATAACAAAGTGAACCTAATTG
1 CAAGTTCAAAGAACAAAATGAACCTAATTG
60313661 CCATAAATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (31 bp):
CAAGTTCAAAGAACAAAATGAACCTAATTGT
Found at i:60313788 original size:191 final size:188
Alignment explanation
Indices: 60313441--60313819 Score: 521
Period size: 191 Copynumber: 2.0 Consensus size: 188
60313431 TGATGAAATA
* *
60313441 CAAGTTCAAAGAACAAAAAGAACCTAATTGCCATAAACTTGACAACTAAATCCATTTTGATCGTA
1 CAAGTTCAAAGAACAAAAAGAACCTAATTGCCATAAAC-TGACAACTAAATCCATTTTGACCCTA
60313506 GAAATTGACAATGTAAACGTTCAATGACGTAACACTATAAGATTGTACCCAGTCATCACCTTTAG
65 GAAATTGACAATGTAAAC-TTCAATGACGTAACACTATAAGATTGTACCCAGTCATCACCTTTAG
* * *
60313571 GTGTCACATTATCAAACTTTGATGAAATACAAGTTCAAAGACCAAAATGAACCTAATTGT
129 GAGTCACATTATCAAACTTTGATGAAATACAAGTTCAAACACCAAAATGAACATAATTGT
* * **
60313631 CAAGTTCAGATAACAAAGTGAACCTAATTGCCATAAA-TGCAACAACTAAATCCATTTTGACCCT
1 CAAGTTCAAAGAACAAAAAGAACCTAATTGCCATAAACTG--ACAACTAAATCCATTTTGACCCT
* * * * *
60313695 TGAAATTGACAAATGCATAAA-TTTAATGATGTGACACTATAAGATTGTA-CCACTTCATCACCT
64 AGAAATTGAC-AATG--TAAACTTCAATGACGTAACACTATAAGATTGTACCCA-GTCATCACCT
* *
60313758 TTAGGAGTCACATTATCAAATTTTGATGAAATTCAAGTTCAAACACCAAAATGAACATAATT
125 TTAGGAGTCACATTATCAAACTTTGATGAAATACAAGTTCAAACACCAAAATGAACATAATT
60313820 ACCATAAACT
Statistics
Matches: 167, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
188 2 0.01
190 66 0.40
191 95 0.57
193 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (188 bp):
CAAGTTCAAAGAACAAAAAGAACCTAATTGCCATAAACTGACAACTAAATCCATTTTGACCCTAG
AAATTGACAATGTAAACTTCAATGACGTAACACTATAAGATTGTACCCAGTCATCACCTTTAGGA
GTCACATTATCAAACTTTGATGAAATACAAGTTCAAACACCAAAATGAACATAATTGT
Found at i:60316886 original size:17 final size:16
Alignment explanation
Indices: 60316853--60316883 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60316843 TTTAAAGTAA
60316853 AAAAATCATTAAAAAT
1 AAAAATCATTAAAAAT
*
60316869 AAAAATTATTAAAAA
1 AAAAATCATTAAAAA
60316884 ATATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATCATTAAAAAT
Found at i:60317273 original size:31 final size:30
Alignment explanation
Indices: 60317228--60317306 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
60317218 ATTAAAATTG
*
60317228 TATTTTAA-TATTCAAAAATGAA-AAAA-AA
1 TATTTTAATTTTTCAAAAAT-AATAAAATAA
60317256 TCA-TTTAACCTTTTTCAAAAATAATAAAATAA
1 T-ATTTTAA--TTTTTCAAAAATAATAAAATAA
60317288 TATTTTAATTTTTCAAAAA
1 TATTTTAATTTTTCAAAAA
60317307 ATTTATAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
28 6 0.14
29 1 0.02
30 13 0.30
31 15 0.35
32 8 0.19
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTTTAATTTTTCAAAAATAATAAAATAA
Found at i:60318151 original size:12 final size:12
Alignment explanation
Indices: 60318122--60318158 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
60318112 TCGTAATATA
60318122 AATTTAATATTAT
1 AATTTAATATT-T
60318135 AATTTAATATTT
1 AATTTAATATTT
*
60318147 AATTTATTATTT
1 AATTTAATATTT
60318159 TGATACTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AATTTAATATTT
Found at i:60323972 original size:14 final size:14
Alignment explanation
Indices: 60323953--60324004 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
60323943 AGAAAACACC
60323953 ATATATATGTATGTAT
1 ATATATATGTATG--T
*
60323969 ATATATATGTACGT
1 ATATATATGTATGT
60323983 ATATATATGTATGT
1 ATATATATGTATGT
*
60323997 ATGTATAT
1 ATATATAT
60324005 ATATAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (14 bp):
ATATATATGTATGT
Found at i:60323974 original size:16 final size:16
Alignment explanation
Indices: 60323953--60324009 Score: 87
Period size: 16 Copynumber: 3.4 Consensus size: 16
60323943 AGAAAACACC
60323953 ATATATATGTATGTAT
1 ATATATATGTATGTAT
*
60323969 ATATATATGTACGTAT
1 ATATATATGTATGTAT
60323985 ATATATGTATGTATGTAT
1 ATATA--TATGTATGTAT
60324003 ATATATA
1 ATATATA
60324010 AAATGTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 22 0.59
18 15 0.41
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (16 bp):
ATATATATGTATGTAT
Found at i:60327521 original size:9 final size:9
Alignment explanation
Indices: 60327501--60327549 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
60327491 GTAGTGATTC
*
60327501 AATTCTGTT
1 AATTCGGTT
*
60327510 AATTCGGGT
1 AATTCGGTT
*
60327519 AATTAGGTT
1 AATTCGGTT
*
60327528 AATTCAGTT
1 AATTCGGTT
60327537 AATTCGGTT
1 AATTCGGTT
60327546 AATT
1 AATT
60327550 TTTAACAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:60333572 original size:16 final size:16
Alignment explanation
Indices: 60333551--60333592 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
60333541 AATTTGTATC
*
60333551 CGAAATAATCTAAACT
1 CGAAATAATCTAAAAT
*
60333567 CGAAATAATTTAAAAT
1 CGAAATAATCTAAAAT
*
60333583 CGAAACAATC
1 CGAAATAATC
60333593 CAATCTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (16 bp):
CGAAATAATCTAAAAT
Found at i:60344687 original size:2 final size:2
Alignment explanation
Indices: 60344640--60344668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60344630 AATTTAATCT
60344640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60344669 GTTCATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60353846 original size:2 final size:2
Alignment explanation
Indices: 60353841--60353881 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
60353831 TGAGATTGTA
60353841 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
60353882 AATTAATTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60354610 original size:46 final size:46
Alignment explanation
Indices: 60354543--60354635 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
60354533 ATCTAGCCTT
60354543 TGTACATAATCCAATTTAACTGAAGCCCTTAGAGTGACTTCCACTA
1 TGTACATAATCCAATTTAACTGAAGCCCTTAGAGTGACTTCCACTA
60354589 TGTACATAATCCAATTTAACTGAAGCCCTTAGAGTGACTTCCACTA
1 TGTACATAATCCAATTTAACTGAAGCCCTTAGAGTGACTTCCACTA
60354635 T
1 T
60354636 AAAAGTCTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (46 bp):
TGTACATAATCCAATTTAACTGAAGCCCTTAGAGTGACTTCCACTA
Found at i:60366048 original size:29 final size:30
Alignment explanation
Indices: 60365989--60366048 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
60365979 CAGCCCCCAA
* *
60365989 TTTAAAAGTAAATTAAAAAAAGTATTCATT
1 TTTAAAAGTAAATTAAAAAAAGTACTAATT
**
60366019 TTTAAAA-TAAATTTTAAAAAGTACTAATT
1 TTTAAAAGTAAATTAAAAAAAGTACTAATT
60366048 T
1 T
60366049 GAAAAAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTAAAAGTAAATTAAAAAAAGTACTAATT
Found at i:60366054 original size:29 final size:28
Alignment explanation
Indices: 60365987--60366054 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 28
60365977 CCCAGCCCCC
* *
60365987 AATTTAAAAGTAAATTAAAAAAAGTATT
1 AATTTAAAAATAAATTAAAAAAAGTACT
* * **
60366015 CATTTTTAAAATAAATTTTAAAAAGTACT
1 -AATTTAAAAATAAATTAAAAAAAGTACT
60366044 AATTTGAAAAA
1 AATTT-AAAAA
60366055 AAGTTGTGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (28 bp):
AATTTAAAAATAAATTAAAAAAAGTACT
Found at i:60370412 original size:57 final size:57
Alignment explanation
Indices: 60370320--60370434 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
60370310 ATTGTTGTCG
* * *
60370320 GGCAATTCGGGATGGCTGAATAAACAGTTCAGACAATTACTAAAACCATCTTTGCCA
1 GGCAATCCGGGATGGCTGAATAAACAGTTCAGACAATTACTAAAACAATCGTTGCCA
* * **
60370377 GGCAATCCGGGATGGTTGAATAAATAGTTTGGACAATTACTAAAACAATCGTTGCCA
1 GGCAATCCGGGATGGCTGAATAAACAGTTCAGACAATTACTAAAACAATCGTTGCCA
60370434 G
1 G
60370435 TCAACTCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (57 bp):
GGCAATCCGGGATGGCTGAATAAACAGTTCAGACAATTACTAAAACAATCGTTGCCA
Found at i:60371344 original size:24 final size:24
Alignment explanation
Indices: 60371317--60371368 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
60371307 AATCAAAGTC
* * *
60371317 AAATATATTATGCTAATAAATGCT
1 AAATACATTATACTAATAAATACT
*
60371341 AAATACATTATACTCATAAATACT
1 AAATACATTATACTAATAAATACT
60371365 AAAT
1 AAAT
60371369 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATACATTATACTAATAAATACT
Found at i:60375754 original size:24 final size:24
Alignment explanation
Indices: 60375727--60375783 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
60375717 AAACCTAATT
60375727 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
* *
60375751 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATG
*
60375775 CTCATAAAT
1 CTAATAAAT
60375784 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:60375789 original size:24 final size:24
Alignment explanation
Indices: 60375739--60375790 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
60375729 AATCAAAGTC
* **
60375739 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
60375763 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
60375787 AAAT
1 AAAT
60375791 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:60383505 original size:30 final size:27
Alignment explanation
Indices: 60383438--60383498 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
60383428 TTTTTGGAGG
* *
60383438 TTAAACTATAATATTGCTATTATTAGT
1 TTAAAATATAATATTACTATTATTAGT
60383465 TTAAAATATAATATTACTATTATTAGT
1 TTAAAATATAATATTACTATTATTAGT
60383492 TTAAAAT
1 TTAAAAT
60383499 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (27 bp):
TTAAAATATAATATTACTATTATTAGT
Found at i:60383513 original size:27 final size:27
Alignment explanation
Indices: 60383456--60383514 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
60383446 TAATATTGCT
** **
60383456 ATTATTAGTTTAAAATATAATATTACT
1 ATTATTAGTTTAAAATATAATAAAAAA
* *
60383483 ATTATTAGTTTAAAATTTTATAAAAAA
1 ATTATTAGTTTAAAATATAATAAAAAA
60383510 ATTAT
1 ATTAT
60383515 ATTTTAAGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
ATTATTAGTTTAAAATATAATAAAAAA
Found at i:60395320 original size:14 final size:14
Alignment explanation
Indices: 60395301--60395327 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60395291 TTATTTCGAC
60395301 TTTTTGACCCCATA
1 TTTTTGACCCCATA
60395315 TTTTTGACCCCAT
1 TTTTTGACCCCAT
60395328 GTTGTAGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.30, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTTTGACCCCATA
Found at i:60402653 original size:21 final size:22
Alignment explanation
Indices: 60402606--60402655 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
60402596 AAACTGTAAT
*
60402606 ACAT-AAAAAAATGTATTTAAA
1 ACATGAAATAAATGTATTTAAA
*
60402627 ATATGAAATAAAT-TATTTAAA
1 ACATGAAATAAATGTATTTAAA
*
60402648 GCATGAAA
1 ACATGAAA
60402656 GAGTTTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (22 bp):
ACATGAAATAAATGTATTTAAA
Found at i:60409165 original size:21 final size:21
Alignment explanation
Indices: 60409118--60409165 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
60409108 TTTATTCGAC
*
60409118 AATTTTTAAAAAAATTCATAA
1 AATTTTTAAAAAAATACATAA
*
60409139 ATATTTTT-TAAAAATACAATAA
1 A-ATTTTTAAAAAAATAC-ATAA
60409161 AATTT
1 AATTT
60409166 CAAGAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTTTAAAAAAATACATAA
Found at i:60411838 original size:29 final size:29
Alignment explanation
Indices: 60411796--60411865 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
60411786 TATAAAAAAT
60411796 TTATAATTTTTTAAGGGGCCAGATTTGAA
1 TTATAATTTTTTAAGGGGCCAGATTTGAA
60411825 TTATAATTTTTTAAGGGGCCAGATTTGAA
1 TTATAATTTTTTAAGGGGCCAGATTTGAA
60411854 TTATAATTTTTT
1 TTATAATTTTTT
60411866 TTGTGATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (29 bp):
TTATAATTTTTTAAGGGGCCAGATTTGAA
Found at i:60412798 original size:3 final size:3
Alignment explanation
Indices: 60412759--60412784 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
60412749 TTTTATACAA
60412759 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
60412785 ACTCTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:60412805 original size:13 final size:14
Alignment explanation
Indices: 60412778--60412806 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
60412768 AATAATAATA
60412778 ATAATAAACTCTTT
1 ATAATAAACTCTTT
60412792 ATAATAAA-TCTTT
1 ATAATAAACTCTTT
60412805 AT
1 AT
60412807 TTTGTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATAAACTCTTT
Done.