Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004701.1 Kokia drynarioides strain JFW-HI SEQ_118263, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42594
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:23884 original size:17 final size:17
Alignment explanation
Indices: 23862--23911 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
23852 TGTTAGTAAG
23862 CATTGTCATTGAA-TTC
1 CATTGTCATTGAATTTC
*
23878 TCATTGTCATTGCATTTC
1 -CATTGTCATTGAATTTC
*
23896 CATTGTCATTGCATTT
1 CATTGTCATTGAATTT
23912 TAATGCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (17 bp):
CATTGTCATTGAATTTC
Found at i:29120 original size:15 final size:15
Alignment explanation
Indices: 29089--29126 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29079 CCTTCATCCA
29089 TGTTCGCAACACAAG
1 TGTTCGCAACACAAG
*
29104 TGTTTGCAACATC-AG
1 TGTTCGCAACA-CAAG
29119 TGTTCGCA
1 TGTTCGCA
29127 TTGTGTGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (15 bp):
TGTTCGCAACACAAG
Found at i:32443 original size:28 final size:28
Alignment explanation
Indices: 32403--32458 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
32393 CTCATCAGGA
32403 AGATGACCACTTCATTGTTTTGGATAAC
1 AGATGACCACTTCATTGTTTTGGATAAC
*
32431 AGATGACCACTTCGTTGTTTTGGATAAC
1 AGATGACCACTTCATTGTTTTGGATAAC
32459 TACAATTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (28 bp):
AGATGACCACTTCATTGTTTTGGATAAC
Found at i:32545 original size:39 final size:39
Alignment explanation
Indices: 32502--33191 Score: 356
Period size: 39 Copynumber: 17.7 Consensus size: 39
32492 TATAGTTGTG
* *
32502 ATCTGCCTCAAGCTCAGGGTAAAAGATCGGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
** * * * ** * **
32541 ATCTGCCCCAAGCTCAAGGTAAGAGATTGGCTAACGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * * * * *
32580 ATCTGCCCCAGGCTCGAGATGAAAGATCAGATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * * * * * * *
32619 ATCTACCTCAGGCTCGAGGTAAGAGATTGGCT-GATG-A
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * *
32656 TGATCTGCCCCAAGCTCGAGGTAAAAGATTGGATGACTGCA
1 --ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* *
32697 ATCTGCCCCAAGCTTGGGGTAAGAA-ATTGGCTGATGG-TG-A
1 ATCTGCCCCAAGCTCGGGGTAA-AAGA-T--CGGATGGCTGCA
* * * * * * *
32737 TTC-ACCCTAGGCTCGGGGTAAAAGATTGGATGGATACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
** * * *
32775 ATCTATCCCATGCTCGGGGTAAGAGATTGGCTGATGG-TG--
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGGATGGCTGCA
* * *
32814 ATCCGCCCCAAGCTGGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * *
32853 ATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGG-TG--
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCG---GATGGCTGCA
* * * **
32892 ATTTGCCCCAAGCTCGAGGTAAGAGATTGACTAATGG-TG--
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGGATGGCTGCA
32931 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* **
32970 ATCTGCCCCAAGCTCGGGGTAAGAGATTAGCTTATGG-TG--
1 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CGGATGGCTGCA
* * * *
33009 ATCTACCCCAAGTTCGGGGTAAAAGATAGAATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * * * * **
33048 ATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGACTGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * *
33087 ATCTACCTCAAGTTCGGGGTAAAAGATCGGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
* * * *
33126 ATCTGCCCCAGGCAT-AGGGTAAAAGATCGGATAGCTGTA
1 ATCTGCCCCAAGC-TCGGGGTAAAAGATCGGATGGCTGCA
* ** * *
33165 ATTTGCTTCAAGCTCAGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGAT
33192 TGGCTGACTA
Statistics
Matches: 492, Mismatches: 124, Indels: 70
0.72 0.18 0.10
Matches are distributed among these distances:
36 19 0.04
37 8 0.02
38 12 0.02
39 415 0.84
40 12 0.02
41 8 0.02
42 18 0.04
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCA
Found at i:32613 original size:78 final size:78
Alignment explanation
Indices: 32499--32996 Score: 474
Period size: 78 Copynumber: 6.4 Consensus size: 78
32489 TTGTATAGTT
* **
32499 GTGATCTGCCTCAAGCTC-AGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCAAGGTAA
1 GTGATCTGCCCCAAGCTCGA-GGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAA
* *
32563 GAGATTGGCTAACG
65 GAGATTGGCTGATG
* * * * * * * * *
32577 GTGATCTGCCCCAGGCTCGAGATGAAAGATCAGATGGCTACAATCTACCTCAGGCTCGAGGTAAG
1 GTGATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
32642 AGATTGGCTGATG
66 AGATTGGCTGATG
* * * *
32655 ATGATCTGCCCCAAGCTCGAGGTAAAAGATTGGATGACTGCAATCTGCCCCAAGCTTGGGGTAAG
1 GTGATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
*
32720 AAATTGGCTGATG
66 AGATTGGCTGATG
* * * * * ** *
32733 GTGAT-T-CACCCTAGGCTCGGGGTAAAAGATTGGATGGATACAATCTATCCCATGCTCGGGGTA
1 GTGATCTGC-CCC-AAGCTCGAGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTA
32796 AGAGATTGGCTGATG
64 AGAGATTGGCTGATG
* * * * *
32811 GTGATCCGCCCCAAGCTGGGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAG
1 GTGATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
**
32876 AGATTGATTGATG
66 AGATTGGCTGATG
* * **
32889 GTGATTTGCCCCAAGCTCGAGGTAAGAGATTGACTAATGG-TG--ATCTGCCCCAAGCTCGGGGT
1 GTGATCTGCCCCAAGCTCGAGGTAAAAGA-T--CGGATGGCTGCAATCTGCCCCAAGCTCGGGGT
* *
32951 AAAAGA-T--CGGATG
63 AAGAGATTGGCTGATG
* *
32964 GCTGCAATCTGCCCCAAGCTCGGGGTAAGAGAT
1 G-TG--ATCTGCCCCAAGCTCGAGGTAAAAGAT
32997 TAGCTTATGG
Statistics
Matches: 348, Mismatches: 61, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
75 5 0.01
76 3 0.01
77 6 0.02
78 320 0.92
79 5 0.01
80 3 0.01
81 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (78 bp):
GTGATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
AGATTGGCTGATG
Found at i:32749 original size:117 final size:118
Alignment explanation
Indices: 32541--33074 Score: 426
Period size: 117 Copynumber: 4.6 Consensus size: 118
32531 GATGGCTGCA
* * * * * ** * * * *
32541 ATCTGCCCCAAGCTCAAGGTAAGAGATTGGCTAAC-GGTGATCTGCCCCAGGCTCGAGATGAAAG
1 ATCTACCCCAAGCTCGAGGTAAAAGATTGGATGACTGGCAATCTGCCCCAAGCTCGGGGTAAAAG
* * * * *
32605 ATCAGATGGCTACAATCTACCTCAGGCTCGAGGTAAGAGATTGGCTGATGATG
66 ATCTGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* *
32658 ATCTGCCCCAAGCTCGAGGTAAAAGATTGGATGACT-GCAATCTGCCCCAAGCTTGGGGTAAGAA
1 ATCTACCCCAAGCTCGAGGTAAAAGATTGGATGACTGGCAATCTGCCCCAAGCTCGGGGTAA-AA
* * * * * **
32722 -ATTGGCTGATGG-TG-ATTC-ACCCTAGGCTCGGGGTAAAAGATTGGATGGAT-ACA
65 GA-T--CTGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATG
* * * * * ** * *
32775 ATCTATCCCATGCTCGGGGTAAGAGATTGGCTGA-TGGTGATCCGCCCCAAGCTGGGGGTAAAAG
1 ATCTACCCCAAGCTCGAGGTAAAAGATTGGATGACTGGCAATCTGCCCCAAGCTCGGGGTAAAAG
** *
32839 ATC-GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGGTG
66 ATCTG-ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * **
32892 ATTTGCCCCAAGCTCGAGGTAAGAGATT-GACT-AATGGTGATCTGCCCCAAGCTCGGGGTAAAA
1 ATCTACCCCAAGCTCGAGGTAAAAGATTGGA-TGACTGGCAATCTGCCCCAAGCTCGGGGTAAAA
* * * * *
32955 GATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTAGCTTATGGTG
65 GATCTGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * * *
33009 ATCTACCCCAAGTTCGGGGTAAAAGATAGAATGGCT-GCAATCTACCCCAAGCTCGGGGTAAGAG
1 ATCTACCCCAAGCTCGAGGTAAAAGATTGGATGACTGGCAATCTGCCCCAAGCTCGGGGTAAAAG
33073 AT
66 AT
33075 TGGCTGACTG
Statistics
Matches: 333, Mismatches: 66, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
113 1 0.00
114 5 0.02
115 2 0.01
116 12 0.04
117 294 0.88
118 12 0.04
119 1 0.00
120 6 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (118 bp):
ATCTACCCCAAGCTCGAGGTAAAAGATTGGATGACTGGCAATCTGCCCCAAGCTCGGGGTAAAAG
ATCTGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
Found at i:32919 original size:156 final size:155
Alignment explanation
Indices: 32499--32920 Score: 531
Period size: 156 Copynumber: 2.7 Consensus size: 155
32489 TTGTATAGTT
* * **
32499 GTGATCTGCCTCAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCAAGGTAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
* * * * ** *
32564 AGATTGGCTAACGGTGATCTGCCCCAGGCTCGAGATGAAAGATCAGATGGCTACAATCTACCTCA
66 AGATTGGCTGATGGTGATTTGCCCCAGGCTCGAGGT-AAAGATTGGATGGATACAATCTACCTCA
32629 GGCTCGAGGTAAGAGATTGGCTGATG
130 GGCTCGAGGTAAGAGATTGGCTGATG
* * * * *
32655 ATGATCTGCCCCAAGCTCGAGGTAAAAGATTGGATGACTGCAATCTGCCCCAAGCTTGGGGTAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
* ** * *
32720 AAATTGGCTGATGGTGATTCACCCTAGGCTCGGGGTAAAAGATTGGATGGATACAATCTATCC-C
66 AGATTGGCTGATGGTGATTTGCCCCAGGCTCGAGGT-AAAGATTGGATGGATACAATCTA-CCTC
* *
32784 ATGCTCGGGGTAAGAGATTGGCTGATG
129 AGGCTCGAGGTAAGAGATTGGCTGATG
* * * *
32811 GTGATCCGCCCCAAGCTGGGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAG
1 GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
** *
32876 AGATTGATTGATGGTGATTTGCCCCAAGCTCGAGGTAAGAGATTG
66 AGATTGGCTGATGGTGATTTGCCCCAGGCTCGAGGTAA-AGATTG
32921 ACTAATGGTG
Statistics
Matches: 223, Mismatches: 41, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
155 2 0.01
156 219 0.98
157 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (155 bp):
GTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAAGCTCGGGGTAAG
AGATTGGCTGATGGTGATTTGCCCCAGGCTCGAGGTAAAGATTGGATGGATACAATCTACCTCAG
GCTCGAGGTAAGAGATTGGCTGATG
Found at i:33723 original size:147 final size:146
Alignment explanation
Indices: 33525--34286 Score: 514
Period size: 147 Copynumber: 5.2 Consensus size: 146
33515 GTACTGGGTC
* * *
33525 CGCCGTTGCTGCCTCAACCTTTCCCTTCATATCTTTTAAGGTACCAAGTTCGCCATTGCGGCCTC
1 CGCCGTTGCGGCCTCAACCTTTCCCTT-ACATCTTTTAAGGTACCGAGTTCGCCATTGCGGCCTC
* * * *
33590 AACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGGCCTTAATCTTTCCCATCACA
65 AACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCAAA
33655 T-TTCATGGTATCGGTTT
130 TCTTCATGGTATCGG-TT
* * *
33672 CGCCGTTGCGGCCTCAACCTTTCTCGTTACATCTTTTAAGGTATCGGGTTCGCCATTGCGGCCTC
1 CGCCGTTGCGGCCTCAACCTTTC-CCTTACATCTTTTAAGGTACCGAGTTCGCCATTGCGGCCTC
* * * * * * ** *
33737 AACCTTTCCCTTCAACATCTTTTAAGGTATCGAGTTCACCGTTGTAACCTCAACCTTTCCCTTCA
65 AACCTTTCCCTT-AAAATC-TTCATGGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCA
*
33802 AATCTTCATGGTACTAGGTT
128 AATCTTCATGGTA-TCGGTT
* * * * * * * * * * * *
33822 CACAGTTACGACCTCAACCTTTCCCAT-CATATTTCATGGTATCGAATTCGCCGTTGTGGCCTCA
1 CGCCGTTGCGGCCTCAACCTTTCCCTTACATCTTTTAAGGTACCGAGTTCGCCATTGCGGCCTCA
* * * * * * * * * *
33886 ATCTTTCTCATCACATCTTC-TGAGGTACCGGATTCACCGTCGCGACCTCAA-TTCTTCCCTTCA
66 ACCTTTCCCTTAAAATCTTCAT--GGTACCGGGTTCACCATTGCGACCTCAACCT-TTCCCATCA
*
33949 AATCTTCATGGTATTGGGTT
128 AATCTTCATGGTA-TCGGTT
* * * * * * * * *
33969 CACCATTGTGGACTCAACCTTTCCCGTCACATCTTTTAAGGTACCGGGTTTGCCGTTGTGGCCTC
1 CGCCGTTGCGGCCTCAACCTTTCCC-TTACATCTTTTAAGGTACCGAGTTCGCCATTGCGGCCTC
* * * * * * * *
34034 AACCTTTCCCTTCAAATGTTCATGTTACCAGGTTCGCCATTGTGGCCTCAACCTTTCCCATCACA
65 AACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCAAA
* *
34099 T-TTCATGGTACCAGATT
130 TCTTCATGGTATC-GGTT
* * * * * * * ** * * *
34116 CGACGTTGTGGCCTCAATCTTTCTCATCACAT-TTTTGAGGTA-CTAGGTTCATCGTTG-TGCAT
1 CGCCGTTGCGGCCTCAACCTTTC-CCTTACATCTTTTAAGGTACCGA-GTTCGCCATTGCGGCCT
* * * ** * * * * * * *
34178 CAACATTTCCCTTTAAATCTTTATGGTACCAAGTTCGCCGTTACAACCTCAACCTTTCTCGTCAC
64 CAACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCAA
* *
34243 ATCTTTTAAGGTATCGGGTT
129 ATC-TTCATGGTATC-GGTT
**
34263 CGCCGTTGCGGGGTCAACCTTTCC
1 CGCCGTTGCGGCCTCAACCTTTCC
34287 TTTCAAATCT
Statistics
Matches: 479, Mismatches: 119, Indels: 35
0.76 0.19 0.06
Matches are distributed among these distances:
145 58 0.12
146 21 0.04
147 205 0.43
148 77 0.16
149 84 0.18
150 31 0.06
151 3 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.35
Consensus pattern (146 bp):
CGCCGTTGCGGCCTCAACCTTTCCCTTACATCTTTTAAGGTACCGAGTTCGCCATTGCGGCCTCA
ACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGACCTCAACCTTTCCCATCAAAT
CTTCATGGTATCGGTT
Found at i:33807 original size:198 final size:195
Alignment explanation
Indices: 33508--34207 Score: 617
Period size: 198 Copynumber: 3.6 Consensus size: 195
33498 CCATCTTGTT
* * * * *
33508 TTCTAAGGTACTGGGTCCGCCGTTGCTGCCTCAACCTTTCCCTTCATATCTTTTAAGGTACCAAG
1 TTCTAAGGTAC-GGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTTTAAGGTATCGAG
* * * *
33573 TTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTCATGGTACCGGGTTCACCATTGCGGCCT
65 TTCACCATTGTGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCATTGCGGCCT
* * * * * *
33638 TAATCTTTCCCATCACATTTCATGGTATCGGTTTCGCCGTTGCGGCCTCAACCTTTCTCGTTACA
130 CAACCTTTCCCATCAAATTTCATGGTATCGG-TTCGCCGTTGTGGCCTCAACCTTTCTCATCACA
33703 TC
194 TC
* *
33705 TTTTAAGGTATCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTCAACATCTTTTAAGGTATCGA
1 TTCTAAGGTA-CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAA-ATCTTTTAAGGTATCGA
* * ** * *
33770 GTTCACCGTTGTAACCTCAACCTTTCCCTTCAAATCTTCATGGTACTAGGTTCA-CAGTTACGAC
64 GTTCACCATTGTGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCA-TTGCGGC
* * *
33834 CTCAACCTTTCCCATCATATTTCATGGTATCGAATTCGCCGTTGTGGCCTCAATCTTTCTCATCA
128 CTCAACCTTTCCCATCAAATTTCATGGTATCG-GTTCGCCGTTGTGGCCTCAACCTTTCTCATCA
33899 CATC
192 CATC
* * * * * * * * * *
33903 TTCTGAGGTACCGGATTCACCGTCGCGACCTCAA-TTCTTCCCTTCAAATC-TTCATGGTATTGG
1 TTCTAAGGTA-CGGGTTCGCCGTTGCGGCCTCAACCT-TTCCCTTCAAATCTTTTAAGGTATCGA
* * * * ** * *
33966 GTTCACCATTGTGGA-CTCAACCTTTCCCGTCACATCTTTTAAGGTACCGGGTTTGCCGTTGTGG
64 GTTCACCATTGT-GACCTCAACCTTTCCCTTCAAATC-TTCATGGTACCGGGTTCACCATTGCGG
* * * * *
34030 CCTCAACCTTTCCCTTCAAATGTTCATGTTACCAGGTTCGCCATTGTGGCCTCAACCTTTCCCAT
127 CCTCAACCTTTCCCATCAAAT-TTCATGGTATC-GGTTCGCCGTTGTGGCCTCAACCTTTCTCAT
34095 CACAT-
190 CACATC
* * * * * * * * * * *
34100 TTC-ATGGTACCAGATTCGACGTTGTGGCCTCAATCTTTCTCATCACAT-TTTTGAGGTA-CTAG
1 TTCTAAGGTA-CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTTTAAGGTATCGA-
* * * * * *
34162 GTTCATCGTTGTG-CATCAACATTTCCCTTTAAATCTTTATGGTACC
64 GTTCACCATTGTGACCTCAACCTTTCCCTTCAAATCTTCATGGTACC
34208 AAGTTCGCCG
Statistics
Matches: 403, Mismatches: 86, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
194 10 0.02
195 17 0.04
196 86 0.21
197 85 0.21
198 204 0.51
199 1 0.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (195 bp):
TTCTAAGGTACGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTTTAAGGTATCGAGT
TCACCATTGTGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCATTGCGGCCTC
AACCTTTCCCATCAAATTTCATGGTATCGGTTCGCCGTTGTGGCCTCAACCTTTCTCATCACATC
Found at i:33991 original size:99 final size:99
Alignment explanation
Indices: 33536--34116 Score: 365
Period size: 99 Copynumber: 5.9 Consensus size: 99
33526 GCCGTTGCTG
* * * * * * *
33536 CCTCAACCTTTCCCTTCATATCTTTTAAGGTACCAAGTTCGCCATTGCGGCCTCAACCTTTCCCT
1 CCTCAACCTTTCCCTTCAAATC-TTCATGGTACCAGGTTCACCATTGTGGCCTCAACCTTTCCCA
* * * * * * *
33601 TAAAATCTTC-ATGGTACCGGGTTCACCATTGCGG
65 TCACATCTTCTAAGGTACCGGATTCACCGTCGCGA
* * * * * * * * * *
33635 CCTTAATCTTTCCCATCACAT-TTCATGGTATC-GGTTTCGCCGTTGCGGCCTCAACCTTTCTCG
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGG-TTCACCATTGTGGCCTCAACCTTTCCCA
* * * * * * * *
33698 TTACATCTTTTAAGGTATCGGGTTCGCCATTGCGG
65 TCACATCTTCTAAGGTACCGGATTCACCGTCGCGA
* * * * **
33733 CCTCAACCTTTCCCTTCAACATCTTTTAAGGTATC-GAGTTCACCGTTGTAACCTCAACCTTTCC
1 CCTCAACCTTTCCCTTCAA-ATC-TTCATGGTACCAG-GTTCACCATTGTGGCCTCAACCTTTCC
* * * * * **
33797 CTTCAAATCTTC-ATGGTACTAGG-TTCACAGTTACGA
63 CATCACATCTTCTAAGGTAC-CGGATTCACCGTCGCGA
* * * * * * * *
33833 CCTCAACCTTTCCCATCATAT-TTCATGGTATC-GAATTCGCCGTTGTGGCCTCAATCTTTCTCA
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAG-GTTCACCATTGTGGCCTCAACCTTTCCCA
*
33896 TCACATCTTCTGAGGTACCGGATTCACCGTCGCGA
65 TCACATCTTCTAAGGTACCGGATTCACCGTCGCGA
* *** * *
33931 CCTCAA-TTCTTCCCTTCAAATCTTCATGGTATTGGGTTCACCATTGTGGACTCAACCTTTCCCG
1 CCTCAACCT-TTCCCTTCAAATCTTCATGGTACCAGGTTCACCATTGTGGCCTCAACCTTTCCCA
* * ** * * *
33995 TCACATCTTTTAAGGTACCGGGTTTGCCGTTGTGG
65 TCACATCTTCTAAGGTACCGGATTCACCGTCGCGA
* * *
34030 CCTCAACCTTTCCCTTCAAATGTTCATGTTACCAGGTTCGCCATTGTGGCCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCACCATTGTGGCCTCAACCTTTCCCAT
* *
34095 CACAT-TTC-ATGGTACCAGATTC
66 CACATCTTCTAAGGTACCGGATTC
34117 GACGTTGTGG
Statistics
Matches: 378, Mismatches: 91, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
96 1 0.00
97 95 0.25
98 69 0.18
99 139 0.37
100 32 0.08
101 41 0.11
102 1 0.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.34
Consensus pattern (99 bp):
CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCACCATTGTGGCCTCAACCTTTCCCAT
CACATCTTCTAAGGTACCGGATTCACCGTCGCGA
Found at i:34003 original size:246 final size:246
Alignment explanation
Indices: 33536--34158 Score: 668
Period size: 246 Copynumber: 2.5 Consensus size: 246
33526 GCCGTTGCTG
* * * * * * * *
33536 CCTCAACCTTTCCCTTCATATCTTTTAAGGTACCAAGTTCGCCATTGCGGCCTCAACCTTTCCCT
1 CCTCAACCTTTCCCTTCAAATC-TTCATGGTACCAGGTTCGACATTACGACCTCAACCTTTCCCA
* * * * * * * *
33601 TAAAATCTTCATGGTACCGGGTTC-ACCATTGCGGCCTTAATCTTTCCCATCACATTTC--ATGG
65 TCACAT-TTCATGGTACCAGATTCGA-CGTTGTGGCCTCAATCTTTCTCATCACATTTCTGA-GG
* * * * * * * * * * *
33663 TATCGGTTTCGCCGTTGCGGCCTCAA-CCTTTCTCGTT-ACATCTTTTAAGGTATCGGGTTCGCC
127 TACCGGATTCACCGTCGCGACCTCAATTC-TTC-CCTTCAAATC-TTCATGGTATCGGGTTCACC
* * *
33726 ATTGCGGCCTCAACCTTTCCCTTCAACATCTTTTAAGGTATCGAGTTCACCGTTGTAA
189 ATTGCGGACTCAACCTTTCCCGTCAACATCTTTTAAGGTACCGAGTTCACCGTTGTAA
*
33784 CCTCAACCTTTCCCTTCAAATCTTCATGGTACTAGGTTC-ACAGTTACGACCTCAACCTTTCCCA
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGACA-TTACGACCTCAACCTTTCCCA
* * *
33848 TCATATTTCATGGTATC-GAATTCGCCGTTGTGGCCTCAATCTTTCTCATCACATCTTCTGAGGT
65 TCACATTTCATGGTACCAG-ATTCGACGTTGTGGCCTCAATCTTTCTCATCACAT-TTCTGAGGT
*
33912 ACCGGATTCACCGTCGCGACCTCAATTCTTCCCTTCAAATCTTCATGGTATTGGGTTCACCATTG
128 ACCGGATTCACCGTCGCGACCTCAATTCTTCCCTTCAAATCTTCATGGTATCGGGTTCACCATTG
* * ** **
33977 TGGACTCAACCTTTCCCGTC-ACATCTTTTAAGGTACCGGGTTTGCCGTTGTGG
193 CGGACTCAACCTTTCCCGTCAACATCTTTTAAGGTACCGAGTTCACCGTTGTAA
* * * ** *
34030 CCTCAACCTTTCCCTTCAAATGTTCATGTTACCAGGTTCGCCATTGTGGCCTCAACCTTTCCCAT
1 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGACATTACGACCTCAACCTTTCCCAT
*
34095 CACATTTCATGGTACCAGATTCGACGTTGTGGCCTCAATCTTTCTCATCACATTTTTGAGGTAC
66 CACATTTCATGGTACCAGATTCGACGTTGTGGCCTCAATCTTTCTCATCACATTTCTGAGGTAC
34159 TAGGTTCATC
Statistics
Matches: 315, Mismatches: 50, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
245 11 0.03
246 170 0.54
247 81 0.26
248 51 0.16
249 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (246 bp):
CCTCAACCTTTCCCTTCAAATCTTCATGGTACCAGGTTCGACATTACGACCTCAACCTTTCCCAT
CACATTTCATGGTACCAGATTCGACGTTGTGGCCTCAATCTTTCTCATCACATTTCTGAGGTACC
GGATTCACCGTCGCGACCTCAATTCTTCCCTTCAAATCTTCATGGTATCGGGTTCACCATTGCGG
ACTCAACCTTTCCCGTCAACATCTTTTAAGGTACCGAGTTCACCGTTGTAA
Found at i:35263 original size:23 final size:23
Alignment explanation
Indices: 35226--35290 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 23
35216 CGACCTCTCC
35226 TTTTCTTTTTCCCATTTTTTTCTA
1 TTTTCTTTTT-CCATTTTTTTCTA
*
35250 TTTTCTTTTTCCA-TTTTTTCTT
1 TTTTCTTTTTCCATTTTTTTCTA
35272 TTTTCTTTTTTCC-TTTTTT
1 TTTTC-TTTTTCCATTTTTT
35291 CTTTCTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 13 0.34
23 15 0.39
24 10 0.26
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTTCCATTTTTTTCTA
Found at i:35273 original size:7 final size:7
Alignment explanation
Indices: 35241--35309 Score: 77
Period size: 7 Copynumber: 9.7 Consensus size: 7
35231 TTTTTCCCAT
35241 TTTTTTC
1 TTTTTTC
*
35248 TATTTTC
1 TTTTTTC
*
35255 TTTTTCC
1 TTTTTTC
35262 ATTTTTTC
1 -TTTTTTC
35270 TTTTTTC
1 TTTTTTC
35277 TTTTTTCC
1 TTTTTT-C
35285 TTTTTTC
1 TTTTTTC
*
35292 TTTCTT-
1 TTTTTTC
*
35298 TTCTTTC
1 TTTTTTC
35305 TTTTT
1 TTTTT
35310 CATTTATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
6 4 0.08
7 34 0.67
8 13 0.25
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:35293 original size:15 final size:14
Alignment explanation
Indices: 35241--35309 Score: 77
Period size: 15 Copynumber: 4.9 Consensus size: 14
35231 TTTTTCCCAT
*
35241 TTTTTTCTATTTTC
1 TTTTTTCTTTTTTC
*
35255 TTTTTCCATTTTTTC
1 TTTTTTC-TTTTTTC
35270 TTTTTTCTTTTTTCC
1 TTTTTTCTTTTTT-C
*
35285 TTTTTTCTTTCTT-
1 TTTTTTCTTTTTTC
*
35298 TTCTTTCTTTTT
1 TTTTTTCTTTTT
35310 CATTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
13 10 0.21
14 12 0.26
15 25 0.53
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:35293 original size:22 final size:23
Alignment explanation
Indices: 35226--35303 Score: 97
Period size: 22 Copynumber: 3.3 Consensus size: 23
35216 CGACCTCTCC
* *
35226 TTTTCTTTTTCCCATTTTTTTCTA
1 TTTTCTTTTTTCCA-TTTTTTCTT
35250 TTTTC-TTTTTCCATTTTTTCTT
1 TTTTCTTTTTTCCATTTTTTCTT
35272 TTTTCTTTTTTCC-TTTTTTCTTT
1 TTTTCTTTTTTCCATTTTTTC-TT
35295 CTTTTCTTT
1 -TTTTCTTT
35304 CTTTTTCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
22 20 0.41
23 16 0.33
24 13 0.27
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTTTCCATTTTTTCTT
Found at i:39260 original size:24 final size:27
Alignment explanation
Indices: 39233--39283 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
39223 ATATTTCATA
39233 GAAAAAGC-AAAGGATCA-ACA-CAAT
1 GAAAAAGCAAAAGGATCATACATCAAT
*
39257 GAAAATGCAAAAGGATCATACATCAAT
1 GAAAAAGCAAAAGGATCATACATCAAT
39284 TTAAATTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 3 0.13
27 4 0.17
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (27 bp):
GAAAAAGCAAAAGGATCATACATCAAT
Found at i:41307 original size:26 final size:26
Alignment explanation
Indices: 41278--41328 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
41268 TCTTGATATT
*
41278 TCGAATCTGACTTTTTATAGACTATC
1 TCGAATCTGACTTTTTATAAACTATC
41304 TCGAATCTGACTTTTTATAAACTAT
1 TCGAATCTGACTTTTTATAAACTAT
41329 GTATTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (26 bp):
TCGAATCTGACTTTTTATAAACTATC
Done.